WO2012094586A2 - Synthetic non-covalently self-assembling bipartite prna chimeras - Google Patents

Synthetic non-covalently self-assembling bipartite prna chimeras Download PDF

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WO2012094586A2
WO2012094586A2 PCT/US2012/020469 US2012020469W WO2012094586A2 WO 2012094586 A2 WO2012094586 A2 WO 2012094586A2 US 2012020469 W US2012020469 W US 2012020469W WO 2012094586 A2 WO2012094586 A2 WO 2012094586A2
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prna
rna
polynucleotide
artificial
sirna
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WO2012094586A3 (en
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Peixuan Guo
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Peixuan Guo
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Priority to PCT/US2012/040823 priority Critical patent/WO2012170372A2/en
Priority to CN201280011209.7A priority patent/CN103403189B/en
Priority to US13/992,714 priority patent/US9297013B2/en
Publication of WO2012094586A2 publication Critical patent/WO2012094586A2/en
Publication of WO2012094586A3 publication Critical patent/WO2012094586A3/en

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    • C12N2310/00—Structure or type of the nucleic acid
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Definitions

  • the presently disclosed invention embodiments relate to RNA nanoparticles and methods for their preparation and use.
  • the present embodiments relate to self-assembling two-piece artificial pRNA polynucleotides that share pRNA secondary structure with wild-type dsDNA viral packaging RNA (pRNA), and their derivatives, for use in assembling and stabilizing biologically active RNA nanoparticles.
  • pRNA wild-type dsDNA viral packaging RNA
  • RNA molecules can be designed and manipulated at a level of simplicity
  • RNA is a suitable candidate for nanotechnological applications.
  • the concept of RNA nanotechnology has been proposed for more than a decade (2, 5, 7, 10-12; for reviews, see 4, 13, 14).
  • Dimeric, trimeric, and hexameric RNA nanoparticles can be assembled through self-assembly of multiple reengineered natural RNA molecules (5).
  • the recognized potential of RNA nanoparticles for use in the treatment of cancer, viral infection, genetics diseases and other human ailments has heightened recent interest in RNA nanotechnology (4).
  • Phi29 ( ⁇ 29) DNA packaging motor uses six pRNAs that form a ring to gear the DNA packaging motor (5, 27-30). Each pRNA molecule contains two domains (Fig. 1A). One of the domains, bases 23-97, located at the central region of pRNA, is involved in intermolecular interactions such as non-covalent, specific intermolecular associative events (27, 28, 31 , 32), and hence is referred to as the intermolecular interaction domain.
  • the two loops (L- loop and R-loop), which are capable of interlocking associations between pRNA monomers to form dimers, trimers and hexamers, reside within this domain.
  • chimeric pRNA may be engineered in a wide variety of ways by which some or all of the pRNA 573' proximate double-stranded helical end may be removed and/or replaced with a heterologous component such as siRNA, a ribozyme, antisense RNA, an RNA aptamer, a peptide nucleic acid, etc., such that the double-stranded helical domain can be used to carry a therapeutic "payload” such as a therapeutic siRNA (Fig. 1A) (23, 24, 34; see also, e.g., U.S. Patent No. 7,655,787, US 2010/0003753, US 2008/0064647, WO 2005/003293, WO 02/016596).
  • a therapeutic siRNA Fig. 1A
  • pRNA escorts the siRNA to cells, to silence genes and to destroy leukemia cells and/or cancer cells of lung, breast, head and neck, as well as other tumors (23-25,35-38).
  • the pRNA system has several advantages including defined structure, controllable stoichiometry, multi-valency, targeted delivery, ideal nanoscale size (-20-40 nm), and minimal immunogenicity ⁇ e.g., poor induction of antibody responses), to enable repeated administration of chimeric pRNA for the treatment of chronic diseases (4).
  • the pRNA is remarkably stable in a wide range of pH (-4-9), temperature, and organic solvents (6).
  • compositions and methods that permit the production and use of high-purity, precisely structurally designed, chemically and physiologically stable pRNA, including chimeric pRNA having particularly useful therapeutic, targeting, stabilizing and/or detectable labeling moieties.
  • chimeric pRNA having particularly useful therapeutic, targeting, stabilizing and/or detectable labeling moieties.
  • At least one heterologous component is selected from (i) a heterologous component that is covalently attached to a P1 5'-end, (ii) a heterologous component that is covalently attached to the P1 3'-end, (iii) a heterologous component that is covalently attached to the P2 5'-end, and (iv) a heterologous component that is covalently attached to a P2 3'-end.
  • the artificial pRNA polynucleotide one or a plurality of modified nucleotides, which modified nucleotide in certain further embodiments is selected from a 2'-fluoro-2'-deoxy nucleotide or a derivative thereof, a phosphorothioate , a 2'-O-methyl ribonucleotide or a derivative thereof, a 2'-NH 2 -2'-deoxy nucleotide or a derivative thereof, and a 2'-CH 3 -2'- deoxy nucleotide or a derivative thereof.
  • the artificial pRNA polynucleotide does not elicit a TLR-mediated response when
  • the heterologous component comprises a Dicer substrate that is processed by a Dicer pathway to yield a siRNA that is capable of specifically interfering with expression of a gene.
  • P1 and P2 self-assemble to form a substantially full-length pRNA.
  • a method of delivering a biologically active moiety to a cell comprising contacting the cell with the above-described artificial pRNA polynucleotide which comprises at least one or at least two heterologous components, under conditions and for a time sufficient for uptake by the cell of the artificial pRNA polynucleotide, wherein the heterologous component comprises the biologically active moiety.
  • Figure 1 shows the structure and characterization of chemically synthesized 2-piece pRNA (P1/P2).
  • P1/P2 2-piece pRNA
  • A The structure of a typical monomeric pRNA nanoparticle comprising P1 and P2 RNAs.
  • Figure 2 shows that the pRNA nanoparticle comprising two-piece (P1 +P2) self-assembled pRNA monomers did not induce an interferon response in vitro.
  • A KB cells were transfected with 50 nM pRNA (2'-F modified vs. non-modified), 50 nM siRNA, and 1 g/mL poly l:C using Fugene- HD. The cells were harvested 24 hours later and semi-quantitative RT-PCR was conducted to test for the expression of the indicated IFN responsive genes.
  • B Human PBMC were incubated with 50 nM pRNA or 1 g/mL poly l:C. After 24 hours, the RNAs were extracted and tested for the upregulation of TLR-3, TLR-7 and TLR-9.
  • KT-107 and KT-108 are pRNA monomers that differ in the sequence of the 573' helical region.
  • C Production of TNF-a in the mouse macrophage cell line RAW-647 after incubation with different concentrations of pRNA and poly l:C. Three hours post-incubation, aliquots from the culture media were used to test for the levels of TNF-a by ELISA.
  • D Activation of TLR-3 pathway as measured using HEK-BlueTM-hTLR3 reporter cell line.
  • pRNA monomers that differed in the length and the extent of modification of the 573' helical region were tested at the concentrations shown and compared to poly l:C.
  • pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers for 24 hours, aliquots from the culture media were used for colorimetric detection of TLR-3 activation.
  • FF 2'- F modified helical region
  • NN non-modified helical region
  • 29 the helical region was 29 nucleotides in length
  • 22 the helical region was 22 nucleotides in length.
  • All pRNA constructs used had a modified intermolecular interaction domain. Poly l:C was used in all these assays as positive control.
  • Figure 3 shows that the Folate-pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers targeted FR+ tumors upon systemic administration.
  • A HeLa xenograft tumor bearing nude mice were injected with 15 nmol ( ⁇ 24mg/kg) of KT-105 (Folate- AlexaFluor647 labeled pRNA nanoparticle) through the tail vein (right). The control mice were injected with either PBS (left) or with folic acid (/.p., 10mg/kg) 10 minutes prior to KT-105 injection (middle). The mice were euthanized 24 hours after injection and whole body imaging was conducted using IVIS® Lumina station.
  • B HeLa xenograft tumor bearing nude mice were injected with 15 nmol ( ⁇ 24mg/kg) of KT-105 (Folate- AlexaFluor647 labeled pRNA nanoparticle) through the tail vein (right). The control mice
  • mice were dissected and the major organs were isolated for imaging .
  • C KB xenograft tumor bearing nude mice were injected with 15 nmol (24 mg/kg)(lower panel) or 3.75 nmol (upper panel)( ⁇ 6mg/kg) of KT-105 through the tail vein. Organs were isolated and imaged as described above.
  • Figure 4 shows plasma concentration of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers upon systemic administration.
  • concentration of the nanoparticle was determined using CGE.
  • the semi-log plot of the plasma concentration vs. time is shown.
  • Figure 5 shows white blood cell counts in mice following injection of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers.
  • Clinical pathology analysis was conducted for the C57B/6 mice upon one-week repeat i.v. administrations of pRNA vs. Poly l:C at the indicated doses. Total cell counts (left) and differentials (right) were displayed.
  • Figure 6 shows capillary gel electrophoretic (CGE) analysis of monomeric and dimeric pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers.
  • CGE capillary gel electrophoretic
  • Figure 7 shows that chemically synthesized 2'F-pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers were metabolically stable.
  • the different forms of nanoparticles were incubated with different concentrations of human serum or with RNase A (1 U, 30 min) for the indicated time periods at 37°C. Aliquots were taken at different time intervals and subjected to phenol :chloroform extraction followed by ethanol precipitation. pRNA was visualized by Sybr® Gold staining of 10%/8 M urea polyacrylamide gels (denatured PAGE).
  • Figure 8 shows cellular uptake of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers with various folate (FA) conjugation.
  • A-l KB cells were incubated with FA-pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers containing folate at the 5'-end of P1 .
  • the pRNA was labeled with fluorescein using Silencer® siRNA labeling kit (Ambion). The cells were incubated with the pRNA (200 nM) in the absence or presence of excess folic acid (FA) (200 fold) for 30 min.
  • the cells were either harvested by trypsinization, fixed, and analyzed by flow cytometry (A-C) or imaged using a confocal microscope (D-l).
  • J-M KB cells were transfected with GFP-Rho-B-expressing cassette to label early and late endosomes (green). After transfection by 24 h, KB cells were incubated with 200 nM Cy5-FA-pRNA nanoparticles (red) for the indicated periods. Cy5 was conjugated to the 5'-end of P1 and folate was conjugated on 5'- end of P2. The cells were imaged by confocal microscopy to determine co- localization of pRNA with the endosomes (yellow) and the extent of endosomal release.
  • FIG. 9 shows the weights of different organs from the C57B/6 mice after 1 week of repeated systemic administration of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers at a dose of 30 mg/kg.
  • Figure 10 shows construction of two-piece RNA assemblies, (a) The structure of pRNA molecules and pRNA/siRNA chimera, (b) The design and sequence of three different two-piece modules for pRNA or pRNA/siRNA chimera, (c) 8% native PAGE showing the self-assembly of two RNA fragments into the pRNA monomer and dimer formation of resulting two-piece RNA assemblies.
  • the monomer control including (1 -1 17) Ab' pRNA and its dimer partner (1 -1 17) Ba' pRNA.
  • the dimer control is the dimer formed by (1 -1 17) Ab' pRNA and Ba' pRNA.
  • the monomer control including (1 -1 17) Ab' pRNA siRNA chimera and its dimer partner (1 -1 17) Ba' pRNA.
  • the dimer control is the dimer formed by (1 -1 17) Ab' pRNA siRNA chimera and Ba' pRNA.
  • Figure 1 1 DNA packaging activity (a) and viral assembly activity (b) of pRNA chimera assembled from two pieces of pRNA fragments, (a) 0.8% agarose gel showing the procapsid protected viral DNA after packaging which indicated the active pRNA components.
  • Lanel is 1 Kb DNA ladder; lane 2 indicated the total amount of input viral genome DNA for the packaging assay; lane 4 is the active packaging served as positive control.
  • Lane3, lane 5 to lane 9 served as negative control for background check which only add monomeric (1 -1 17) Ab'(1 -1 17) Ba' or two-piece pRNA assemblies without presence of dimer partner.
  • Lane 10 to lane 12 showing the active packaging activity of all three two-piece pRNA assemblies (b) Viral assembly activity is reflected by the plaque formation unit per milliliter (PFU/mL).
  • the no RNA, no ATP, monomeric pRNA (Ab' and Ba' pRNA) or two-piece pRNA assemblies served as negative control for checking the background plaque formation.
  • All three two-piece pRNA assemblies together with their dimer partner (1 -1 17)Ba' pRNA can assemble mature virons to infect the host bacteria and form plaque which is comparable to the wild type dimer (1 -1 17)Ab' pRNA plus (1 -1 17)Ba' served as positive control.
  • FIG. 12 Gene silencing assay for pRNA/siRNA(eGFP) assembled from two pieces of RNA fragments, (a) The eGFP gene silencing knock-down effects by two-piece pRNA/siRNA(eGFP) chimera and its mutant controls. Nucleotides in red indicate the mutation, (b) 8% native PAGE showing the self-assembly of two RNA fragments into the pRNA siRNA chimera and its mutant controls (lane 1 : monomer control; lane 2: pRNA siRNA(eGFP); lane 3: pRNA siRNA(eGFP) with sense strand mutant; lane 4:
  • pRNA siRNA(eGFP) dimer lane 7: dimer of pRNA siRNA(eGFP) with sense strand mutant; lane 8: dimer of pRNA siRNA(eGFP) with antisense strand mutant; lane 9: dimer of pRNA/siRNA(eGFP) with both sense strand and antisense strand mutant; and lane 10: dimer control).
  • the no RNA, no plasmid DNA control served as the system blank for the assay.
  • DNA1 is the plasmid pGL3 harboring firefly luciferase gene and
  • DNA2 is the plasmid pRL- TK harboring renilla luciferase.
  • the relative firefly luciferase activity is to normalize firefly luciferase activity using the internal control renilla luciferase activity which reflected the level of luciferase gene expression.
  • Figure 14 The survivin silencing effects of two-piece pRNA siRNA chimera assayed by Western Blot.
  • Cells were treated with different concentration of RNAs (5nM, 20nM and 40nM) respectively including two-piece pRNA siRNA(survivin), two-piece pRNA/scramble control as well as according intact pRNA siRNA(survivin) and its scrambled control.
  • Column 2 of the figure only included two concentration of RNA treatment (5nM and 20nM).
  • the reduced survivin gene expression was displayed as the lighter band after blotting.
  • Figure 15 The reduced survivin gene expression was displayed as the lighter band after blotting.
  • Figure 16 shows an autoradiogram showing the Dicer processing of the [32P] labeled pRNA siRNA chimeras assembled from two pieces of RNA fragments.
  • an artificial double-stranded DNA bacteriophage packaging RNA (pRNA) polynucleotide is produced as a two-piece, self-assembling pRNA monomer having a break between the 3'-end of the first piece (P1 ) and the 5'- end of the second piece (P2), wherein the break is situated in a pRNA single- stranded loop that is formed by nucleotides corresponding to nucleotide positions 53-58 of a wild-type pRNA sequence such as the wild-type pRNA of bacteriophage phi29 pRNA.
  • pRNA DNA bacteriophage packaging RNA
  • P1 and P2 can each be structurally modified by the addition of additional RNA sequences or other chemical moieties ⁇ e.g., heterologous (i.e., non-naturally present) components such as biologically active moieties including siRNA, ribozymes, antisense RNA, aptamers, targeting moieties, peptide nucleic acids, detectable labels, therapeutic agents, endosome-disrupting agents, stabilizing nucleotides such as 2'-fluoro-2'-deoxy nucleotide derivatives, phosphorothioates, 2'-O-methyl ribonucleotides, 2'-NH 2 - 2'-deoxy nucleotide derivatives, 2'-CH 3 -2'-deoxy nucleotide derivatives, etc.) at the 5'-end and/or the 3'-end whilst still retaining the ability to self-assemble into an artificial pRNA monomer that retains wild-type pRNA function such as dimer, trim
  • the herein described artificial two-piece pRNA monomers unexpectedly accommodate structural modifications at the 5'-ends and/or the 3'-ends of P1 and P2, including in particular retention of the ability of siRNA so attached ⁇ e.g., as a heterologous component that is attached, directly or indirectly via a linker or spacer sequence, to the 5'-end of P1 and/or to the 3'- end of P2, and/or to the 3'-end of P1 and/or to the 5'-end of P2) to mediate gene-silencing or gene-inhibiting ⁇ e.g., decreasing gene product expression in a statistically significant manner) activity.
  • siRNA sequences present in the herein described artificial two-piece pRNA monomers may be processed by the intracellular Dicer pathway to result in functional RNA interference.
  • the herein described artificial pRNA polynucleotides comprising two-piece (P1 +P2) self-assembled pRNA monomers will find uses in therapeutics and diagnostics, and in patient screening and biological/ biomedical research applications.
  • Certain preferred embodiments contemplate use of the herein described artificial pRNA
  • polynucleotides comprising two-piece (P1 +P2) self-assembled pRNA
  • certain of the herein described invention embodiments contemplate a flexible and versatile modular system for targeted delivery of therapeutic and/or diagnostic agents, based on the ability to attach different heterologous components to the 5'-ends and/or to the 3'-ends of P1 and/or P2, which then self-assemble non-covalently to form a two-piece pRNA monomer having a wild-type pRNA secondary structure, and which monomers may then be mixed and matched to form a wide range of pRNA nanoparticulate dimers, trimers and/or hexamers.
  • the herein described artificial pRNA polynucleotides are non-immunogenic in certain preferred embodiments, such that repeated therapeutic and/or diagnostic administration may be practiced in a subject without eliciting undesirable immune responses that might otherwise counteract the purpose for which the pRNA is being used.
  • polynucleotides to be produced in certain embodiments, wholly through non- enzymatic chemical synthesis, according to certain preferred embodiments.
  • Synthetic chemical production of polynucleotides is known in the art and, currently, typically permits efficient synthesis of high-purity, substantially homogeneous (e.g., greater than at least 95, 96, 97, 98 or 99% homogeneous according to the detection capability of available analytical chemistry
  • Chemical synthesis also permits more precise implementation of chemical modifications at specific locations in the pRNA molecular structure, relative to that which can be achieved by enzymatic pRNA synthesis. Accordingly, it will be appreciated that previously described pRNA monomers, which typically exceed 100 nucleotides in length, are not currently amenable to efficient, non- enzymatic chemical synthesis, a problem that is overcome by the present two- piece pRNA monomers.
  • the break ⁇ e.g., opening, interruption, discontinuity) between P1 and P2 in the structure of the herein described self-assembled two-piece pRNA monomer is situated in the well recognized single-stranded loop, which loop is described, for instance, in US 2010/0003753 as the "head loop” in Fig. 2B therein, and as “loop 24" in paragraph [01 14] (referring to Fig. 4C) therein, and for which several clearly corresponding single-stranded loops at
  • pRNA can be dissected into a two-piece chimeric construct, in which two individual RNA oligonucleotides, one encompassing the R-loop and the other the L-loop, were clamped together via a six-nucleotide duplex (39).
  • two individual RNA oligonucleotides one encompassing the R-loop and the other the L-loop
  • a six-nucleotide duplex 39.
  • no break was present in the "head loop”
  • one of the two pieces was located in the middle of the pRNA.
  • This requirement for a duplex clamp made the resulting RNA unsuitable for the construction of therapeutic RNA nanoparticles harboring siRNA or other heterologous components, and also precluded their application to drug delivery.
  • These earlier "clamped" pRNA constructs also failed to exhibit pRNA
  • the present two-piece pRNA chimeric monomers can be used to generate full-length functional pRNAs that are not only competent for driving the phi29 DNA packaging motor, but that are also proficient for therapeutic and diagnostic purposes such as those described herein.
  • the resulting two- piece pRNA monomer was fully competent in associating with other interacting pRNAs to form dimers, as demonstrated by the packaging of DNA via the nanomotor and the assembly of phi29 viruses in vitro.
  • the monomeric pRNA subunits could be assembled from two-piece fragments harboring siRNA or receptor-binding ligands, and these subunits were equally competent at assembling into dimers.
  • the subunits carrying different functionalities were able to bind cancer cells specifically, to enter the cells, and to silence specific genes of interest.
  • the pRNA nanoparticles formed from the present non- covalently self-assembling two-piece pRNA monomer were processed by Dicer to release the siRNA embedded within the nanoparticle.
  • US 2010/0003753 discloses that the pRNA intermolecular interaction domain (sometimes referred to as the pRNA region) has a compact stable secondary structure characteristic of bacteriophage pRNA sequences.
  • the pRNA region may, in certain embodiments, include pRNA of a bacteriophage selected from phi29, SF5', B103, PZA, M2, NF and GA1 .
  • the pRNA region may include: (i) in the 5' to 3' direction beginning at the covalent linkage of the pRNA with the 3' end of the double-stranded helical domain (sometimes referred to as the spacer region) a first loop; a second loop (e.g., the head loop); and a lower stem-loop structure comprising a bulge, a first stem section and a third loop; (ii) a second stem section interposed between the spacer region and the stem-loop structure; (iii) a third stem section interposed between the stem-loop structure and the first loop; and (iv) a fourth stem section interposed between the first loop and the second loop.
  • nucleotide sequence SEQ ID NO:1 in US 2010/0003753 of native full length phi29 pRNA (Guo et al., Nucl. Acids Res. 15:7081 -7090 (1987)), as well as its predicted base-paired secondary structure, are disclosed in US 2010/0003753 (see also, e.g., Zhang et al., RNA 3:315-323 (1997);
  • the intermolecular interaction domain is present within the procapsid binding domain, which is located at the central part of the pRNA molecule at bases 23- 97 (Garver et al., RNA 3:1068-79 (1997); Chen et a ⁇ ., J Biol Chem 275:17510- 16 (2000)), while the double-stranded helical (or "DNA translocation") domain is located at the 573' paired ends.
  • Exogenous RNA e.g., a heterologous component
  • Exogenous RNA can be connected to the 3' or 5' end of the pRNA without affecting pRNA folding; this foreign RNA molecule also folds independently (Hoeprich et al., Gene Therapy, 10(15):1258- 1267 (2003); Shu et al., J Nanosci and Nanotech (JNN), 4:295-302 (2003); Guo, J. Nanosci Nanothechnol, 2005, 5(12):1964-1982).
  • Phylogenetic analysis of pRNAs from phages SF5', B103, phi29, PZA, M2, NF and GA1 shows very low sequence identity and few conserved bases, yet the family of pRNAs appears to have strikingly similar and stable predicted secondary structures (see, e.g., Fig. 3 in US 2010/0003753).
  • the pRNAs from bacteriophages SF5' (SEQ ID NOS:1 1 and 28 in US 2010/0003753), B103 (SEQ ID NOS:12 and 29 in US 2010/0003753), phi29/PZA (SEQ ID NOS:13 and 30 in US 2010/0003753), M2/NF (SEQ ID NOS:14 and 31 in US 2010/0003753), GA1 (SEQ ID NOS:15 and 32 in US 2010/0003753) of Bacillus subtilis (Chen et al., RNA 5:805-818 (1999); and aptRNA (SEQ ID NOS:16 and 33 in US 2010/0003753) are all predicted to have a secondary structure that exhibits essentially the same structural features as has been shown for phi29 pRNA (US 2010/0003753; Chen et al., RNA 5:805-818 (1999)). All have native 5' and 3' ends at the left end of a stem structure (as shown in Fig. 3 in US 2010/0003753) and
  • the pRNAs of these bacteriophages thus share a single stable secondary structure.
  • RNA base pairs commonly include G-C, A-T and U-G.
  • Predictions of secondary structure are preferably made according to the method of Zuker and Jaeger, for example by using a program known by the trade designation RNASTRUCTURE 3.6, written by David H. Mathews
  • RNA can be characterized by stems, loops and bulges.
  • stem is a double-stranded section of two lengths of base-paired ribonucleotides. Stem sections contain at least 2 base pairs and are limited in size only by the length of the RNA molecule.
  • a single secondary structure is dictated by a number of different primary sequences in predictable and well-understood ways.
  • single or pairs of nucleotides can generally be added, removed, or substituted without altering the overall base pairing interactions within the RNA molecule and without interfering with its biological function. This is particularly true if one or a few base pairs of nucleotides are removed, added or substituted along double-stranded hybridized length of the molecule, or if one or more
  • nucleotides are removed, added or substituted in the single-stranded loop regions.
  • GC base pairs and AT base pairs differ slightly in their thermodynamic stability, one can generally be substituted for another at a site within the double-stranded length without altering the secondary structure of an RNA molecule.
  • GC base pairs are preferred in the stem region due to their added stability.
  • Changes in secondary structure as a result of addition, deletion or modification of nucleotides can be readily assessed by applying the secondary structure prediction algorithm of Zuker and Jaeger as described above.
  • the 573' double-stranded helical region of the pRNA can accommodate substantial variation in primary sequence without an appreciable change in secondary structure.
  • Typical pRNAs that may be substantially full-length pRNAs comprise about 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 019, 1 10, 1 1 1 , 1 12, 1 13, 1 14, 1 15, 1 16, 1 17, 1 18, 1 19, 120, 121 , 122, 123, 124, 125, 126, 127, 128, 129 or 130 nucleotides in length, although shorter and longer pRNAs are disclosed and contemplated herein, such as artificial pRNA polynucleotides that self-assemble from a first pRNA piece P1 and a second pRNA piece P2, each of which comprises at least about 29-62 nucleotides that form a pRNA domain having the secondary structure of a pRNA intermolecular interaction domain, and each of which may further comprise a heterologous component such as additional 5'-end and/or
  • the pRNA chimera such as a pRNA chimera that comprises a presently disclosed self-assembled two-piece pRNA monomer which further comprises one or more heterologous component is useful as a vehicle to carry and deliver one or more biologically active moieties, detectable labels, and the like to a target molecule, cell or location.
  • the biologically active moieties, detectable labels and the like are considered herein as "heterologous" components of the pRNA chimera (that is, they are not present in the naturally occurring pRNA) and are sometimes referred to herein as the "cargo" or "payload” that is delivered by, carried by or incorporated into the pRNA chimera.
  • Heterologous components of a pRNA chimera may be, like the pRNA itself, RNAs that are sometimes referred to herein as "daughter" RNAs or biologically active RNAs.
  • the cargo components can be oligonucleotides, polynucleotides, peptides, polypeptides, carbohydrates, lipids, hormones, labeling agents, small organic molecules, and the like, without limitation, and any pRNA, including in certain embodiments a P1 and/or a P2 of a herein described self-assembling two-piece pRNA monomer, that has been derivatized with, conjugated to, or otherwise contains or is associated with a cargo component is considered a "pRNA chimera” or a "chimeric pRNA".
  • the chimeric pRNAs can advantageously be considered as "building blocks” that can be customized, selected, mixed and matched to produce multimeric, polyvalent pRNA complexes tailor-made for a desired application or purpose.
  • a pRNA chimera which comprises a herein described self-assembling two-piece pRNA monomer may include an intermolecular interaction domain (pRNA region) having the secondary structure exemplified in Fig. 3 of US 2010/0003753 and
  • the spacer region is termed "heterologous” because all or a portion of its nucleotide sequence is engineered or is obtained from an organism other than the bacteriophage. It is the presence of the heterologous spacer region that renders certain artificial pRNA polynucleotides "chimeric" according to certain herein described embodiments. Where both ends of the cargo RNA may, in certain
  • the cargo such as an siRNA or a ribozyme
  • the cargo may be protected from degradation when exposed, for example, to a physiological milieu; this configuration may, according to non-limiting theory, also assist the biologically active moiety to fold appropriately.
  • the ability of the pRNA chimera to perform its intended function of protecting and carrying a biologically active moiety depends not on the primary nucleotide sequence of the pRNA intermolecular interaction domain (the primary structure), but on the secondary structure (base pairing
  • the "pRNA region" of the pRNA chimera is thus so termed because it has a secondary structure, although not necessarily an RNA sequence, characteristic of a native bacteriophage pRNA molecule. Therefore, unless otherwise specified, the term "pRNA region" as used herein includes naturally occurring (native) pRNA sequences, nonnaturally occurring (nonnative) sequences, and combinations thereof provided that they yield the secondary structure characteristic of naturally occurring (native) bacteriophage pRNA as described herein.
  • pRNA region is not intended to be limited to only those particular nucleotide sequences native to pRNA.
  • the pRNA region can thus contain any nucleotide sequence which results in the secondary structure shown in Fig. 4 of US 2010/0003753.
  • Nucleotide sequences that fold into the aforesaid secondary structure include naturally occurring sequences, those that are derived by modifying naturally occurring pRNA sequences, and those that are designed de novo, as well as
  • nucleotide sequence will fold into the secondary structure shown in Fig. 4 of US 2010/0003753 and described herein by applying a secondary structure algorithm, such as RNASTRUCTURE as described above, to the nucleotide sequence.
  • a secondary structure algorithm such as RNASTRUCTURE as described above. Examples of nucleotide sequences that, when folded, yield the secondary structure of the pRNA region of the pRNA chimera of the invention are shown in Fig. 3 of US 2010/0003753.
  • pRNA sequences from bacteriophages SF5' SEQ ID NOS:1 1 and 28 of US 2010/0003753
  • B103 SEQ ID NOS:12 and 29 of US 2010/0003753
  • .phi29/PZA SEQ ID NOS:13 and 30 of US 2010/0003753
  • M2/NF SEQ ID NOS:14 and 31 of US
  • pRNA region of the pRNA chimera is defined by its secondary structure
  • still other examples of a pRNA chimera can be readily made by "mixing and matching" nucleotide fragments from, for example, SEQ ID NO:s 1 , 2, 7, 1 1 , 12, 14, 15 and 16 of US 2010/0003753 that fold into particular secondary structural features (bulges, loops, stem-loops, etc.) provided that the resulting nucleotide sequence folds into the overall secondary structure as shown in Fig. 4 of US 2010/0003753.
  • nucleotides encoding bulge loop 22 from bacteriophage SF5' pRNA (SEQ ID NO:1 1 of US 2010/0003753) could be substituted for the nucleotides encoding bulge loop 22 in the phi29 pRNA (SEQ ID NO:1 of US 2010/0003753) to yield a pRNA region as described herein.
  • any number of artificial sequences can be substituted into SEQ ID NO:s 1 , 2, 7, 1 1 , 12, 14, 15 and 16 of US
  • pRNA region 1 is shown in detail in Fig. 4(c) of US 2010/0003753.
  • pRNA region 1 is characterized by a stem-loop secondary structure, wherein the single-stranded loop formed by nucleotides corresponding to nucleotide positions 53-58 in a wild-type pRNA sequence such as the phi29 wild-type pRNA sequence, also referred to as the head loop or loop 24 in US 2010/0003753, is relatively small and the base-pairing in the stem (essentially stem sections 20, 21 and 23 of US 2010/0003753) is interrupted by structures on either side of loop 24.
  • Bulge loop 22 of US 2010/0003753, the "right hand loop" is positioned 5' of loop 24.
  • Positioned 3' of loop 24 is a stem-loop structure that contains bulge 25, stem 26 and loop 27, the "left hand loop", as disclosed in US 2010/0003753.
  • stem section 20 (as shown in US
  • the "cargo" carried by the chimeric pRNA takes the form of stem section 20 itself, which constitutes biologically active siRNA.
  • stem section 20 can be derivatized at either or both of its 5'- and 3'- ends with a biologically active moiety, detectable label, or the like, as its heterologous component "cargo".
  • the 5' end of P1 in the pRNA polynucleotide that is self-assembled from two pieces, P1 and P2, to form a two-piece pRNA monomer can be derivatized with folate (to facilitate targeting to folate receptor-bearing cells) or with a fluorescent label (to facilitate detection of the pRNA monomer, including detection of a pRNA nanoparticle that comprises such a monomer).
  • folate to facilitate targeting to folate receptor-bearing cells
  • a fluorescent label to facilitate detection of the pRNA monomer, including detection of a pRNA nanoparticle that comprises such a monomer.
  • certain embodiments contemplate multimeric pRNA complexes that may comprise one or more of the herein described artificial pRNA polynucleotides comprising a self-assembled two- piece pRNA monomer, in which complexes the interactions between the right and left hand loops of the various monomers can be controlled by engineering into their structures the desired left/right loop complementarity, advantageously resulting in customized dimers, trimers, and hexamers, such as for use in particular therapeutic and/or diagnostic applications.
  • the artificial pRNA polynucleotide contains at least 8, more preferably at least 15, most preferably at least 30 consecutive ribonucleotides found in native SF5' pRNA, B103 pRNA, phi29/PZA pRNA, M2/NF pRNA, GA1 pRNA, or aptRNA, or native phi29 pRNA, sequences of which are disclosed in US 2010/0003753.
  • the pRNA region may in certain preferred embodiments be formed from: a first pRNA piece P1 that comprises a RNA polynucleotide of at least 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56 or 57 nucleotides and that includes a P1 intermolecular interaction domain of about 29 nucleotides comprising the P1 3'- end, and which piece P1 may further comprise one or more heterologous components attached at the 3'-end and/or at the 5'-end and independently comprising an additional polynucleotide of up to about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250 or more nucleotides; and a second pRNA piece P2 that comprises a RNA
  • P1 and/or P2 are produced by non- enzymatic chemical synthesis; it is accordingly believed without wishing to be limited that economically efficient non-enzymatic synthesis in quantities and of a quality sufficient for pharmaceutical (including therapeutic and diagnostic) purposes currently may be feasible for polynucleotides of not more than about 100, 95, 90, 85 or 80 nucleotides in length.
  • P1 and P2 each contain a portion of the phi29 pRNA sequence that starts at ribonucleotide 23, preferably at
  • P1 and/or P2 each comprise a portion of the phi29 nucleotide sequence that is preferably at least 60% identical to, more preferably 80% identical to, even more preferably 90% identical to, and most preferably 95% identical to a portion of the nucleotide sequence of a corresponding native SF5' pRNA, B103 pRNA, phi29/PZA pRNA, M2/NF pRNA, GA1 pRNA, the aptRNA chimera or phi29 pRNA (particularly bases 20-97); these sequences are disclosed in US 2010/0003753.
  • Percent identity is determined by aligning two polynucleotides to optimize the number of identical nucleotides along the lengths of their sequences; gaps in either or both sequences are permitted in making the alignment in order to optimize the number of shared nucleotides, although the nucleotides in each sequence must nonetheless remain in their proper order.
  • the two nucleotide sequences are readily compared using the Blastn program of the BLAST 2 search algorithm, as described by Tatusova et al. (FEMS Microbiol Lett 1999, 174:247-250).
  • the covalent linkages between the heterologous component for example, an RNA that comprises a biologically active moiety such as a siRNA or a ribozyme, and P1 or P2 can be direct or indirect but preferably are indirect.
  • the spacer region includes additional string(s) of ribonucleotides at one or both ends of the biologically active moiety. These ribonucleotide strings, if present, contain preferably at least about 3
  • the strings can contain any desired ribonucleotides, however it is preferably that ribonucleotide
  • compositions are selected so as to prevent the ribonucleotide strings on either side of the biological moiety from base pairing with each other or with other parts of the pRNA chimera formed by the artificial pRNA monomer and the heterologous component.
  • Exemplary biologically active moieties include, without limitation, DNA, RNA, DNA or RNA analogs, including a ribozyme, a siRNA, an RNA aptamer, or an antisense RNA, peptide nucleic acid (PNA), a peptide, a protein such as an antibody, a polysaccharide, a lipid, a virus, a plasmid, a cofactor, or a combination thereof.
  • Biologically active moieties can be selected without limitation, and include those having desired activity or characteristic, such as binding activity, enzymatic activity, and the like.
  • the biological activity of the biologically active moieties is an enzymatic activity or binding activity or both; for example, the biologically active moiety may function as or encode a ribozyme or other catalytic moiety.
  • siRNA is a double-stranded RNA
  • the effective siRNA moiety could include any sequence to replace the 573' paired helical region.
  • the biologically active moiety is preferably a polynucleotide.
  • a preferred biologically active polynucleotide is a polyribonucleotide, more preferably the biologically active polynucleotide is a siRNA or a ribozyme such as a hammerhead ribozyme or a hairpin ribozyme.
  • Antisense RNA and other bioactive RNAs are also preferred.
  • nucleotide encompass DNA, RNA, or combinations thereof, unless otherwise indicated.
  • DNA and RNA should be understood to include not only naturally occurring nucleic acids, but also sequences containing nucleotide analogs or modified
  • nucleotides such as those that have been chemically or enzymatically modified, for example DNA phosphorothioates, RNA phosphorothioates, and 2'- O-methyl ribonucleotides.
  • one or more nucleotide derivatives such as 2'-NH 2 -2'-deoxy CTP, 2'-CH 3 -2'-deoxy CTP, 2'-F-2' deoxy CTP, 2'-F-2' deoxy UTP, and aptmers (L-nucleotide aptamers) are incorporated into the pRNA during synthesis to produce stable RNA products that are resistant to RNase digestion.
  • the stabilizing modification is preferably made at the 2' position of the ribonucleotide or at other positions.
  • incorporation of the stabilizing nucleotide derivatives is not expected to significantly interfere with dimerization or trimerization of the pRNAs to form a multimeric complex, nor is it expected to adversely impact the activity or function of the "cargo" moiety. Since biological function of the pRNA itself (other than its ability to form multimeric complexes) is not a concern, inclusion of non-natural nucleotide derivatives is suitable, especially for the receptor-binding aptamers selected from a random pool ⁇ e.g., using SELEX).
  • the cargo RNA can be synthesized with regular nucleotides and ligated to the pRNA molecule.
  • a ribozyme is generally characterized by: arm 1 -active enzyme center-arm 2 where arm 1 and arm 2 are sequences complementary to the target substrate to be cleaved by the ribozyme, and the active enzyme center is the catalytic center that cleaves the target RNA.
  • the "arms" of the ribozyme typically contain at least about 7 nucleotides, preferably at least about 12 nucleotides; and typically contain at most about 100 nucleotides, preferably at most about 30 nucleotides.
  • the nucleotide sequence of the arms can be engineered to hybridize to the nucleotide sequence of any desired target nucleic acid.
  • siRNA was achieved using complementary siRNA attached at positions 29 and 91 to form the paired helical region, and with the siRNA attached at positions 21 and 99 to form the paired helical region (see US 2010/0003753). Accordingly in the present embodiments it is important that the siRNA not intrude into the intermolecular interaction region (containing the right hand and left hand loops) such that it interferes with the interactions of the right and left hand loops in the formation of dimers, trimers and hexamers.
  • Labeling at least one component of a multimeric pRNA complex allows the complex to be detected.
  • a therapeutic agent such as a radionuclide
  • a therapeutic agent can be linked at or near a 5' or 3' end of an artificial two-piece pRNA monomer, a pRNA chimera formed therefrom or a modified pRNA to effect treatment of a subject once the multimeric complex has bound to and/or been internalized by the target cell.
  • a pRNA may be truncated (at either the 5' or 3' ends) with respect to a naturally occurring pRNA, or it may have one or more additional nucleotides added to its 5' and/or 3' end when compared to a naturally occurring pRNA.
  • derivatization may be of the first and/or last nucleotides of the linear pRNA; i.e., the 5' and/or the 3' nucleotides of P1 and/or P2 that form that particular pRNA molecule, or, when the pRNA polynucleotide is produced by non-enzymatic chemical synthesis, derivatization may be effected in the course of the synthesis at any other desired position in the molecular structure.
  • heterologous component can be linked either covalently or noncovalently to the pRNA at or near the 5' or 3' end of the pRNA, for example, at the 5'- and/or 3'-ends of P1 and/or P2.
  • linkage is covalent, except in the case where a complementary
  • oligonucleotide constitutes the heterologous component, as discussed in US 2010/0003753.
  • cancers e.g., solid tumors such as epithelial cancers, epithelioma, adenocarcinoma, cervical cancer, prostate cancer, sarcoma, chondrosarcoma, neuroblastoma, lung, kidney, colon, pancreatic, bone or other cancer, etc., circulating or liquid tumors such as leukemia, lymphoma, ascites tumors, etc.) or infectious disease, including viral infections such as those caused by human immunodeficiency virus (HIV) and hepatitis virus, particularly hepatitis B virus (HBV), also human papilloma virus, influenza and other viruses.
  • HCV human immunodeficiency virus
  • HBV hepatitis virus
  • HBV hepatitis B virus
  • siRNA directed against the gene encoding survivin.
  • Survivin inhibits apoptosis in certain cancer cells, thus survivin siRNA, which silences survivin, induces apoptosis of cancer cells.
  • the dimeric, trimeric and hexameric polyvalent pRNA complexes of the invention are thus ideally suited for therapeutic RNAs or other chemical drugs for the treatment of cancers, viral infections and genetic diseases. Applications of multiple therapeutic agents are expected to enhance the efficiency of the in vivo therapy.
  • RNA molecules are known as "RNA aptamers.”
  • RNA aptamers Starting with a library containing random RNA sequences, in vitro evolution techniques allow for the selection of the RNA molecules that are able to bind a specific pre-identified substrate, such as a ligand or receptor (Ciesiolka et al., RNA 1 :538-550 (1995); Klug and Famulok, Molecular Biology Reports 20:97-107 (1994).
  • the SELEX system is used to identify RNA aptamers that bind specifically to proteins, polysaccharides, lipids, ATP, chemicals and
  • this approach can be generalized well beyond being a means to deliver an endosome disrupting agent or bind a target cell surface receptor, as it provides a way to link essentially any desired molecule (typically, a non-nucleic acid) to the pRNA delivery vehicle once an RNA aptamer that binds it has been identified.
  • the linkage between an RNA aptamer and its target molecule is noncovalent, but cross-linking can, if desired, be achieved in some instances after the initial binding step has taken place.
  • RNA aptamers for specific binding
  • functional groups such as biotin, --SH, or -NH.sub.2 can be linked to the end of the pRNA.
  • endosome disrupting agents or other desired molecules, particularly non- nucleic acid molecules
  • streptavidin- biotin interaction or by chemical crosslinking (--SH/maleimide or - NH.sub.2/NHS ester).
  • the hexamer could harbor up to five other components. These could include poly(amino ester)(n-PAE) (Lim et al., Bioconjug. Chem, 13:952- 957 (2002)), synthetic peptides (Mastrobattista et al., J Biol Chem, 277:27135- 27143 (2002); Plank et al., J Biol Chem, 269:12918-12924 (1994); and Van Rossenberg et al., J Biol Chem, 277:45803-45810 (2002)), virus-derived particles (Nicklin et al., Circulation, 102:231 -237 (2000)) for lysosome escape, adjuvants, drugs or toxins. Using the same principle, dimers or trimers could be utilized. Even the hexamer-bound empty procapsid could prove useful, serving as a nanocapsule to harbor
  • RNA is uniquely suitable for use in treating chronic diseases since it has a low or undetectable level of immunogenicity except when complexed with protein.
  • RNA nanoparticles such as a nanoparticle comprising the herein described artificial pRNA polynucleotide, for example a nanoparticle comprising one or more siRNA polynucleotides that are capable of interfering with target polypeptide expression, may also be used to modulate ⁇ e.g., inhibit or potentiate) target polypeptide activity in a patient.
  • a "patient" may be any mammal, including a human, and may be afflicted with a condition associated with undesired target polypeptide activity or may be free of detectable disease. Accordingly, the treatment may be of an existing disease or may be prophylactic.
  • Non-limiting examples of conditions associated with inappropriate activity of specific siRNA target polypeptides may include disorders associated with cell proliferation, including cancer, graft- versus-host disease (GVHD), autoimmune diseases, allergy or other conditions in which immunosuppression may be involved, metabolic diseases, abnormal cell growth or proliferation, infectious diseases, obesity, impaired glucose tolerance and diabetes, and cell cycle abnormalities.
  • GVHD graft- versus-host disease
  • RNA nanoparticles for administration to a patient, such as (in certain preferred embodiments) a nanoparticle comprising the herein described artificial pRNA polynucleotide, or (in certain other
  • compositions comprised in an appropriate vector ⁇ e.g., including a vector which comprises a DNA sequence from which the subunits of the RNA nanoparticle can be transcribed and then self-assembled
  • a pharmaceutical composition may be a sterile aqueous or non-aqueous solution, suspension or emulsion, which additionally comprises a physiologically acceptable carrier (i.e., a nontoxic material that does not interfere with the activity of the active ingredient).
  • physiologically acceptable carrier i.e., a nontoxic material that does not interfere with the activity of the active ingredient.
  • Such compositions may be in the form of a solid, liquid or gas (aerosol).
  • compositions of the present embodiments may be formulated as a lyophilizate or compounds may be encapsulated within liposomes using well known technology.
  • Pharmaceutical compositions within the scope of the present invention may also contain other components, which may be
  • buffers e.g., neutral buffered saline or phosphate buffered saline
  • carbohydrates e.g., glucose, mannose, sucrose or dextrans
  • mannitol proteins
  • polypeptides or amino acids such as glycine
  • antioxidants e.g., EDTA or glutathione
  • stabilizers e.g., sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium tartrate, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite, sodium metabisulfite
  • compositions of the present invention Any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of the present invention.
  • Carriers for therapeutic use are well known, and are described, for example, in Remingtons Pharmaceutical Sciences, Mack Publishing Co. (A.R. Gennaro ed. 1985).
  • the type of carrier is selected based on the mode of administration.
  • Pharmaceutical compositions may be formulated for any appropriate manner of administration, including, for example, topical, oral, nasal, intrathecal, rectal, vaginal, sublingual or parenteral administration, including subcutaneous, intravenous, intramuscular, intrasternal,
  • the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer.
  • any of the above carriers or a solid carrier such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, kaolin, glycerin, starch dextrins, sodium alginate, carboxymethylcellulose, ethyl cellulose, glucose, sucrose and/or magnesium carbonate, may be employed.
  • a pharmaceutical composition ⁇ e.g., for oral administration or delivery by injection may be in the form of a liquid ⁇ e.g., an elixir, syrup, solution, emulsion or suspension).
  • a liquid pharmaceutical composition may include, for example, one or more of the following: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium,
  • polyethylene glycols, glycerin, propylene glycol or other solvents such as polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose.
  • a parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. The use of physiological saline is preferred, and an injectable pharmaceutical composition is preferably sterile.
  • a therapeutic agent comprising an RNA nanoparticles comprising the herein described artificial pRNA polynucleotide as described herein (or, e.g., a recombinant nucleic acid construct comprising a polynucleotide encoding one or more of the RNA subunits of such a nanoparticle) may be linked to any of a variety of
  • such an agent may be linked to a targeting moiety ⁇ e.g., a small molecule ligand, an aptamer, a monoclonal or polyclonal antibody, a protein or a liposome) that facilitates the delivery of the agent to the target site.
  • a targeting moiety may be any substance (such as a compound or cell) that, when linked to an agent enhances the transport of the agent to a target cell or tissue, thereby increasing the local concentration of the agent.
  • Targeting moieties include small molecule ligands ⁇ e.g., folate), aptamers, antibodies or fragments thereof, receptors, ligands and other molecules that bind to cells of, or in the vicinity of, the target tissue.
  • An antibody targeting agent may be an intact (whole) molecule, a fragment thereof, or a functional equivalent thereof. Examples of antibody fragments are F(ab')2, Fab', Fab and F[v] fragments, which may be produced by conventional methods or by genetic or protein engineering.
  • Linkage is generally covalent and may be achieved by, for example, direct condensation or other reactions, or by way of bi- or multi-functional linkers.
  • Targeting moieties may be selected based on the cell(s) or tissue(s) toward which the agent is expected to exert a therapeutic benefit.
  • Pharmaceutical compositions may be administered in a manner appropriate to the disease to be treated (or prevented).
  • An appropriate dosage and a suitable duration and frequency of administration will be determined by such factors as the condition of the patient, the type and severity of the patient's disease, the particular form of the active ingredient and the method of administration.
  • an appropriate dosage and treatment regimen provides the agent(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit ⁇ e.g., an improved clinical outcome, such as more frequent complete or partial remissions, or longer disease-free and/or overall survival, or a lessening of symptom severity).
  • a dose should be sufficient to prevent, delay the onset of or diminish the severity of a disease associated with cell proliferation.
  • Optimal dosages may generally be determined using experimental models and/or clinical trials.
  • the amount of RNA nanoparticles (comprising the herein described artificial pRNA polynucleotide) that is present in a dose, or that is produced in situ by DNA present in a dose ⁇ e.g., from a recombinant nucleic acid construct comprising an encoding polynucleotide), ranges from about 0.01 ⁇ g to about 100 ⁇ g per kg of host, typically from about 0.1 ⁇ g to about 10 ⁇ g.
  • the use of the minimum dosage that is sufficient to provide effective therapy is usually preferred.
  • Patients may generally be monitored for therapeutic or prophylactic effectiveness using assays suitable for the condition being treated or prevented, which will be familiar to those having ordinary skill in the art. Suitable dose sizes will vary with the size of the patient, but will typically range from about 10 mL to about 500 mL for 10-60 kg animal.
  • an agent includes one agent, as well as two or more agents; and so forth.
  • Standard techniques may be used for recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation ⁇ e.g., electroporation, lipofection).
  • Enzymatic reactions and purification techniques may be performed according to manufacturer's specifications or as commonly accomplished in the art or as described herein. These and related techniques and procedures may be generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification. See e.g., Sambrook et ai, 2001 , MOLECULAR CLONING: A LABORATORY MANUAL, 3d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Current Protocols in Molecular Biology (Greene Publ.
  • the 2'-F-pRNA monomer molecule was first chemically synthesized as two pieces with an approximate length of ⁇ 55nt of P1 and -60 nt of P2 (depending on the particular pRNA monomer) by Trilink Biotechnologies (San Diego, CA).
  • the first oligonucleotide (P1 ) had a 3'-OH group.
  • the second oligonucleotide (P2) had a 5'-phosphate group (Fig. 1A).
  • P1 and P2 were simply mixed and/or annealed at an equal molar ratio at the desired concentration.
  • P1 and P2 oligonucleotides were dissolved in 1 X T4 RNA ligase buffer (New England BioLabs, Ipswich, MA) at 50 ⁇ final concentration for each oligo. The oligonucleotides were annealed by heating to 90°C for 10 min followed by slow cooling to room temperature over the course of 45 minutes.
  • T4 RNA ligase I (1 .2 ⁇ / ⁇ _) (New England BioLabs, Ipswich, MA) was added and the reaction carried out at 37°C overnight to form the pRNA monomer.
  • the ligated product was extracted using phenol :chloroform followed by ethanol precipitation and subsequent 10%/8M urea PAGE purification.
  • the purified product was quantified by UV absorbance at 260 nm using a NanoDrop ND-1000 spectrophotometer. Cellular uptake ofpRNA nanoparticle by confocol
  • Fluorescently-labeled pRNA nanoparticles were used for cellular uptake studies. Essentially, two labeling methods were used. First, direct coupling of fluorescence at 5' end of the oligonucleotides was used as described above. Second, the pRNA was labeled with fluorescein using the Label IT® kit and purified according to the manufacturer's instructions
  • KB cells were grown in a folate-free RPMI-1640 medium (Invitrogen, Eugene, OR) supplemented with 10% FBS.
  • the cells were cultured in eight-well-chambered slides (LabTek®; Nunc, Roskilde, Denmark) at a density of 1x104 cells/well. Twenty-four hours later, the culture media was replaced with fresh 200 uL folate-free media, and the fluorescently labeled folate-pRNA nanoparticles were added at a final concentration of 200 nM, either in the absence or in the presence of 200-fold excess of free folic acid. After incubation of the cells at 37°C for 30 min, confocal microscopy was conducted. Images were recorded with an inverted Nikon A1 confocal microscope using a 40x objective. Images were processed using NIS software provided by Nikon.
  • PBMCs mononuclear cells
  • 2'-F modified pRNA and poly l:C as a positive control.
  • the expression levels of human TLR receptors were analyzed by semi-quantitative RT-PCR using TLR RT-Primer Set (Invivogen, San Diego, CA), as described herein.
  • Mouse macrophage cell line, RAW-246 (ATCC, Manassas, VA), was plated at a density of 30,000 cells/well in 200 ⁇ _ DMEM medium supplemented with 10% (v/v) FBS in 96 well plate. The cells were incubated with pRNA nanoparticles at final concentrations of 400, 100, 4 g/mL for 3 h at 37°C. Aliquots (20 ⁇ _) from the culture medium were taken and analyzed using the ELISA kit for murine TNF-a, per the manufacturer's instruction (Antigenix America, NY).
  • HEK-BlueTM- hTLR3 (Invivogen, San Diego, CA) cells were set up at a density of 300,000 cells/mL in a test medium containing DMEM, 4.5 g/L glucose, 100 g/mL NormocinTM, 2 mM L-glutamine, 10% (v/v) heat inactivated FBS.
  • the cell suspension (180 ⁇ _) was mixed with a 20 ⁇ _ pRNA solution and plated in each well of a 96 well plate with final concentrations of 1000, 100, and 10 ng/mL, followed by overnight incubation at 37 °C.
  • mice Balb/c nude male mice (3 mice total) were each injected with 600 ⁇ g of AlexaFluor647-labeled pRNA monomer (24 mg/kg) through the tail vein.
  • Blood was collected (up to 20 ⁇ _) through the lateral saphenous vein at 5 min, 30 min, 2hr, 5hr, and 24hr time points. Blood samples were collected in BD Vacutainer® SSTTM Serum Separation Tubes. The tubes were inverted five times and left for 30 minutes at room temperature (to allow the blood to clot), followed by centrifugation at 1000-1300 g for 10 minutes. Two ⁇ _ supernatant serums were mixed with 1 ⁇ _ of proteinase-K and 37 ⁇ _ of water.
  • the mixture was incubated at 37°C for 30 minutes before loading onto the capillary gel electrophoresis (CGE) machine.
  • CGE capillary gel electrophoresis
  • the pRNA in the blood was quantified by CGE through measurement of the fluorescence intensity using a P/ACE MDQ capillary electrophoresis system with a 635 nm laser suitable for AlexaFluor647 fluorophores (Beckman Coulter, Inc., Fullerton, California).
  • the capillaries used were 32 cm in length and 100 ⁇ in diameter. Samples were loaded by voltage injection for 40 s at 4 kV and allowed to run for 25 min at 7.8 kV. The gel was replaced after every run.
  • the buffer and the non-denaturing gel were purchased from Beckman Coulter (dsDNA 1000 Kit).
  • the electropherograms produced were integrated using the software "32 Karat” version 7 provided by Beckman Coulter.
  • the pRNA concentrations were calculated from a standard curve.
  • the serum concentration profiles were fitted with an IV bolus non- compartmental model using the Kinetica program (Fisher Scientific, Inc.), and the key secondary pharmacokinetic parameters were deduced.
  • mice 3 groups of 4 immunocompetent female C57B/6 mice (Harlan) aged 10 weeks were injected via tail vein with PBS, Ba'-2'-F-sur-pRNAi (KT-108) at 30mg/kg and KT- 108 at 10mg/kg.
  • the blood was collected by cardiac puncture 3 hrs post injection.
  • the plasma was prepared and analyzed for mouse TNF-a and IL-6 using ELISA assay
  • mice were intravenously injected (tail vein) with: 1 ) PBS, 2) poly l:C at 30mg/kgm (Sigma, MO), 3) KT-108 at 30 mg/kg, and 4) KT-108 at 10 mg/kg.
  • the mice were treated once every 48hr for 7 days (4 doses total). The mice were monitored for clinical signs and body weights. On day 7, 3 h post the fourth injection, the mice were euthanized per protocol and blood samples were collected by cardiac puncture for standard panel clinical chemistry (including PT, aPTT) and clinical pathology analysis.
  • 6-week-old male nude mice (nu/nu) were purchased from NCI/Frederick and maintained on a folate-free diet for a total of 2 weeks before the start of the experiment.
  • the mice were injected with different cancer cells (KB cells ⁇ 3 x 106 cells per mouse, HeLa cells ⁇ 1 x 107 cells per mouse in 40 % matrigel in a folate free RPMI-1640 medium.
  • the tumors reached -500 mm3
  • the mice were injected intravenously through the tail vein with a single dose of 15 nmol (24 mg/kg) of KT-105 (FA-AlexaFluor647 labeled-pRNA).
  • T4-RNA ligase 2 -F-P1 and -P2 are efficiently ligated by T4-RNA ligase into the full-length pRNA.
  • the synthetic strategy produced two new termini (P1 -OH-3' and 5'-PO4-P2) that could be readily ligated to form a full-length molecule if desired.
  • a correctly folded pRNA monomer would present the T4 RNA ligase with an intramolecular ligation step instead of the regular
  • the chemically synthesized P1/P2 complex with or without ligation formed a dimer with other pRNA.
  • a correctly folded 2-piece pRNA monomer (Ba') or the 2-F modified pRNA monomer have been shown to form a dimer with a complementary (Ab') monomer (16, see Example 3).
  • a two-piece 2'-F-Sur-pRNAi Ba' monomer was mixed with a 2'F-pRNA Ab' monomer at a 1 :1 molar ratio, followed by native PAGE analysis.
  • the results demonstrated that the two monomers, whether ligated or non-ligated, formed a dimer (Fig. 1 D).
  • Fluorescent based capillary electrophoresis a technique milder and more sensitive than regular slab gel, indicated that the efficiency of 2'-F-pRNA dimer formation was as high as 99% (Fig. 6).
  • the 2'-F-pRNA nanoparticle (two-piece) was stable.
  • the stability of a pharmaceutical product is particularly important for manufacturing, storage, transportation, and potency maintenance (expiration date), etc.
  • thermostability is also the foundation for diverse and robust modularizations. Furthermore, thermostability can also affect the behavior of nanoparticles inside the body upon administration.
  • a functional nucleic acid agent such as pRNA
  • the most important aspect of its stability lies in the stability of its folding, particularly the two-pieces folding together.
  • Melting temperature (Tm) studies reveal that the nonligated 2'-F two-piece pRNA was stable.
  • the 2'-F-pRNA was metabolically stable in the presence of serum or RNase A.
  • the purpose of chemical modification was to make the pRNA nanoparticle metabolically stable in biological fluids (e.g. plasma). Previous data have shown that the 2'-F-modified pRNA generated by in vitro transcription was indeed significantly stabilized in the biological milieus (16).
  • this particle was incubated with culture media containing 10% and 50% human serum for various periods, followed by denaturing urea-PAGE analysis. A large proportion of the 2'-F-pRNAi remained intact for up to 24 hours (Fig. 7), in contrast to the non-modified RNA, which degraded rapidly. The enhanced stability was further confirmed by incubating the 2'-F pRNA with RNaseA, where the majority of full-length pRNAi remained intact (Fig. 7). These results demonstrated that the chemically synthesized 2'-F-pRNA was metabolically stable.
  • the pRNA nanoparticles did not induce IFN response in cultured DCis in vitro.
  • a safety profile is a key aspect of any nanodelivery system for systemic applications.
  • a concern with a nucleic acid based system is the non-specific activation of interferon response (IFN) pathways.
  • IFN interferon response
  • the potential induction of IFN responses was assessed in vitro using several cell-based systems. Since polyinosinic:polycytidylic acid (Poly l:C), a synthetic double-stranded RNA, is a ligand to Toll-like receptor (TLR)-3 and a potential inducer of cytokines (IFN, IL-6 and TNF-a, etc.) (33), it was used as a positive control in all tests.
  • TLR Toll-like receptor
  • HEK-BlueTM-hTLR3 is a reporter 293-cell line that over-expresses the human TLR3 gene (hTLR3) and secretes reporter embryonic alkaline phosphatase (SEAP), whose gene is under the control of an NF- ⁇ and AP-1 inducible promoter.
  • SEAP reporter embryonic alkaline phosphatase
  • the SEAP in the culture media provides a colorimetric readout of the activation of TLR3-induced pathways.
  • pRNA was incubated with HEK-BlueTM- hTLR3 overnight, and then quantified the SEAP production.
  • pRNA did not induce the TLR-3 pathway, in contrast to the poly l:C induced dose responsive induction of the TLR-3 pathway (Fig. 2D).
  • pRNA nanoparticles did not induce interferon response in multiple cell types at all tested dose levels in vitro.
  • pRNA with a longer double strand region did not cause any IFN response.
  • RNA nanoparticles One important utility of nanoparticles for therapeutic or diagnostic applications is that different functional modules can be incorporated into a single nanoparticle.
  • a robust nanodelivery system may in certain embodiments desirably have these features: 1 ) the incorporation should not change the structures and functions of either the nanoparticle core or the modules; 2) the modularization can still be achieved by a simple bottom-up self-assembly process using the same basic building blocks but with different pre-incorporated functional modules; 3) a chemical synthesis process can facilitate precisely controlled modulation of the building blocks.
  • the herein described pRNA nanoparticles had these three features, exemplified by the following functional modularizatons.
  • RNA can be readily labeled by fluorescence using a commercially available kit, such as the one that uses a fluorescent platinum reagent that can non- specifically label any G base in a nucleic acid sequence (e.g. the Silencer® Labeling Kit from Ambion).
  • a fluorescent platinum reagent that can non- specifically label any G base in a nucleic acid sequence
  • this process is hardly stoichiometric, and the number of fluorescent tags per pRNA monomer is difficult to control, which in turn may affect folding, cause physical hindrance in intermolecular interaction, and/or disturb interaction with cell surface receptors.
  • Fluorescent tags were able to be introduced (such as Cy5, Cy3, FITC and AlexaFluor647) at the 5'-end as well as at the 3'-end or in the middle of the sequence of both P1 and P2.
  • FIG. 1A shows examples of these fluorescent tags incorporated at the 5'- end of P1 and P2 using this method.
  • These fluorescently labeled P1 or P2 were self-assembled with 5'-folate-P1 or P2 to form a fluorescently labeled folate- pRNA monomeric pRNA nanoparticle to be used for in vitro and in vivo imaging experiments.
  • Folate receptors are widely over-expressed in many cancer cell surfaces. Folate ligand binds to FR with high affinity (Kd of 0.1 -1 nM) (37).
  • folate has been broadly tested as a targeting mechanism for delivering chemotherapeutic drugs, liposome, siRNA, or imaging reporters to tumors (38-42). Therefore, the folate- pRNA nanoparticle was tested for specific targeting to FR+ tumors.
  • phosphoramidite was first synthesized in collaboration with Berry & Associates, Inc. The folate phosphoramidite was then coupled into pRNA-P1 at the last step during regular automated chemical synthesis with coupling efficiencies > 90% (Fig. 1A). This efficiency is difficult to achieve by other methods.
  • P2 could also be labeled with folate by a direct coupling method to create 5'-folate-pRNA P2.
  • the folate-pRNA P1 self-assembled with pRNA-P2 to form the folate-pRNA monomer, similar to the non-folate modified pRNA monomer (Fig. 1A).
  • Folate-pRNA nanoparticles specifically targeted FR+ human xenograft tumors in immunocompromised mice upon systemic exposure.
  • a ligand labeled pRNA nanopartide was tested for beneficial tissue distribution and the advantage of self-delivery to the disease tissues of interest upon systemic administration.
  • the nanoparticles contained a specific ligand that could target only disease tissue; they were relatively small in size and hydrophilic, so as not to be trapped in the liver and spleen by the
  • RES reticuloendothelial system
  • AlexaFluor647-folate-pRNA fluorescence-labeled folate-pRNA nanopartide
  • the Alexa Fluor-647 was chosen as a near infrared fluorescent dye for its brightness, photo-stability and far-red emission spectrum that did not overlap with autofluorescence levels in tissue to be conjugated to pRNA (5'-P2, see above) by direct coupling during the last step of P2 synthesis. Twenty-four hours post-administration, the animals were imaged using MS® Lumina station.
  • PK analysis of 2'-F-pRNA nanoparticle Pharmacokinetic (PK) parameters describe the fate and/or behavior of a drug in the in vivo
  • the 2'-F modified pRNA nanoparticles had significantly enhanced metabolic stability.
  • the dimensions of the monomeric pRNA nanoparticles were > 1 1 nm, which was above the threshold of kidney filtration.
  • a PK analysis was carried out for the folate-2'-F-pRNA nanopartide in tumor bearing mice upon systemic administration (a single intravenous injection), in which P1 was fluorescently labeled (AlexaFluor647) at the 5'-end (Fig. 1A). Fluorescence labeling was to ensure sensitive detection and quantification of nanoparticles in plasma sample, as compared to the low sensitivity of UV detection/quantification.
  • the labeled folate-2'-F-pRNA was injected via the tail vein at time 0, followed by blood collection at different time points post administration (5 min, 30 min, 2hrs, 5hrs, 24hrs).
  • the fluorescent nanopartide concentration in serum was then determined using capillary gel electrophoresis (CGE). The choice of using CGE was to ensure the
  • the Plasma concentration-time plot demonstrated a typical two- phase kinetics with an initial rapid distribution phase, followed by a relatively slow elimination phase (Fig. 4).
  • the secondary PK parameters were calculated using a non-compartmental model, as shown in Table 1 . The results
  • mice Two toxicological assessments of pRNA were performed in mice. The rationale for choosing mice was to be consistent with both PK and tumor targeting studies.
  • three groups of four immunocompetent C57B/6 mice each were injected via the tail-vein with PBS (group 1 ), pRNA at 30mg/kg (group 2), and pRNA at 10mg/kg (group 3) respectively.
  • group 1 three groups of four immunocompetent C57B/6 mice each were injected via the tail-vein with PBS (group 1 ), pRNA at 30mg/kg (group 2), and pRNA at 10mg/kg (group 3) respectively.
  • the plasma samples from the treated animals were analyzed for mouse TNF-a and IL-6 induction by ELISA. The results showed no induction of TNF-a and IL-6 at the tested dose levels.
  • RNA nanoparticles have several important features (for Review, see (5)).
  • RNA can fold into well-defined and stable 3° structures. For example, kissing-loop interactions can be 2-3 fold more stable than the RNA duplex of the same sequence (27,28).
  • RNA as an informational molecule, can be fabricated in different sizes, structures and functions, which are all coded in its sequences.
  • RNAi trigger and self-folding RNA scaffolds mimicking ribozymes and aptamers.
  • useful functional modules e.g. RNAi trigger and self-folding RNA scaffolds mimicking ribozymes and aptamers.
  • RNA modularity is hierarchically manifested at chemical, structural, and supramolecular levels, a desired RNA nanostructure with multiple substructures and functions, in principle, can be predesigned and constructed by a bottom-up process using programmable basic building blocks.
  • scalable total synthetic chemistry procedures are now available for industrial manufacturing and precise modifications of these predesigned building blocks.
  • RNA is completely biocompatible, biodegradable and non-immunogenic
  • modified RNA is resistant to degradation by ribonucleases without altering the original structure/functions in many cases (16).
  • RNA nanotechnology faces practical challenges because of its extreme flexibility and variability.
  • Each RNA nucleotide has eight degrees of freedom, and there are competitions between the favorable stacking interaction and the non-favorable
  • the pRNA secondary structure (1 , 4, 6, 21 ) has been demonstrated by the present studies to be retained in chemically synthesized two-piece pRNA monomers that were tightly folded and highly stable. These are believed to be the first RNA nanoparticles to have been comprehensively examined pharmacologically in vivo, and to be demonstrated to be safe with favorable PK and biodistribution profiles, as well as self delivery to tumor tissues by a specific targeting mechanism.
  • RNA nanoparticles biocompartibility profiles as RNA nanoparticles. Aptamer attachment to herein described RNA nanoparticles did not disrupt the structures and/or functions of either the nanoparticle or the aptamer (data not shown).
  • pRNA nanoparticles thus will find advantageous use in therapeutic delivery, with synthetic uniformity, particle size, PK properties, and immunological/ toxicological properties that are superior to naked siRNA and to other polymeric or liposomal delivery platforms; these and other properties also provide advantages for imaging targeted disease tissues as demonstrated in this study.
  • fluorescent dyes other reporters such as radioactive isotopes or contrasting agents can also be incorporated for a variety of imaging applications, including PET and NMR.
  • the 1 17-nucleotide RNA called the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor, has been shown to be an efficient vector for the construction of RNA nanoparticles for the delivery of siRNA into specific cancer or viral infected cells.
  • pRNA packaging RNA
  • chemical synthesis of 1 17- nucleotide RNA is not feasible commercially.
  • labeling at specific locations on pRNA requires the understanding of its modular organization.
  • the resulting two-piece pRNA was fully competent in associating with other interacting pRNAs to form dimers, as demonstrated by the packaging of DNA via the nanomotor and the assembly of phi29 viruses in vitro.
  • the pRNA subunit assembled from two-piece fragments harboring siRNA or receptor- binding ligands were equally competent in assembling into dimers.
  • the subunits carrying different functionalities were able to bind cancer cells specifically, enter the cell, and silence specific genes of interest.
  • the pRNA nanoparticles were subsequently processed by Dicer to release the siRNA embedded within the nanoparticle.
  • RNA molecules can be designed and manipulated at a level of simplicity characteristic of DNA, while possessing the flexibility in structure and function or enzymatic activity similar to that of proteins.
  • RNA is a suitable candidate for nanotechnological applications (1 -5).
  • the concept of RNA nanotechnology has been proposed for more than a decade (2, 4, 6-9)(for review, see ref (1 , 10, 1 1 ).
  • the first evidence was reported in 1998 showing that dimeric, trimeric, and hexameric RNA nanopartides can be assembled through self-assembly of multiple reengineered natural RNA molecules (2).
  • the field of RNA nanotechnology becomes more and more popular due to the recognition of the potential of RNA nanopartides in the treatment of cancer, viral infection, genetics diseases and other human ailment (1 ).
  • RNA-based therapeutic approaches using small interfering RNA (siRNA) (12-15), and hbozymes(16-20) have been shown to down-regulate specific gene expression in cancerous or viral-infected cells.
  • RNA aptamer has been shown to bear functions similar to that of antibodies in their ability to recognize specific ligands (organic compounds, nucleotides, or peptides) for targeted delivery through the formation of binding pockets(21 ,22). This has led to heightened interest in the scientific community and the rapid development of siRNA-based therapeutics.
  • pRNA packetaging RNA
  • Phi29 DNA packaging motor uses six pRNAs that form a ring to gear the DNA packaging motor(2,27- 30). Each pRNA molecule contains two domains (Fig. 10a). One of the domains, bases 23-97, located at the central region of pRNA, is for
  • the two interlocking loops reside within this domain.
  • the second domain is for the binding of the DNA packaging enzyme gp16 (33). This domain is located at the 573' ends that pair to form a double-stranded helical region(34). Removal of this domain does not affect the formation of dimer, trimer and hexamer(27,32). Therefore, the pRNA 573' proximate double-stranded helical end(34) could serve to carry a therapeutic siRNA (Fig. 10a) (23,24).
  • pRNA could escort the siRNA to silence genes and to destroy cancer cells of leukemia, lung, breast, head and neck, as well as others (23-25, 35-38).
  • the pRNA system has several advantages including defined structure, controllable stoichiometry, multi- valency, targeted delivery, ideal nanoscale size (-20-40 nm), and minimal induction of antibody response to enable repeated treatments of chronic diseases (1 ).
  • the pRNA is remarkably stable in a wide range of pH (-4-9), temperature, and organic solvents(3).
  • RNA subunit is about 1 17 nucleotides, which is beyond the limit of currently available commercial chemical RNA synthesis technologies
  • RNA polymerase RNA polymerase
  • the pRNA can be dissected into a two-piece chimeric construct, in which two individual RNA oligonucleotides, one encompassing the R-loop and the other the L-loop, are clamped together via a six-nucleotide duplex(39).
  • one of these pieces is located in the middle of the pRNA; this made the resulting RNA not suitable for the construction of therapeutic RNA nanoparticles harboring siRNA or other modules, and also not feasible for applications in drug delivery.
  • we further develop the two-piece chimeric constructs to generate full-length functional pRNAs that are not only competent for driving the phi29 DNA packaging motor but also proficient for therapeutic and diagnostic purposes.
  • RNA fragments were transcribed by T7 RNA polymerase using dsDNA templates from PCR, as described previously (3).
  • dsDNA templates from PCR, as described previously (3).
  • RNA complex pRNA/siRNA(GFP), pRNA siRNA(luciferase), and pRNA siRNA(survivin) were assembled from the synthesized RNA fragments either by direct mixing of two fragments at 1 :1 molar ratio in TMS (10 mM Mg2+) buffer at room temperature for more than 30 mins or by annealing the two fragments in TMS through heating at 75 °C for 5 min, followed by slow cooling to room temperature. RNA complexes assembled from the two pieces were then purified from 10% native polyacrylamide gel(28).
  • Assay for pRNA dimer formation The potential of dimer formation is one way to verify correct folding of the pRNA assembled from two pieces of RNA fragments.
  • the pRNA construct Ab' monomer was mixed with their interacting partner pRNA Ba' in TBM buffer (89 mM Tris-HCI (pH 7.6), 0.2 M Boric Acid, and 5 mM MgCI2) at equal mole ratio, and incubated at room temperature for 30 min. The dimer formation was then assayed, followed by purification in 10% native polyacrylamide gel.
  • the mature viral particles could be obtained by mixing two-piece pRNA Ab' monomer, (1 -1 17)pRNA Ba', viral procapsid, gp16, and DNA-gp3, 10mM ATP as well as other two components gp9 and gp1 1 -14 were incubated at room temperature. The mixture was plated on host Bacillus subtilis su+44. After 12-14hrs incubation at 37 °C, the plaque formation per plate was count and the viral assembly activity was calculated by PFU/mL.
  • Human nasopharyngeal carcinoma KB cells (American Type Culture Collection, ATCC, Manassas, VA) are routinely maintained in RPMI 1640 medium (Invitrogen, Carlsbad, CA) and
  • FBS fetal bovine serum
  • GFP reporter assay to test the potential of the two-piece pRNA complex in escorting siRNA delivered into specific cells.
  • 105 cells were seeded in 24- well plates.
  • GFP-expressing plasmid pGFP-N2 (Clontech Laboratories, Inc., Mountain View, CA)
  • two-piece pRNA AbVsiRNA(GFP) and different kind of mutant controls were co-transfected into cells by using lipofactamine 2000 (Invitrogen, Carlsbad, CA) 24 hours after seeding. The effect was measured at the level of eGFP expression, as observed by fluorescence microscopy(23,24).
  • Dual-Luciferase assays to test the potential of the two-piece pRNA complex in escorting siRNA delivered specifically into cells via folate receptors.
  • KB cells were seeded in 24-well plates.
  • Gene silencing assays were performed by co-transfecting two- piece chimeric pRNA/siRNA(luciferase) with both plasmid pGL3 and pRL-TK (Promega, Madison, Wl) coding for firefly and renilla luciferase, respectively. The latter served as an internal control to normalize the luciferase data (Dual- Luciferase Reporter Assay System, Promega, Madison, Wl).
  • KB Cells were seeded into 24-well plates overnight and transfected with 5nM, 20nM and 40nM two-piece pRNA siRNA(survivin) chimera as well as the scrambled control by Lipofectamine 2000. After 48 hrs, cells were rinsed and harvested in lysis buffer. Protein concentrations were determined and equal amounts of proteins were loaded onto a 15% polyacrylamide gel.
  • Membranes were blocked, incubated with primary antibody to survivin and ⁇ - actin (R&D Systems, Minneapolis, MN), and conjugated to a secondary antibody (Sigma-Aldrich Corp., St. Louis, MO). Membranes were then blotted by ECL kit (Millipore, Billerica, MA) and exposed to film for autoradiography.
  • RNA complexes were grown on glass coverslides in folate-free RPMI-1640 medium overnight. Two-piece pRNA/folate and control two-piece pRNA/NH2 with siRNA were each incubated with the cells at 37°C for 2-3 hrs. After PBS wash, the cells were fixed by 4% paraformaldehyde and stained by Alexa Fluor® 488 phalloidin (Invitrogen, Carlsbad, CA) for cytoskeleton and TO- PRO®-3 iodide (642/661 ) (Invitrogen, Carlsbad, CA) for nucleus, staining as per the manufacturer's instructions. Cells were then assayed for binding and entry of the RNA complexes by the Zeiss LSM 510 laser scanning confocal microscope (Carl Zeiss).
  • Dicer processing of the two-piece pRNA/siRNA complex The procedure for in vitro Dicer processing assay has been reported previously (23).
  • the 5'-end [32P] labeled two-piece pRNA siRNA chimera or the intact pRNA siRNA chimera was treated with the recombinant Dicer (Genlantis/Gene Therapy Systems, San Diego, CA) and separated by 16% Urea/PAGE gel for subsequent autoradiography.
  • the pRNA constructs used in this work are identified by: (i) the R-loop and/or L-loop sequence(s); and (ii) the started/ended nucleotide number.
  • a particular R-loop sequence is assigned an upper case letter (i.e., A, B, ..), and a particular L-loop sequence is assigned a lower case letter with a prime (i.e., a', b', ..).
  • the same set of letters i.e., Aa' designates complementary sequences in the R/L loop, while different letters indicate lack of sequence complementarities.
  • Ab' indicates that the pRNA assemblies contain a right-hand loop A and the left hand loop b' for inter-RNA interaction with Ba' in the assembly of the pRNA dimer.
  • the 1 17-nt intact pRNA with various R-loop and L-loop is designated as (1 -1 17) Rl' (i.e., 1 -1 17 Ab').
  • FIG. 10b Three two-piece pRNA assemblages (Fig. 10b) are designated as (1 -28)/(30-1 17) Ab', (1 -55)/(56-1 17) Ab' and (1 -71 )/(75-1 17) Ab'.
  • Three two- piece pRNA chimeras (Fig. 10b) are designated as (1 -28)/(30-1 17) Ab' pRNA/siRNA (eGFP), (1 -55)/(56-1 17) Ab' pRNA/siRNA (eGFP) and (1 -71 )/(75- 1 17) Ab' pRNA/siRNA (eGFP).
  • pRNA/siRNA(eGFP) represents a pRNA chimera that harbors a siRNA targeting the eGFP gene while pRNA/siRNA (luciferase) and pRNA/siRNA (survivin) represent pRNA chimeras that harbor siRNAs targeting the firefly luciferase gene and survivin gene respectively.
  • (1 - 28) and (30-1 17) refer to start and stop of the RNA fragment one and fragment two, respectively, using phi29 pRNA seqAuence number as a reference.
  • RNA assemblies by bottom-up approach using synthetic pRNA fragments.
  • the goal of the construction of pRNA assemblies is two-fold: driving the DNA packaging motor of phi29 and harboring RNA moieties, functionalities, or chemical groups for therapeutic purposes.
  • RNA chimeras there are two important elements: the first one serves as the directing core to guide the folding and assembly of the resulting pRNA chimeras, whereas the second one functions to deliver these particles for medical applications.
  • each fragment of the two-piece RNAs should be smaller than 100nt and suitable for chemical synthesis.
  • All the selected breaks are located at the less structural constraint and more flexible region. And the breaks should avoid the sequences involved in the intermolecular interaction, some important bulges responsible for viral packaging or the region which is for holding functional moieties such as siRNA insertion.
  • Phi29 DNA packaging motor uses six pRNAs that form a ring to gear the DNA packaging motor (2, 27-30). It has been reported previously that dimers are the building blocks in the assembly of the phi29 DNA packaging motor (28). Also, this self-assembling property can be used for the fabrication of reengineered dimeric pRNA chimeras that can serve as polyvalent vehicles for specific targeting and delivery of siRNA or ribozyme to cancer cells(10,23-25,36). Thus, it is crucial to find out whether pRNA constructs can form dimers, which would provide direct evidence that pRNA monomeric subunits constructed by the two-piece approach retain the self- assembling property of the intact pRNA.
  • the two-piece monomeric Ab' pRNA subsequently formed dimer, in the presence of its interacting partner (1 -1 17)Ba' pRNA and migrated into the upper dimer band which was at the same position as wild-type pRNA dimer Ab'-Ba'.
  • the phi29 DNA packaging assay (41 , 42) was carried out by replacing one of the subunits of the pRNA dimer with the two- piece pRNA assemblies. After in vitro assembly of the functional DNA packaging motor, the double-stranded viral genome was packaged into the viral prohead. The mixture was then treated by DNase I and separated by 0.8% agarose gel. The DNA successfully packaged was protected from DNase digestion and can be observed on the gel (Fig. 1 1 a).
  • the viral assembly assay also carried out by replacing one of the subunits of the dimer with the two-piece pRNA assemblies, the functional dimer will drive the DNA packaging motor to gear the viral genome into the procapsid and subsequently form the mature virons to infect the host bacteria and form plaques.
  • the plaque forming units (PFU) per milliliter was used to reflect the RNA activity during the phi29 viral assembly.
  • the control pRNA dimer showed 107 PFU/mL viral assembly activity while all three types of the two-piece Ab' pRNA assembled from two RNA fragments still exhibited around 106 PFU/mL viral assembly activity, thereby demonstrating that the chimeric dimers were indeed functional.
  • Fig. 13 functionality targeting the experimental reporter, firefly luciferase gene (Fig. 13). This included the constructions (1 -28)/(30-1 17)Ab' pRNA/siRNA(firefly luciferase), (1 -55)/(55-56)Ab' pRNA/siRNA(firefly luciferase) and (1 -71 )/(75- 1 17)Ab' pRNA/siRNA(firefly luciferase). Compared to the eGFP gene knockdown assay, the dual-Luciferase report system can quantitatively measure the gene silencing effects of these three two-piece pRNA siRNA assemblies.
  • the relative lucifrease activity was used to reflect the expression level of firefly luciferase gene by normalizing the firefly luciferase activity with the internal control, Renilla luciferase activity.
  • the two-piece (1 -28)/(30-1 17) pRNA/siRNA(survivin) assembly showed similar silencing effects on the survivin gene expression as the intact pRNA siRNA(survivin) which is demonstrated by Western Blot assay; a two-piece pRNA siRNA assembly harboring scrambled survivin siRNA served as negative control (Fig. 14).
  • This two-piece pRNA siRNA was processed efficiently by Dicer in vitro to release the end RNA fragment (23nt ⁇ 27nt), as shown in Fig. 16. The processed small RNA fragments were confirmed to harbor the siRNA sequence by Northern Blot assay (data not shown).
  • RNA nanoparticles Many cancer cell lines, especially those of epithelial or myelocytic origin, overexpress the folate receptor (FR) on their surface(43). Folate has been used extensively as cancer cell delivery agent via folate receptor-mediated endocytosis(25, 37,44). Human nasopharyngeal epidermal carcinoma KB cells which have overexpressed FR on the cell surface(37) were used as the cell model and the fluorescently labeled two-piece pRNA folate was used to test its cell binding efficiency. A fluorescent two-piece pRNA NH2 that did not contain folate group was used as the negative control. Flow cytometry data showed that the binding efficiency of the fluorescent two- piece pRNA/folate was close to 100% (Fig.
  • Rational design of two-piece RNA assemblies followed multiple cpRNA designs (40). All these cpRNAs showed comparable DNA packaging and viral assembly activity which indicated the new opening/break along the pRNA chain have no or less affects on the correct folding as well as the function of pRNA. Other criteria were also considered.
  • the final assemblies generated by two-piece designs should: 1 ) still maintain the correct structure folding; and 2) maintain the similar function as intact particles.
  • phi29 bacteriophage pRNA can be engineered to harbor therapeutic modules and efficiently assembled into higher order structures with defined stoichiometry using a two-piece construction approach. This method overcomes the current limitations in chemical synthesis of long RNA molecules, while retaining the structural and functional integraty and chemical stability of both wild type pRNAs and the therapeutic pRNA chimeras.
  • the two-piece pRNA constructs were structurally competent, evidenced by efficient dimer formation. However, the two-piece modules showed lower DNA packaging and viral assembly activity (-10 fold) compared to the wild type pRNA.
  • the multivalent chimeric constructs harboring targeting, detection, and therapeutic moieties were functionally proficient, as
  • the intact pRNA/siRNA can only be processed to generate the RNA fragment larger than 23nt, while the two- piece module could be processed to generate -23 nt RNA fragment since the single nucleotide gap between nucleotide 28 and 30 within the two-piece pRNA siRNA molecule might facilitate the siRNA processing by Dicer.
  • siRNA alone might be unstable in cytoplasm compared to the two- piece pRNA/siRNA chimera which folded into the strong secondary/tertiary structure resistant to various conditions (3) and might protect the embedded siRNA from fast degradation and resulting in an enhanced RNAi (RNA interference) function inside the cells.
  • flow cytometry and confocal images demonstrated that the therapeutic two-piece pRNA modules were strongly bound to the target cells and subsequently internalized into cancer cells with high efficiency.
  • the results showed the feasibility of the two-piece approach in assembling functional RNA nanoparticles with high yield.
  • the bottom-up self-assembly of pRNA using the two-piece approach demonstrated the addressable and programmable nature of pRNA.
  • the constructed two- piece pRNA/siRNA and two-piece pRNA-folate chimera can further assemble into dimeric particles for targeted delivery of therapeutics into folate receptor positive cancer cells. This approach can be extended in the future to build more complex multifunctional nanoparticles for a wide range of therapeutic, detection, and diagnosis applications.
  • RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35: 849-857.

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Abstract

Artificial packaging RNA (pRNA) polynucleotides that share secondary structure with dsDNA bacteriophage pRNA (e.g., phi29 pRNA) are formed by non-covalent self-assembly from two RNA pieces to form pRNA monomers that may include heterologous sequences to form chimeric pRNA monomers. The two RNA pieces (P1 and P2) can be made by non-enzymatic chemical synthesis and the resulting monomer includes a break in the single- stranded head loop corresponding to positions 53-58 in a wild-type phi29 pRNA. The synthetic pRNA monomers can be assembled into multimeric polyvalent nanoparticles and may include as heterologous components payloads such as siRNA, ribozymes, aptamers, antisense RNA, detectable labels, therapeutic drugs and the like, as well as targeting moieties, endosome- disrupting agents and other moieties.

Description

SYNTHETIC NON-COVALENTLY SELF-ASSEMBLING BIPARTITE PRNA
CHIMERAS
CROSS-REFERENCE TO RELATED APPLICATION
This application claims the benefit under 35 U.S.C. § 1 19(e) of U.S. Provisional Patent Application No. 61/430,892 filed January 7, 201 1 , where this provisional application is incorporated herein by reference in its entirety.
STATEMENT OF GOVERNMENT INTEREST
This invention was made with government support under Grant Nos. SBIR1 R43GM087081 -01 , EB003730, CA151648 and GM059944 awarded by the National Institutes of Health. The government has certain rights in this invention.
BACKGROUND
Technical Field
The presently disclosed invention embodiments relate to RNA nanoparticles and methods for their preparation and use. In particular, the present embodiments relate to self-assembling two-piece artificial pRNA polynucleotides that share pRNA secondary structure with wild-type dsDNA viral packaging RNA (pRNA), and their derivatives, for use in assembling and stabilizing biologically active RNA nanoparticles.
Description of the Related Art
Research in nanotechnology involves modification, engineering, and/or assembly of organized materials on the nanometer scale (1 ). RNA molecules can be designed and manipulated at a level of simplicity
characteristic of DNA (2-7), while possessing the flexibility in structure and function or enzymatic activity similar to that of proteins (8,9). Thus, RNA is a suitable candidate for nanotechnological applications. The concept of RNA nanotechnology has been proposed for more than a decade (2, 5, 7, 10-12; for reviews, see 4, 13, 14). Dimeric, trimeric, and hexameric RNA nanoparticles can be assembled through self-assembly of multiple reengineered natural RNA molecules (5). The recognized potential of RNA nanoparticles for use in the treatment of cancer, viral infection, genetics diseases and other human ailments has heightened recent interest in RNA nanotechnology (4).
Several RNA-based therapeutic approaches using small interfering RNA (siRNA)(15-17), ribozymes (18-20) and anti-sense RNA (21 ,22) have been shown to down-regulate specific gene expression in cancerous or viral-infected cells, and has led in particular to the rapid development of siRNA- based therapeutics. Although methods for gene silencing with high efficacy and specificity have been achieved in vitro, the effective delivery of RNA to specific cells in vivo still remains challenging. Specific delivery of siRNA to target cells has been achieved using the pRNA (packaging RNA) of the double stranded DNA bacteriophage phi29 (φ29; 23-25), which forms dimers and trimers via the interaction of the left (L-loop) and right (R-loop) interlocking loops that are present in the pRNA structure (5, 26, 27).
Phi29 (φ29) DNA packaging motor uses six pRNAs that form a ring to gear the DNA packaging motor (5, 27-30). Each pRNA molecule contains two domains (Fig. 1A). One of the domains, bases 23-97, located at the central region of pRNA, is involved in intermolecular interactions such as non-covalent, specific intermolecular associative events (27, 28, 31 , 32), and hence is referred to as the intermolecular interaction domain. The two loops (L- loop and R-loop), which are capable of interlocking associations between pRNA monomers to form dimers, trimers and hexamers, reside within this domain. The second domain contains regions of duplexed (double-stranded) RNA in wild-type pRNA and mediates binding of the pRNA to the DNA packaging enzyme gp16 (33). This domain is located at the 573' ends that pair to form a double-stranded helical region, and so may be referred to as the 573' duplex domain or double-stranded helical domain. Removal of this domain does not affect the formation of pRNA dimers, trimers and hexamers (27, 32). Therefore, chimeric pRNA may be engineered in a wide variety of ways by which some or all of the pRNA 573' proximate double-stranded helical end may be removed and/or replaced with a heterologous component such as siRNA, a ribozyme, antisense RNA, an RNA aptamer, a peptide nucleic acid, etc., such that the double-stranded helical domain can be used to carry a therapeutic "payload" such as a therapeutic siRNA (Fig. 1A) (23, 24, 34; see also, e.g., U.S. Patent No. 7,655,787, US 2010/0003753, US 2008/0064647, WO 2005/003293, WO 02/016596).
Using this chimera technology, pRNA escorts the siRNA to cells, to silence genes and to destroy leukemia cells and/or cancer cells of lung, breast, head and neck, as well as other tumors (23-25,35-38). The pRNA system has several advantages including defined structure, controllable stoichiometry, multi-valency, targeted delivery, ideal nanoscale size (-20-40 nm), and minimal immunogenicity {e.g., poor induction of antibody responses), to enable repeated administration of chimeric pRNA for the treatment of chronic diseases (4). In addition, the pRNA is remarkably stable in a wide range of pH (-4-9), temperature, and organic solvents (6). One current drawback, however, in the development of chimeric pRNA-based therapies is the requirement for relatively large quantities of high purity, high quality chimeric pRNA products, which are not readily produced by conventional recombinant methodologies employing enzymatic synthesis. The wild-type pRNA subunit of bacteriophage phi29 is about 1 17 nucleotides in length, a size which is beyond the limit of currently available commercial chemical RNA synthesis technologies (which typically offer a maximum polynucleotide length of about 80 nucleotides with low yield). At this time, most pRNA or engineered pRNA chimeras are synthesized enzymatically using RNA polymerase. Enzymatic synthesis, however, in addition to presenting problems with product purity and
consistency, also suffers from its inability efficiently to permit reliable and accurate chemical modification of RNA products in a precise, accurate and site- specific manner. For example, if placed at particular positions within the pRNA structure, certain chemically modified nucleotides may desirably improve pRNA resistance to degradation when the pRNA is subsequently introduced in vivo, but such site-specific placement is not readily afforded by enzymatic synthesis.
Clearly there is a need in the art for improved compositions and methods that permit the production and use of high-purity, precisely structurally designed, chemically and physiologically stable pRNA, including chimeric pRNA having particularly useful therapeutic, targeting, stabilizing and/or detectable labeling moieties. The presently described invention embodiments address this need and provide other related advantages.
BRIEF SUMMARY
In certain embodiments of the invention described herein, there is provided an artificial pRNA polynucleotide, comprising a first pRNA piece P1 , and a second pRNA piece P2, wherein: P1 and P2 self-assemble non- covalently to form a two-piece pRNA monomer having a wild-type pRNA secondary structure and a break between a P1 3'-end and a P2 5'-end, said break being situated in a single-stranded loop formed by nucleotides
corresponding to nucleotide positions 53-58 in a wild-type pRNA sequence; P1 comprises a RNA polynucleotide of at least 29-57 nucleotides and includes a P1 internnolecular interaction domain of about 29 nucleotides comprising the P1 3'-end; P2 comprises a RNA polynucleotide of at least 39-62 nucleotides and includes a P2 internnolecular interaction domain of about 39 nucleotides comprising the P2 5'-end; and the P1 internnolecular interaction domain and the P2 internnolecular interaction domain interact non-covalently to form the artificial pRNA polynucleotide.
In certain embodiments the artificial pRNA polynucleotide is produced by non-enzymatic chemical synthesis. In certain embodiments the artificial pRNA polynucleotide is capable of forming a pRNA dimer. In certain embodiments the artificial pRNA polynucleotide is capable of mediating double- stranded DNA phage motor-driven DNA packaging and virion assembly. In certain further embodiments the artificial pRNA polynucleotide comprises at least one heterologous component or at least two heterologous components. In certain further embodiments at least one heterologous component is selected from (i) a heterologous component that is covalently attached to a P1 5'-end, (ii) a heterologous component that is covalently attached to the P1 3'-end, (iii) a heterologous component that is covalently attached to the P2 5'-end, and (iv) a heterologous component that is covalently attached to a P2 3'-end. In certain further embodiments the heterologous component is selected from an siRNA, a targeting moiety, a ribozyme, an RNA aptamer, an antisense RNA, a peptide nucleic acid, a detectable label, a therapeutic agent and an endosome-disrupting agent.
In certain embodiments the artificial pRNA polynucleotide one or a plurality of modified nucleotides, which modified nucleotide in certain further embodiments is selected from a 2'-fluoro-2'-deoxy nucleotide or a derivative thereof, a phosphorothioate , a 2'-O-methyl ribonucleotide or a derivative thereof, a 2'-NH2-2'-deoxy nucleotide or a derivative thereof, and a 2'-CH3-2'- deoxy nucleotide or a derivative thereof. In certain embodiments the artificial pRNA polynucleotide does not elicit a TLR-mediated response when
administered to a mammal.
In certain embodiments the heterologous component comprises a Dicer substrate that is processed by a Dicer pathway to yield a siRNA that is capable of specifically interfering with expression of a gene. In certain embodiments of the above-described artificial pRNA polynucleotide, P1 and P2 self-assemble to form a substantially full-length pRNA.
In certain other embodiments there is provided a method of delivering a biologically active moiety to a cell, comprising contacting the cell with the above-described artificial pRNA polynucleotide which comprises at least one or at least two heterologous components, under conditions and for a time sufficient for uptake by the cell of the artificial pRNA polynucleotide, wherein the heterologous component comprises the biologically active moiety. These and other aspects and embodiments of the present invention will become apparent upon reference to the following detailed description and attached drawings. All references disclosed herein are hereby incorporated by reference in their entirety as if each was incorporated
individually.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
Figure 1 shows the structure and characterization of chemically synthesized 2-piece pRNA (P1/P2). A. The structure of a typical monomeric pRNA nanoparticle comprising P1 and P2 RNAs. Folate (FA) and
Alexafluor647 can be optionally conjugated to the 5'-ends of P1 and/or P2. B. Native PAGE analysis of P1 , P2, unligated P1/P2 and ligated P1/P2. C.
Dimerization of pRNA-AbVpRNA-Ba', as analyzed using TBM native PAGE as described (26).
Figure 2 shows that the pRNA nanoparticle comprising two-piece (P1 +P2) self-assembled pRNA monomers did not induce an interferon response in vitro. A: KB cells were transfected with 50 nM pRNA (2'-F modified vs. non-modified), 50 nM siRNA, and 1 g/mL poly l:C using Fugene- HD. The cells were harvested 24 hours later and semi-quantitative RT-PCR was conducted to test for the expression of the indicated IFN responsive genes. B: Human PBMC were incubated with 50 nM pRNA or 1 g/mL poly l:C. After 24 hours, the RNAs were extracted and tested for the upregulation of TLR-3, TLR-7 and TLR-9. KT-107 and KT-108 are pRNA monomers that differ in the sequence of the 573' helical region. C: Production of TNF-a in the mouse macrophage cell line RAW-647 after incubation with different concentrations of pRNA and poly l:C. Three hours post-incubation, aliquots from the culture media were used to test for the levels of TNF-a by ELISA. D: Activation of TLR-3 pathway as measured using HEK-Blue™-hTLR3 reporter cell line.
pRNA monomers that differed in the length and the extent of modification of the 573' helical region were tested at the concentrations shown and compared to poly l:C. After incubation with pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers for 24 hours, aliquots from the culture media were used for colorimetric detection of TLR-3 activation. FF = 2'- F modified helical region; NN = non-modified helical region; 29 = the helical region was 29 nucleotides in length; 22 = the helical region was 22 nucleotides in length. All pRNA constructs used had a modified intermolecular interaction domain. Poly l:C was used in all these assays as positive control.
Figure 3 shows that the Folate-pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers targeted FR+ tumors upon systemic administration. A: HeLa xenograft tumor bearing nude mice were injected with 15 nmol (~24mg/kg) of KT-105 (Folate- AlexaFluor647 labeled pRNA nanoparticle) through the tail vein (right). The control mice were injected with either PBS (left) or with folic acid (/.p., 10mg/kg) 10 minutes prior to KT-105 injection (middle). The mice were euthanized 24 hours after injection and whole body imaging was conducted using IVIS® Lumina station. B. following whole body imaging, the mice were dissected and the major organs were isolated for imaging . Lv = liver; K = kidney; H = heart; L = lung; S = spleen; I = intestine; M = muscle; T = tumor. C: KB xenograft tumor bearing nude mice were injected with 15 nmol (24 mg/kg)(lower panel) or 3.75 nmol (upper panel)(~6mg/kg) of KT-105 through the tail vein. Organs were isolated and imaged as described above.
Figure 4 shows plasma concentration of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers upon systemic administration. Tumor bearing mice (n = 3) were i.v. injected with 15 nmol of KT-105 (Folate-Alexafluora 647 pRNA nanoparticles). Blood was collected at different timepoints post-administration (5 min, 30 min, 2hrs, 5hrs, 24h) through the lateral saphenous vein. The serum was isolated and the serum
concentration of the nanoparticle was determined using CGE. The semi-log plot of the plasma concentration vs. time is shown.
Figure 5 shows white blood cell counts in mice following injection of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers. Clinical pathology analysis was conducted for the C57B/6 mice upon one-week repeat i.v. administrations of pRNA vs. Poly l:C at the indicated doses. Total cell counts (left) and differentials (right) were displayed.
Figure 6 shows capillary gel electrophoretic (CGE) analysis of monomeric and dimeric pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers.
Figure 7 shows that chemically synthesized 2'F-pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers were metabolically stable. The different forms of nanoparticles were incubated with different concentrations of human serum or with RNase A (1 U, 30 min) for the indicated time periods at 37°C. Aliquots were taken at different time intervals and subjected to phenol :chloroform extraction followed by ethanol precipitation. pRNA was visualized by Sybr® Gold staining of 10%/8 M urea polyacrylamide gels (denatured PAGE).
Figure 8 shows cellular uptake of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers with various folate (FA) conjugation. A-l: KB cells were incubated with FA-pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers containing folate at the 5'-end of P1 . The pRNA was labeled with fluorescein using Silencer® siRNA labeling kit (Ambion). The cells were incubated with the pRNA (200 nM) in the absence or presence of excess folic acid (FA) (200 fold) for 30 min. The cells were either harvested by trypsinization, fixed, and analyzed by flow cytometry (A-C) or imaged using a confocal microscope (D-l). J-M: KB cells were transfected with GFP-Rho-B-expressing cassette to label early and late endosomes (green). After transfection by 24 h, KB cells were incubated with 200 nM Cy5-FA-pRNA nanoparticles (red) for the indicated periods. Cy5 was conjugated to the 5'-end of P1 and folate was conjugated on 5'- end of P2. The cells were imaged by confocal microscopy to determine co- localization of pRNA with the endosomes (yellow) and the extent of endosomal release. A positive control panel (M) is shown where chloroquine (chQ) was added 4 hours post incubation to induce endosomal release. Figure 9 shows the weights of different organs from the C57B/6 mice after 1 week of repeated systemic administration of pRNA nanoparticles comprising two-piece (P1 +P2) self-assembled pRNA monomers at a dose of 30 mg/kg.
Figure 10 shows construction of two-piece RNA assemblies, (a) The structure of pRNA molecules and pRNA/siRNA chimera, (b) The design and sequence of three different two-piece modules for pRNA or pRNA/siRNA chimera, (c) 8% native PAGE showing the self-assembly of two RNA fragments into the pRNA monomer and dimer formation of resulting two-piece RNA assemblies. The monomer control including (1 -1 17) Ab' pRNA and its dimer partner (1 -1 17) Ba' pRNA. The dimer control is the dimer formed by (1 -1 17) Ab' pRNA and Ba' pRNA. (d) 8% native PAGE showing the self-assembly of two RNA fragments into the pRNA/siRNA chimera and dimer formation of resulting two-piece RNA assemblies. The monomer control including (1 -1 17) Ab' pRNA siRNA chimera and its dimer partner (1 -1 17) Ba' pRNA. The dimer control is the dimer formed by (1 -1 17) Ab' pRNA siRNA chimera and Ba' pRNA.
Figure 1 1 . DNA packaging activity (a) and viral assembly activity (b) of pRNA chimera assembled from two pieces of pRNA fragments, (a) 0.8% agarose gel showing the procapsid protected viral DNA after packaging which indicated the active pRNA components. Lanel is 1 Kb DNA ladder; lane 2 indicated the total amount of input viral genome DNA for the packaging assay; lane 4 is the active packaging served as positive control. Lane3, lane 5 to lane 9 served as negative control for background check which only add monomeric (1 -1 17) Ab'(1 -1 17) Ba' or two-piece pRNA assemblies without presence of dimer partner. Lane 10 to lane 12 showing the active packaging activity of all three two-piece pRNA assemblies, (b) Viral assembly activity is reflected by the plaque formation unit per milliliter (PFU/mL). The no RNA, no ATP, monomeric pRNA (Ab' and Ba' pRNA) or two-piece pRNA assemblies served as negative control for checking the background plaque formation. All three two-piece pRNA assemblies together with their dimer partner (1 -1 17)Ba' pRNA can assemble mature virons to infect the host bacteria and form plaque which is comparable to the wild type dimer (1 -1 17)Ab' pRNA plus (1 -1 17)Ba' served as positive control.
Figure 12. Gene silencing assay for pRNA/siRNA(eGFP) assembled from two pieces of RNA fragments, (a) The eGFP gene silencing knock-down effects by two-piece pRNA/siRNA(eGFP) chimera and its mutant controls. Nucleotides in red indicate the mutation, (b) 8% native PAGE showing the self-assembly of two RNA fragments into the pRNA siRNA chimera and its mutant controls (lane 1 : monomer control; lane 2: pRNA siRNA(eGFP); lane 3: pRNA siRNA(eGFP) with sense strand mutant; lane 4:
pRNA siRNA(eGFP) with antisense strand mutant; lane 5: pRNA/siRNA(eGFP) with both sense strand and antisense strand mutant as well as dimer formation of resulting two-piece RNA assemblies accordingly; lane 6:
pRNA siRNA(eGFP) dimer; lane 7: dimer of pRNA siRNA(eGFP) with sense strand mutant; lane 8: dimer of pRNA siRNA(eGFP) with antisense strand mutant; lane 9: dimer of pRNA/siRNA(eGFP) with both sense strand and antisense strand mutant; and lane 10: dimer control).
Figure 13. Dual-luciferase assay for pRNA siRNA(firefly luciferase) assembled from two pieces of RNA fragments. The no RNA, no plasmid DNA control served as the system blank for the assay. DNA1 is the plasmid pGL3 harboring firefly luciferase gene and DNA2 is the plasmid pRL- TK harboring renilla luciferase. The relative firefly luciferase activity is to normalize firefly luciferase activity using the internal control renilla luciferase activity which reflected the level of luciferase gene expression.
Figure 14. The survivin silencing effects of two-piece pRNA siRNA chimera assayed by Western Blot. Cells were treated with different concentration of RNAs (5nM, 20nM and 40nM) respectively including two-piece pRNA siRNA(survivin), two-piece pRNA/scramble control as well as according intact pRNA siRNA(survivin) and its scrambled control. Column 2 of the figure only included two concentration of RNA treatment (5nM and 20nM). The reduced survivin gene expression was displayed as the lighter band after blotting. Figure 15. Flow cytometry (a) and confocal microscopy imaging (b) of KB cells showing the binding and entry of the pRNA/folate chimera assembled from two pieces of RNA fragments, (a) The shifted cells in blue color indicated the strong binding of the two-piece pRNA folate campared to the two-piece pRNA NH2 control, (b) The green color indicated the region of the cell cytoplasmatic portion and blue color indicated the nucleus. The fluorescent labeled two-piece pRNA folate shown in red.
Figure 16 shows an autoradiogram showing the Dicer processing of the [32P] labeled pRNA siRNA chimeras assembled from two pieces of RNA fragments.
DETAILED DESCRIPTION
Disclosed herein for the first time are invention embodiments according to which an artificial double-stranded DNA bacteriophage packaging RNA (pRNA) polynucleotide is produced as a two-piece, self-assembling pRNA monomer having a break between the 3'-end of the first piece (P1 ) and the 5'- end of the second piece (P2), wherein the break is situated in a pRNA single- stranded loop that is formed by nucleotides corresponding to nucleotide positions 53-58 of a wild-type pRNA sequence such as the wild-type pRNA of bacteriophage phi29 pRNA.
Surprisingly, such two-piece artificial pRNA monomers retain wild- type pRNA secondary structure and are capable of wild-type pRNA functions, including dimer, trimer and hexamer assembly via interactions between the L- loop and R-loop structures of the pRNA domain, and also including mediation of dsDNA phage DNA packaging motor-driven DNA packaging and virion assembly. Also surprisingly, P1 and P2 can each be structurally modified by the addition of additional RNA sequences or other chemical moieties {e.g., heterologous (i.e., non-naturally present) components such as biologically active moieties including siRNA, ribozymes, antisense RNA, aptamers, targeting moieties, peptide nucleic acids, detectable labels, therapeutic agents, endosome-disrupting agents, stabilizing nucleotides such as 2'-fluoro-2'-deoxy nucleotide derivatives, phosphorothioates, 2'-O-methyl ribonucleotides, 2'-NH2- 2'-deoxy nucleotide derivatives, 2'-CH3-2'-deoxy nucleotide derivatives, etc.) at the 5'-end and/or the 3'-end whilst still retaining the ability to self-assemble into an artificial pRNA monomer that retains wild-type pRNA function such as dimer, trimer and hexamer assembly.
The herein described artificial two-piece pRNA monomers unexpectedly accommodate structural modifications at the 5'-ends and/or the 3'-ends of P1 and P2, including in particular retention of the ability of siRNA so attached {e.g., as a heterologous component that is attached, directly or indirectly via a linker or spacer sequence, to the 5'-end of P1 and/or to the 3'- end of P2, and/or to the 3'-end of P1 and/or to the 5'-end of P2) to mediate gene-silencing or gene-inhibiting {e.g., decreasing gene product expression in a statistically significant manner) activity. For example, siRNA sequences present in the herein described artificial two-piece pRNA monomers may be processed by the intracellular Dicer pathway to result in functional RNA interference.
In these and related embodiments, the herein described artificial pRNA polynucleotides comprising two-piece (P1 +P2) self-assembled pRNA monomers will find uses in therapeutics and diagnostics, and in patient screening and biological/ biomedical research applications. Certain preferred embodiments contemplate use of the herein described artificial pRNA
polynucleotides comprising two-piece (P1 +P2) self-assembled pRNA
monomers for targeted delivery of therapeutic "payloads" such as a siRNA that is capable of silencing a gene target in a diseased cell such as a cancer cell or a virus-infected cell, including such monomers that are designed to contain a heterologous component that may be a targeting moiety such as an RNA aptamer, a ligand for a known specific receptor that is present on the target cell, an antibody or antigen-binding fragment thereof, or other targeting moiety.
Accordingly, certain of the herein described invention embodiments contemplate a flexible and versatile modular system for targeted delivery of therapeutic and/or diagnostic agents, based on the ability to attach different heterologous components to the 5'-ends and/or to the 3'-ends of P1 and/or P2, which then self-assemble non-covalently to form a two-piece pRNA monomer having a wild-type pRNA secondary structure, and which monomers may then be mixed and matched to form a wide range of pRNA nanoparticulate dimers, trimers and/or hexamers. For instance, P1 and P2 components as described herein may be prepared that carry one or more particular siRNA sequences, such as siRNA directed against a target gene that is important to cancer cell survival, and/or that also carry one or more particular targeting moieties, such as a specific ligand or counter-receptor for a receptor that may be present on cancer cells, and/or that also carry one or more detectable labels, such as a fluorescent, radiochemical or other detectable moiety that permits assessment of pRNA nanoparticle delivery to and uptake by cancer cells, and/or that also carry one or more modified nucleotides such as chemically modified nucleotides that resist degradation under physiological conditions or otherwise stabilize the pRNA.
Advantageously, the herein described artificial pRNA polynucleotides are non-immunogenic in certain preferred embodiments, such that repeated therapeutic and/or diagnostic administration may be practiced in a subject without eliciting undesirable immune responses that might otherwise counteract the purpose for which the pRNA is being used.
Those skilled in the art will also recognize that certain advantages are obtained by the ability of the herein described artificial pRNA
polynucleotides to be produced, in certain embodiments, wholly through non- enzymatic chemical synthesis, according to certain preferred embodiments. Synthetic chemical production of polynucleotides is known in the art and, currently, typically permits efficient synthesis of high-purity, substantially homogeneous (e.g., greater than at least 95, 96, 97, 98 or 99% homogeneous according to the detection capability of available analytical chemistry
instrumentation) preparations of polynucleotides of at least about 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89 or 90 nucleotides.
Chemical synthesis also permits more precise implementation of chemical modifications at specific locations in the pRNA molecular structure, relative to that which can be achieved by enzymatic pRNA synthesis. Accordingly, it will be appreciated that previously described pRNA monomers, which typically exceed 100 nucleotides in length, are not currently amenable to efficient, non- enzymatic chemical synthesis, a problem that is overcome by the present two- piece pRNA monomers. Additionally, it will be appreciated that the presently disclosed embodiments include the surprising features that a two-piece pRNA monomer can be assembled from two pieces even with the presence of a break in the single-stranded loop formed by nucleotides corresponding to nucleotide positions 53-58 in a wild-type pRNA sequence such as the wild-type phi29 pRNA sequence.
pRNA structure is well known and has been described, for example, in U.S. Patent No. 7,655,787, and in US 2010/0003753, US
2008/0064647, WO 2005/003293, WO 02/016596, Hoeprich et al. (2002 J. Biol. Chem. 277:20794); Zhang et al. (1995 Virol. 207:442), Hoeprich et al. (2003 Gene Therap. 10:1258), Guo (2002 Prog. Nucl. Ac. Res. Mol. Biol. 72:415), Guo (2005 Meths. Mol. Biol. 300:285), Guo (2005 Hum. Gene Therap. 16:1097) and Chen et al. (2000 J. Biol. Chem. 275:17510). Therein are described the pRNA primary and secondary structures, including, importantly, the disclosure that although pRNA primary sequences may differ considerably among the various dsDNA bacteriophages, there is an overall conservation of secondary structure that has been established for pRNA.
Where the three-dimensional (secondary) structure of pRNA is well known, it will be understood that from the present disclosure, persons familiar with the pRNA art will recognize the occurrence of a single-stranded loop that is formed by nucleotides at positions 53-58 in a wild-type pRNA sequence (such as the phi29 wild-type pRNA), and so will appreciate that similar single-stranded loops are found in other pRNA structures, even where such loops may or may not be formed by nucleotides at exactly positions 53-58 in such other structures, so long as they are present in a "corresponding" position. Hence, the break {e.g., opening, interruption, discontinuity) between P1 and P2 in the structure of the herein described self-assembled two-piece pRNA monomer is situated in the well recognized single-stranded loop, which loop is described, for instance, in US 2010/0003753 as the "head loop" in Fig. 2B therein, and as "loop 24" in paragraph [01 14] (referring to Fig. 4C) therein, and for which several clearly corresponding single-stranded loops at
comparable positions in additional pRNA sequences are presented in Fig. 3A-F therein.
The present embodiments offer certain advantages over previous reports that pRNA can be dissected into a two-piece chimeric construct, in which two individual RNA oligonucleotides, one encompassing the R-loop and the other the L-loop, were clamped together via a six-nucleotide duplex (39). In such earlier two-piece constructs, however, no break was present in the "head loop", and one of the two pieces was located in the middle of the pRNA. This requirement for a duplex clamp made the resulting RNA unsuitable for the construction of therapeutic RNA nanoparticles harboring siRNA or other heterologous components, and also precluded their application to drug delivery. These earlier "clamped" pRNA constructs also failed to exhibit pRNA
functionality such as the ability to mediate dsDNA phage motor-driven DNA packaging. By contrast, the present two-piece pRNA chimeric monomers can be used to generate full-length functional pRNAs that are not only competent for driving the phi29 DNA packaging motor, but that are also proficient for therapeutic and diagnostic purposes such as those described herein.
The 1 17-nucleotide RNA, called the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor, has been shown to be an efficient vector for the construction of RNA nanoparticles for the delivery of siRNA into specific cancer or viral infected cells. Currently, however, non-enzymatic chemical synthesis of 1 17-nucleotide RNA is not feasible commercially. In addition, labeling the molecule at specific locations on pRNA requires the understanding of its modular organization and is not readily accomplished by enzymatic synthesis. Multiple approaches are disclosed herein for the construction of a functional pRNA monomer, including a 1 17-base pRNA, using two synthetic RNA fragments with variable modifications. The resulting two- piece pRNA monomer was fully competent in associating with other interacting pRNAs to form dimers, as demonstrated by the packaging of DNA via the nanomotor and the assembly of phi29 viruses in vitro. The monomeric pRNA subunits could be assembled from two-piece fragments harboring siRNA or receptor-binding ligands, and these subunits were equally competent at assembling into dimers. The subunits carrying different functionalities were able to bind cancer cells specifically, to enter the cells, and to silence specific genes of interest. The pRNA nanoparticles formed from the present non- covalently self-assembling two-piece pRNA monomer were processed by Dicer to release the siRNA embedded within the nanoparticle.
As noted above, US 2010/0003753 (U.S.A.N. 1 1/989,590) discloses that the pRNA intermolecular interaction domain (sometimes referred to as the pRNA region) has a compact stable secondary structure characteristic of bacteriophage pRNA sequences. The pRNA region may, in certain embodiments, include pRNA of a bacteriophage selected from phi29, SF5', B103, PZA, M2, NF and GA1 . The pRNA region may include: (i) in the 5' to 3' direction beginning at the covalent linkage of the pRNA with the 3' end of the double-stranded helical domain (sometimes referred to as the spacer region) a first loop; a second loop (e.g., the head loop); and a lower stem-loop structure comprising a bulge, a first stem section and a third loop; (ii) a second stem section interposed between the spacer region and the stem-loop structure; (iii) a third stem section interposed between the stem-loop structure and the first loop; and (iv) a fourth stem section interposed between the first loop and the second loop.
Bacteriophage phi29 (φ29) is a double-stranded DNA virus that encodes packaging RNA or "pRNA", a120 base RNA that plays a key role in phi29 DNA packaging (Guo et al. 1987 Science 236:690-694). pRNA binds to viral procapsids at the portal vertex (the site where DNA enters the procapsid) (Guo et al., 1987 Nucl. Acids Res. 15:7081 -7090) and is not present in the mature phi29 virion. The tertiary structure of the pRNA monomer and dimer has been reported (Zhang et al., V/'ro/ogy 81 :281 -93 (2001 ); Trottier et al., RNA 6(9):1257-1266 (2000); Chen et al. J. Biol. Chem. 275(23): 17510-17516 (2000); Garver et al., J. Biol. Chem. 275(4): 2817-2824 (2000)). A computer model of the three-dimensional structure of a pRNA monomer has been constructed (Hoeprich and Guo, J. Biol. Chem. 277:20794-803 (2002)) based on experimental data derived from photo-affinity cross-linking (Garver and Guo, RNA 3:1068-79 (1997); Chen and Guo, J Virol 71 :495-500(1997)); chemical modification and chemical modification interference (Mat-Arip et al., J Biol Chem 276:32575-84 (2001 ); Zhang et al., Virology 281 :281 -93 (2001 ); Trottier et al., RNA 6:1257-66 (2000)); complementary modification (Zhang et al., RNA 1 :1041 -50 (1995); Zhang et al., Virology 201 :77-85 (1994); Zhang et al., RNA 3:315-22 (1997); Reid et al., J Biol Chem 269:18656-61 (1994); Wichitwechkarn et al., Mol B/'o/ 223:991 -98 (1992)); nuclease probing (Chen and Guo, J Virol 71 :495-500 (1997); Reid et al., J Biol Chem 269:5157-62 (1994); Zhang et al., Virology 21 1 :568-76 (1995)); oligo targeting competition assays (Trottier and Guo, J Virol 71 :487-94 (1997); Trottier et al., J Virol 70:55-61 (1996)) and cryo- atomic force microscopy (Mat-Arip et al., J Biol Chem 276:32575-84 (2001 ); Trottier et al., RNA 6:1257-66 (2000); Chen et a\., J Biol Chem 275:17510-16 (2000)). pRNA hexamer docking with the connector crystal structure reveals a very impressive match with available biochemical, genetic, and physical data concerning the 3D structure of pRNA (Hoeprich and Guo, J. Biol. Chem
277:20794-803 (2002)).
The nucleotide sequence (SEQ ID NO:1 in US 2010/0003753) of native full length phi29 pRNA (Guo et al., Nucl. Acids Res. 15:7081 -7090 (1987)), as well as its predicted base-paired secondary structure, are disclosed in US 2010/0003753 (see also, e.g., Zhang et al., RNA 3:315-323 (1997);
Zhang et al., Virology 207:442-451 (1995)). The predicted secondary structure has been partially confirmed (Zhang et al., RNA 1 :1041 -1050 (1995); Reid et al., J. Biol. Chem. 269:18656-18661 (1994); Zhang et al., V/ro/ogy 201 :77-85 (1994); Chen et al., J. Virol. 71 : 495-500 (1997)). The intermolecular interaction domain facilitates the interactions {e.g., dimerization, trimerization) of pRNA molecules and includes a right hand loop and a left hand loop that are important in the interaction between pRNAs, as described in US 2010/0003753. The intermolecular interaction domain is present within the procapsid binding domain, which is located at the central part of the pRNA molecule at bases 23- 97 (Garver et al., RNA 3:1068-79 (1997); Chen et a\., J Biol Chem 275:17510- 16 (2000)), while the double-stranded helical (or "DNA translocation") domain is located at the 573' paired ends. The 5' and 3' ends have been found to be proximate to one another, and several kinds of circularly permuted pRNA have been constructed (Zhang et al., RNA 3:315-22 (1997); Zhang et al., Virology 207:442-51 (1995); Guo, Prog in Nucl Acid Res Mol Biol 72:415-72 (2002)). These two domains are compact and fold independently, such that exogenous RNA can be connected to the end of the pRNA without affecting pRNA folding, and that phi29 pRNA can be used as a vector to escort and chaperone small therapeutic RNA molecules. Indeed, removal of the DNA translocating domain does not change the nature of pRNA's intermolecular interaction, i.e., replacement or insertion of nucleotides before residue #23 or after residue #97 does not interfere with the formation of dimers, trimers, and hexamers
(Hoeprich et al., Gene Therapy, 10(15):1258-1267 (2003); Chen et al., RNA, 5:805-818 (1999); and Shu et al., J Nanosci and Nanotech (JNN), 4:295-302 (2003)). Exogenous RNA (e.g., a heterologous component) can be connected to the 3' or 5' end of the pRNA without affecting pRNA folding; this foreign RNA molecule also folds independently (Hoeprich et al., Gene Therapy, 10(15):1258- 1267 (2003); Shu et al., J Nanosci and Nanotech (JNN), 4:295-302 (2003); Guo, J. Nanosci Nanothechnol, 2005, 5(12):1964-1982).
Phylogenetic analysis of pRNAs from phages SF5', B103, phi29, PZA, M2, NF and GA1 (Chen et al., RNA 5:805-818 (1999)) shows very low sequence identity and few conserved bases, yet the family of pRNAs appears to have strikingly similar and stable predicted secondary structures (see, e.g., Fig. 3 in US 2010/0003753). The pRNAs from bacteriophages SF5' (SEQ ID NOS:1 1 and 28 in US 2010/0003753), B103 (SEQ ID NOS:12 and 29 in US 2010/0003753), phi29/PZA (SEQ ID NOS:13 and 30 in US 2010/0003753), M2/NF (SEQ ID NOS:14 and 31 in US 2010/0003753), GA1 (SEQ ID NOS:15 and 32 in US 2010/0003753) of Bacillus subtilis (Chen et al., RNA 5:805-818 (1999); and aptRNA (SEQ ID NOS:16 and 33 in US 2010/0003753) are all predicted to have a secondary structure that exhibits essentially the same structural features as has been shown for phi29 pRNA (US 2010/0003753; Chen et al., RNA 5:805-818 (1999)). All have native 5' and 3' ends at the left end of a stem structure (as shown in Fig. 3 in US 2010/0003753) and contain the same structural features positioned at the same relative locations.
The pRNAs of these bacteriophages thus share a single stable secondary structure.
Secondary structure in an RNA molecule is formed by base pairing among ribonucleotides. RNA base pairs commonly include G-C, A-T and U-G. Predictions of secondary structure are preferably made according to the method of Zuker and Jaeger, for example by using a program known by the trade designation RNASTRUCTURE 3.6, written by David H. Mathews
(Mathews et al., J. Mol. Biol. 288:91 1 -940 (1999); see also Zuker, Science 244:48-52 (1989); Jaeger et al., Proc. Natl. Acad. Sci. USA 86:7706-7710 (1989); Jaeger et al., Meth. Enzymol. 183:281 -306 (1990)). This program is publicly available on the worldwide web at the homepage of the laboratory of Douglas Turner at the University of Rochester at
ma.chem.rochester.edu/RNAstructure.html and runs on MS Windows 95, 98, ME, 2000 and NT4. The program is also publicly available on the worldwide web at Michael Zuker's homepage at Rensselaer Polytechnic Institute
(bioinfo. math. rpi.edu/.about.zukerm/home. html); his homepage offers online folding and a version of the algorithm that can be compiled on Silicon Graphics, Sun, or DEC Alpha workstations. The structure with the lowest energy (i.e., the optimal structure) is chosen. Secondary structures of RNA can be characterized by stems, loops and bulges. A "stem" is a double-stranded section of two lengths of base-paired ribonucleotides. Stem sections contain at least 2 base pairs and are limited in size only by the length of the RNA molecule. A "loop" is a single- stranded section that typically includes at least 3 ribonucleotides and is also limited in size only by the length of the RNA molecule. In a "stem loop", the 5' and 3' ends of the loop coincide with the end of a base-paired stem section. In a "bulge loop", the loop emerges from along the length of a stem section. The 5' and 3' ends of a bulge loop are typically not base paired although they may potentially be (see, e.g., G40 and C48 of the bulge loop in the phi29 pRNA structure; Fig. 2 in US 2010/0003753). A "bulge" is an unpaired single stranded section of about 1 to about 6 ribonucleotides present along the length of (or between) stem sections. Note that there is no clear line between a large "bulge" and a small "bulge loop." Herein, where the term "bulge" is used, it also includes a small "bulge loop" (i.e., a bulge loop of less than about 7
ribonucleotides).
The secondary structure of an RNA molecule is determined by the nature and location of the base pairing options along its length. RNA
secondary structure is degenerate; that is, different primary ribonucleotide sequences can yield the same base pairing configurations and hence the same secondary structure. In a way, it is akin to the way multiple amino acid sequences can produce the same secondary structure, for example an alpha- helix.
A single secondary structure is dictated by a number of different primary sequences in predictable and well-understood ways. For example, single or pairs of nucleotides can generally be added, removed, or substituted without altering the overall base pairing interactions within the RNA molecule and without interfering with its biological function. This is particularly true if one or a few base pairs of nucleotides are removed, added or substituted along double-stranded hybridized length of the molecule, or if one or more
nucleotides are removed, added or substituted in the single-stranded loop regions. For example, although GC base pairs and AT base pairs differ slightly in their thermodynamic stability, one can generally be substituted for another at a site within the double-stranded length without altering the secondary structure of an RNA molecule. GC base pairs are preferred in the stem region due to their added stability. Changes in secondary structure as a result of addition, deletion or modification of nucleotides can be readily assessed by applying the secondary structure prediction algorithm of Zuker and Jaeger as described above. The 573' double-stranded helical region of the pRNA can accommodate substantial variation in primary sequence without an appreciable change in secondary structure.
Typical pRNAs that may be substantially full-length pRNAs comprise about 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 , 102, 103, 104, 105, 106, 107, 108, 019, 1 10, 1 1 1 , 1 12, 1 13, 1 14, 1 15, 1 16, 1 17, 1 18, 1 19, 120, 121 , 122, 123, 124, 125, 126, 127, 128, 129 or 130 nucleotides in length, although shorter and longer pRNAs are disclosed and contemplated herein, such as artificial pRNA polynucleotides that self-assemble from a first pRNA piece P1 and a second pRNA piece P2, each of which comprises at least about 29-62 nucleotides that form a pRNA domain having the secondary structure of a pRNA intermolecular interaction domain, and each of which may further comprise a heterologous component such as additional 5'-end and/or 3'-end polynucleotide sequences (e.g., siRNA, antisense RNA, ribozyme, aptamer, spacer oligonucleotide sequence, linker oligonucleotide sequence, overhang oligonucleotide sequence, complementarity oligonucleotide sequence for nanoparticle assembly, etc.) and/or chemical modifications {e.g., detectable label, therapeutic drug, targeting moiety such as a ligand, receptor or counter- receptor, antibody, etc.).
The pRNA chimera such as a pRNA chimera that comprises a presently disclosed self-assembled two-piece pRNA monomer which further comprises one or more heterologous component is useful as a vehicle to carry and deliver one or more biologically active moieties, detectable labels, and the like to a target molecule, cell or location. The biologically active moieties, detectable labels and the like are considered herein as "heterologous" components of the pRNA chimera (that is, they are not present in the naturally occurring pRNA) and are sometimes referred to herein as the "cargo" or "payload" that is delivered by, carried by or incorporated into the pRNA chimera. Heterologous components of a pRNA chimera may be, like the pRNA itself, RNAs that are sometimes referred to herein as "daughter" RNAs or biologically active RNAs. The cargo components can be oligonucleotides, polynucleotides, peptides, polypeptides, carbohydrates, lipids, hormones, labeling agents, small organic molecules, and the like, without limitation, and any pRNA, including in certain embodiments a P1 and/or a P2 of a herein described self-assembling two-piece pRNA monomer, that has been derivatized with, conjugated to, or otherwise contains or is associated with a cargo component is considered a "pRNA chimera" or a "chimeric pRNA". As described in more detail below, the chimeric pRNAs can advantageously be considered as "building blocks" that can be customized, selected, mixed and matched to produce multimeric, polyvalent pRNA complexes tailor-made for a desired application or purpose.
In certain contemplated embodiments, a pRNA chimera which comprises a herein described self-assembling two-piece pRNA monomer may include an intermolecular interaction domain (pRNA region) having the secondary structure exemplified in Fig. 3 of US 2010/0003753 and
schematically depicted in Fig. 4 of US 2010/0003753, as described therein), flanking a heterologous spacer region that contains a biologically active moiety, preferably an RNA such as an siRNA, an RNA aptamer for targeting to a cell- surface receptor and/or a ribozyme.
The secondary structure of the pRNA region of the pRNA chimera is the common secondary structure that characterizes the pRNA from
bacteriophages phi29, SF5', B103, PZA, M2, NF and GA1 . The spacer region is termed "heterologous" because all or a portion of its nucleotide sequence is engineered or is obtained from an organism other than the bacteriophage. It is the presence of the heterologous spacer region that renders certain artificial pRNA polynucleotides "chimeric" according to certain herein described embodiments. Where both ends of the cargo RNA may, in certain
embodiments, be connected to pRNA, the cargo, such as an siRNA or a ribozyme, may be protected from degradation when exposed, for example, to a physiological milieu; this configuration may, according to non-limiting theory, also assist the biologically active moiety to fold appropriately.
Notably, the ability of the pRNA chimera to perform its intended function of protecting and carrying a biologically active moiety depends not on the primary nucleotide sequence of the pRNA intermolecular interaction domain (the primary structure), but on the secondary structure (base pairing
interactions) that the pRNA region assumes as a result of its primary
ribonucleotide sequence. As also noted above, the "pRNA region" of the pRNA chimera is thus so termed because it has a secondary structure, although not necessarily an RNA sequence, characteristic of a native bacteriophage pRNA molecule. Therefore, unless otherwise specified, the term "pRNA region" as used herein includes naturally occurring (native) pRNA sequences, nonnaturally occurring (nonnative) sequences, and combinations thereof provided that they yield the secondary structure characteristic of naturally occurring (native) bacteriophage pRNA as described herein.
Stated another way, the term "pRNA region" is not intended to be limited to only those particular nucleotide sequences native to pRNA. The pRNA region can thus contain any nucleotide sequence which results in the secondary structure shown in Fig. 4 of US 2010/0003753. Nucleotide sequences that fold into the aforesaid secondary structure include naturally occurring sequences, those that are derived by modifying naturally occurring pRNA sequences, and those that are designed de novo, as well as
combinations thereof. One of skill in the art can readily determine whether a nucleotide sequence will fold into the secondary structure shown in Fig. 4 of US 2010/0003753 and described herein by applying a secondary structure algorithm, such as RNASTRUCTURE as described above, to the nucleotide sequence. Examples of nucleotide sequences that, when folded, yield the secondary structure of the pRNA region of the pRNA chimera of the invention are shown in Fig. 3 of US 2010/0003753. They include pRNA sequences from bacteriophages SF5' (SEQ ID NOS:1 1 and 28 of US 2010/0003753), B103 (SEQ ID NOS:12 and 29 of US 2010/0003753), .phi29/PZA (SEQ ID NOS:13 and 30 of US 2010/0003753), M2/NF (SEQ ID NOS:14 and 31 of US
2010/0003753), GA1 (SEQ ID NOS:15 and 32 of US 2010/0003753) as well as the aptRNA (SEQ ID NOS:16 and 33 of US 2010/0003753).
Further, since the pRNA region of the pRNA chimera is defined by its secondary structure, still other examples of a pRNA chimera can be readily made by "mixing and matching" nucleotide fragments from, for example, SEQ ID NO:s 1 , 2, 7, 1 1 , 12, 14, 15 and 16 of US 2010/0003753 that fold into particular secondary structural features (bulges, loops, stem-loops, etc.) provided that the resulting nucleotide sequence folds into the overall secondary structure as shown in Fig. 4 of US 2010/0003753. For example, nucleotides encoding bulge loop 22 from bacteriophage SF5' pRNA (SEQ ID NO:1 1 of US 2010/0003753) could be substituted for the nucleotides encoding bulge loop 22 in the phi29 pRNA (SEQ ID NO:1 of US 2010/0003753) to yield a pRNA region as described herein. Likewise, any number of artificial sequences can be substituted into SEQ ID NO:s 1 , 2, 7, 1 1 , 12, 14, 15 and 16 of US
2010/0003753 to replace nucleotide sequences that fold into one or more structural features (or portions thereof) to form a pRNA region as described herein. See, for example, aptRNA (Fig. 3(f) of US 2010/0003753) which was derived in that fashion from phi29 pRNA. The overarching principle is that the overall secondary structure of the pRNA region is the secondary structure common to the bacteriophage pRNAs, as schematically depicted in Fig. 4 of US 2010/0003753.
pRNA region 1 is shown in detail in Fig. 4(c) of US 2010/0003753. Overall, pRNA region 1 is characterized by a stem-loop secondary structure, wherein the single-stranded loop formed by nucleotides corresponding to nucleotide positions 53-58 in a wild-type pRNA sequence such as the phi29 wild-type pRNA sequence, also referred to as the head loop or loop 24 in US 2010/0003753, is relatively small and the base-pairing in the stem (essentially stem sections 20, 21 and 23 of US 2010/0003753) is interrupted by structures on either side of loop 24. Bulge loop 22 of US 2010/0003753, the "right hand loop" is positioned 5' of loop 24. Positioned 3' of loop 24 is a stem-loop structure that contains bulge 25, stem 26 and loop 27, the "left hand loop", as disclosed in US 2010/0003753.
As also disclosed in of US 2010/0003753, the stem section 20 can be any number of ribonucleotides in length and can contain an unlimited number of bulges provided it is still able to base pair. Preferably and in certain embodiments, stem section 20 contains at least about 4, more preferably at least about 10 base pairs; further, it preferably contains at most about 50, more preferably at most about 40 base pairs. Preferably stem section 20 contains about 0 to about 8 bulges; more preferably it contains about 0 to about 4 bulges.
In certain embodiments, stem section 20 (as shown in US
2010/0003753) can be replaced by a double-stranded siRNA. In this embodiment of the chimeric pRNA, the "cargo" carried by the chimeric pRNA takes the form of stem section 20 itself, which constitutes biologically active siRNA. In certain other embodiments, stem section 20 can be derivatized at either or both of its 5'- and 3'- ends with a biologically active moiety, detectable label, or the like, as its heterologous component "cargo". For example, according to the present disclosure the 5' end of P1 in the pRNA polynucleotide that is self-assembled from two pieces, P1 and P2, to form a two-piece pRNA monomer, can be derivatized with folate (to facilitate targeting to folate receptor-bearing cells) or with a fluorescent label (to facilitate detection of the pRNA monomer, including detection of a pRNA nanoparticle that comprises such a monomer).
Tertiary interactions within an RNA molecule may result from nonlocal interactions of areas of the RNA molecule that are not near to each other in the primary sequence. Although native bacteriophage pRNA appears to exhibit tertiary interactions between the "right hand" loop and the "left hand" loop of the pRNA intermolecular interaction domain (Chen et al., RNA 5:805- 818 (1999); Guo et al, Mol. Cell. 2:149-155 (1998)), it should be understood that the pRNA chimeras contemplated herein are not intended to be limited to RNA molecules exhibiting any particular tertiary interactions. On the other hand, it will be appreciated that these intramolecular, tertiary interactions can be used to advantage. For example, certain embodiments contemplate multimeric pRNA complexes that may comprise one or more of the herein described artificial pRNA polynucleotides comprising a self-assembled two- piece pRNA monomer, in which complexes the interactions between the right and left hand loops of the various monomers can be controlled by engineering into their structures the desired left/right loop complementarity, advantageously resulting in customized dimers, trimers, and hexamers, such as for use in particular therapeutic and/or diagnostic applications.
In certain embodiments, the artificial pRNA polynucleotide contains at least 8, more preferably at least 15, most preferably at least 30 consecutive ribonucleotides found in native SF5' pRNA, B103 pRNA, phi29/PZA pRNA, M2/NF pRNA, GA1 pRNA, or aptRNA, or native phi29 pRNA, sequences of which are disclosed in US 2010/0003753.
The pRNA region may in certain preferred embodiments be formed from: a first pRNA piece P1 that comprises a RNA polynucleotide of at least 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56 or 57 nucleotides and that includes a P1 intermolecular interaction domain of about 29 nucleotides comprising the P1 3'- end, and which piece P1 may further comprise one or more heterologous components attached at the 3'-end and/or at the 5'-end and independently comprising an additional polynucleotide of up to about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250 or more nucleotides; and a second pRNA piece P2 that comprises a RNA
polynucleotide of at least 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 or 62 nucleotides and that includes a P2 intermolecular interaction domain of about 39 nucleotides comprising the P2 5'- end, and which piece P2 may further comprise one or more heterologous components attached at the 3'-end and/or at the 5'-end and independently comprising an additional polynucleotide of up to about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250 or more nucleotides; "about" is understood to include the recited value and also to include a value that is more or less than the recited value by 1 , 2, 5, 10, 15, 20 or 25 percent. In preferred embodiments P1 and/or P2 are produced by non- enzymatic chemical synthesis; it is accordingly believed without wishing to be limited that economically efficient non-enzymatic synthesis in quantities and of a quality sufficient for pharmaceutical (including therapeutic and diagnostic) purposes currently may be feasible for polynucleotides of not more than about 100, 95, 90, 85 or 80 nucleotides in length.
In certain embodiments P1 and P2 each contain a portion of the phi29 pRNA sequence that starts at ribonucleotide 23, preferably at
ribonucleotide 20, and ends at ribonucleotide 95, preferably ribonucleotide 97; the phi29 pRNA sequence is set forth in Fig. 2 of US 2010/0003753. In certain embodiments, P1 and/or P2 each comprise a portion of the phi29 nucleotide sequence that is preferably at least 60% identical to, more preferably 80% identical to, even more preferably 90% identical to, and most preferably 95% identical to a portion of the nucleotide sequence of a corresponding native SF5' pRNA, B103 pRNA, phi29/PZA pRNA, M2/NF pRNA, GA1 pRNA, the aptRNA chimera or phi29 pRNA (particularly bases 20-97); these sequences are disclosed in US 2010/0003753.
Percent identity is determined by aligning two polynucleotides to optimize the number of identical nucleotides along the lengths of their sequences; gaps in either or both sequences are permitted in making the alignment in order to optimize the number of shared nucleotides, although the nucleotides in each sequence must nonetheless remain in their proper order. For example, the two nucleotide sequences are readily compared using the Blastn program of the BLAST 2 search algorithm, as described by Tatusova et al. (FEMS Microbiol Lett 1999, 174:247-250). Preferably, the default values for all BLAST 2 search parameters are used, including reward for match=1 , penalty for mismatch=-2, open gap penalty=5, extension gap penalty=2, gap
x_dropoff=50, expect=10, wordsize=1 1 , and filter on.
The covalent linkages between the heterologous component, for example, an RNA that comprises a biologically active moiety such as a siRNA or a ribozyme, and P1 or P2 can be direct or indirect but preferably are indirect. In an indirect linkage, the spacer region includes additional string(s) of ribonucleotides at one or both ends of the biologically active moiety. These ribonucleotide strings, if present, contain preferably at least about 3
ribonucleotides; and preferably contain at most about 300, more preferably at most about 30 ribonucleotides. Compositionally, the strings can contain any desired ribonucleotides, however it is preferably that ribonucleotide
compositions are selected so as to prevent the ribonucleotide strings on either side of the biological moiety from base pairing with each other or with other parts of the pRNA chimera formed by the artificial pRNA monomer and the heterologous component.
Exemplary biologically active moieties include, without limitation, DNA, RNA, DNA or RNA analogs, including a ribozyme, a siRNA, an RNA aptamer, or an antisense RNA, peptide nucleic acid (PNA), a peptide, a protein such as an antibody, a polysaccharide, a lipid, a virus, a plasmid, a cofactor, or a combination thereof. Biologically active moieties can be selected without limitation, and include those having desired activity or characteristic, such as binding activity, enzymatic activity, and the like. Preferably the biological activity of the biologically active moieties is an enzymatic activity or binding activity or both; for example, the biologically active moiety may function as or encode a ribozyme or other catalytic moiety. Since siRNA is a double-stranded RNA, the effective siRNA moiety could include any sequence to replace the 573' paired helical region.
The biologically active moiety is preferably a polynucleotide. A preferred biologically active polynucleotide is a polyribonucleotide, more preferably the biologically active polynucleotide is a siRNA or a ribozyme such as a hammerhead ribozyme or a hairpin ribozyme. Antisense RNA and other bioactive RNAs are also preferred.
It should be understood that the terms "nucleotide," "oligonucleotide," and "polynucleotide" as used herein encompass DNA, RNA, or combinations thereof, unless otherwise indicated. Further, the terms DNA and RNA should be understood to include not only naturally occurring nucleic acids, but also sequences containing nucleotide analogs or modified
nucleotides, such as those that have been chemically or enzymatically modified, for example DNA phosphorothioates, RNA phosphorothioates, and 2'- O-methyl ribonucleotides.
In a preferred embodiment, one or more nucleotide derivatives, such as 2'-NH2-2'-deoxy CTP, 2'-CH3-2'-deoxy CTP, 2'-F-2' deoxy CTP, 2'-F-2' deoxy UTP, and spiegelmers (L-nucleotide aptamers) are incorporated into the pRNA during synthesis to produce stable RNA products that are resistant to RNase digestion. The stabilizing modification is preferably made at the 2' position of the ribonucleotide or at other positions. In most cases, incorporation of the stabilizing nucleotide derivatives is not expected to significantly interfere with dimerization or trimerization of the pRNAs to form a multimeric complex, nor is it expected to adversely impact the activity or function of the "cargo" moiety. Since biological function of the pRNA itself (other than its ability to form multimeric complexes) is not a concern, inclusion of non-natural nucleotide derivatives is suitable, especially for the receptor-binding aptamers selected from a random pool {e.g., using SELEX). If the incorporation of RNase- resistant nucleotide derivatives into a heterologous component that comprises a therapeutic RNA tethered to the pRNA does happen to interfere with the biological activity, such as a catalytic function of a cargo RNA, for example, the cargo RNA can be synthesized with regular nucleotides and ligated to the pRNA molecule.
A ribozyme is generally characterized by: arm 1 -active enzyme center-arm 2 where arm 1 and arm 2 are sequences complementary to the target substrate to be cleaved by the ribozyme, and the active enzyme center is the catalytic center that cleaves the target RNA. The "arms" of the ribozyme typically contain at least about 7 nucleotides, preferably at least about 12 nucleotides; and typically contain at most about 100 nucleotides, preferably at most about 30 nucleotides. The nucleotide sequence of the arms can be engineered to hybridize to the nucleotide sequence of any desired target nucleic acid.
The artificial pRNA polynucleotides described herein can be synthesized chemically or enzymatically using standard laboratory protocols and are preferably the products of non-enzymatic chemical synthesis. When enzymatic synthesis is employed, the pRNA region may be transcribed from a DNA template that encodes it. Artificial pRNA polynucleotides may be assembled from RNA fragments (modular components) that have been chemically synthesized (see, e.g., Fang et al., Biochemistry, 2005, 44(26):9348- 9358). If synthesized chemically, the artificial pRNA polynucleotide may optionally contain nonnative nucleotides {e.g., derivatized or substituted nucleotides) and/or nonnative bonds analogous to the phosphodiester bonds that characterize naturally occurring nucleic acids. The inclusion of nonnative nucleotides or nonnative bonds can increase the stability of the pRNA
polynucleotide and make it more resistant to enzymatic degradation.
In a pRNA chimera that comprises the herein described artificial pRNA polynucleotide monomer that is self-assembled from P1 and P2, the "cargo" moiety {e.g., siRNA, RNA aptamer or ribozyme) may be positioned in the spacer region, or in another embodiment the "cargo" moiety may be incorporated into, or attached elsewhere in, the pRNA structure.
When replacing the 573' paired helical region of a pRNA with an siRNA, substantial tolerance has been observed concerning the positions in the pRNA sequence at which the siRNA strands can be attached. It has been shown, for example, that the addition or deletion of nucleotides at the 5' end preceding nucleotide 23, and at the 3' end following nucleotide 97, does not affect the correct folding of the intermolecular interaction (procapsid binding) domain (Zhang et al., RNA 1995; 1 :1041 -1050). For example, gene silencing was achieved using complementary siRNA attached at positions 29 and 91 to form the paired helical region, and with the siRNA attached at positions 21 and 99 to form the paired helical region (see US 2010/0003753). Accordingly in the present embodiments it is important that the siRNA not intrude into the intermolecular interaction region (containing the right hand and left hand loops) such that it interferes with the interactions of the right and left hand loops in the formation of dimers, trimers and hexamers.
Covalent attachment of a folate moiety to pRNA chimeras as a targeting moiety is described in US 2010/0003753 and may similarly be employed to target pRNA nanoparticles formed from the herein described pRNA polynucleotides. Another moiety that can be attached at or near the 5' and/or 3' end of a pRNA is a detectable label. One or more 5' or 3' end of a pRNA or a pRNA chimera {e.g., a pRNA that incorporates an siRNA as the paired helical region) may also be derivatized to include a detectable label, such as a fluorescent label, a radioactive label, or a paramagnetic label.
Labeling at least one component of a multimeric pRNA complex allows the complex to be detected. Likewise, a therapeutic agent, such as a radionuclide, can be linked at or near a 5' or 3' end of an artificial two-piece pRNA monomer, a pRNA chimera formed therefrom or a modified pRNA to effect treatment of a subject once the multimeric complex has bound to and/or been internalized by the target cell.
It should be understood that derivatization of a pRNA at or near its 5' or 3' end encompasses linking the cargo moiety to whatever nucleotide presently constitutes the 5' or 3' end of the pRNA polynucleotide. In other words, a pRNA may be truncated (at either the 5' or 3' ends) with respect to a naturally occurring pRNA, or it may have one or more additional nucleotides added to its 5' and/or 3' end when compared to a naturally occurring pRNA. In either event, derivatization may be of the first and/or last nucleotides of the linear pRNA; i.e., the 5' and/or the 3' nucleotides of P1 and/or P2 that form that particular pRNA molecule, or, when the pRNA polynucleotide is produced by non-enzymatic chemical synthesis, derivatization may be effected in the course of the synthesis at any other desired position in the molecular structure.
Furthermore, it should be understood that the heterologous component can be linked either covalently or noncovalently to the pRNA at or near the 5' or 3' end of the pRNA, for example, at the 5'- and/or 3'-ends of P1 and/or P2. Preferably, the linkage is covalent, except in the case where a complementary
oligonucleotide constitutes the heterologous component, as discussed in US 2010/0003753.
The uptake of extracellular macromolecules and particles by receptor-mediated endocytosis (RME) is a process common to almost all eukaryotic cells. The mechanism for receptor-mediated endocytosis has been subjected to intense scrutiny and its overall feasibility for the delivery of therapeutic molecules, such as antibodies (Becerril et al.,
Biochem.Biophys.Res. Commun., 255:386-393 (1999) and Poul et al., J Mol. Biol., 301 :1 149-1 161 (2000)), drugs or RNA aptamers (Homann et al., Bioorg. Med Chem, 9:2571 -2580 (2001 )) has been reported. However, difficulties in exploiting receptor-mediated endocytosis (RME) for the targeting and delivery of therapeutic agents have been encountered and include 1 ) lack of specificity for the targeted cell versus healthy cells; 2) lysosomal degradation of the therapeutic molecules in the endocytic pathway; 3) instability of the targeting and delivery system in the body, and 4) adverse immunological response associated with repeated doses.
The ability of a pRNA chimera, comprising the herein described artificial pRNA polynucleotide fromed from a two-piece pRNA monomer, to form dimers, trimers, tetramers and hexamers, provides additional embodiments whereby individual pRNA chimeras can be viewed as "building blocks". These building blocks can be designed and selected to serve as components of a customized or "designer" multimeric pRNA complex. The monomeric building blocks may be engineered to include right hand and left hand loops in the intermolecular interacting domain that promote the desired interactions {e.g., A- b', B-e', E-a' to form a trimer). See Shu et al., Nano Letters 2004;4:1717-1724; WO2005/035760. The polyvalent nature of these multimeric complexes makes possible an integrated, multi-faceted approach to treatment and/or diagnosis, as described in US 2010/0003753.
Therapeutic agent(s) {e.g., a biologically active RNA such as a ribozyme or a siRNA, or other drug) can be carried by another of the pRNA monomers that make up a dimeric, trimeric or hexameric polyvalent pRNA chimera. Therapeutic agents can include biologically active RNAs, enzymes, chemotherapeutic drugs, and the like. They can be selected to be effective against cancer {e.g., solid tumors such as epithelial cancers, epithelioma, adenocarcinoma, cervical cancer, prostate cancer, sarcoma, chondrosarcoma, neuroblastoma, lung, kidney, colon, pancreatic, bone or other cancer, etc., circulating or liquid tumors such as leukemia, lymphoma, ascites tumors, etc.) or infectious disease, including viral infections such as those caused by human immunodeficiency virus (HIV) and hepatitis virus, particularly hepatitis B virus (HBV), also human papilloma virus, influenza and other viruses. An example of a therapeutic agent can be incorporated into a pRNA chimera for use as a component of an anti-cancer multimeric complex is siRNA directed against the gene encoding survivin. Survivin inhibits apoptosis in certain cancer cells, thus survivin siRNA, which silences survivin, induces apoptosis of cancer cells. The dimeric, trimeric and hexameric polyvalent pRNA complexes of the invention are thus ideally suited for therapeutic RNAs or other chemical drugs for the treatment of cancers, viral infections and genetic diseases. Applications of multiple therapeutic agents are expected to enhance the efficiency of the in vivo therapy.
One type of targeting moiety contemplated for use in certain embodiments as a heterologous component that may be incorporated into the herein described artificial pRNA polynucleotides is a class of RNA molecules that bind other molecules (such as cell surface receptor-binding RNA molecules or RNA molecules that bind endosome disrupting agents), which can, for example, be identified and isolated through SELEX (Systematic Evolution of Ligands by Exponential Enrichment) (Tuerk et al., Science 249:505-510 (1990); and Ellington et al., Nature 346:818-822 (1990)). Such RNA molecules are known as "RNA aptamers." Starting with a library containing random RNA sequences, in vitro evolution techniques allow for the selection of the RNA molecules that are able to bind a specific pre-identified substrate, such as a ligand or receptor (Ciesiolka et al., RNA 1 :538-550 (1995); Klug and Famulok, Molecular Biology Reports 20:97-107 (1994).
The SELEX system is used to identify RNA aptamers that bind specifically to proteins, polysaccharides, lipids, ATP, chemicals and
theoretically any substance that has a well defined molecular structure (Bouvet, Methods Mol. Biol, 148:603-610 (2001 ); Ciesiolka et al., RNA, 1 :538-550 (1995); Davis et al., Methods Enzymol., 267:302-314 (1996); Gold, Harvey Lect., 91 :47-57 (1995); Kraus et al., J Immunol., 160:5209-5212 (1998); Shu et al., J Biol.Chem., 278(9):71 19-7125 (2003); Shultzaberger et al., Nucleic Acids Res., 27:882-887 (1999); Wang et al., Sheng Wu Hua Xue.Yu Sheng Wu Wu Li Xue.Bao. (Shanghai), 30:402-404 (1998); and Zhen et al., Sheng Wu Hua Xue. Yu Sheng Wu Wu Li Xue.Bao. (Shanghai), 34:635-642 (2002)). Indeed, this approach can be generalized well beyond being a means to deliver an endosome disrupting agent or bind a target cell surface receptor, as it provides a way to link essentially any desired molecule (typically, a non-nucleic acid) to the pRNA delivery vehicle once an RNA aptamer that binds it has been identified. The linkage between an RNA aptamer and its target molecule is noncovalent, but cross-linking can, if desired, be achieved in some instances after the initial binding step has taken place.
Instead of or in addition to using SELEX to identify RNA aptamers for specific binding, functional groups such as biotin, --SH, or -NH.sub.2 can be linked to the end of the pRNA. Once the pRNA has been derivatized, endosome disrupting agents (or other desired molecules, particularly non- nucleic acid molecules) can be linked to the end of pRNA by the streptavidin- biotin interaction or by chemical crosslinking (--SH/maleimide or - NH.sub.2/NHS ester). The ability, disclosed herein, to design pRNA molecules that assemble to hexamers in a preprogrammed, intentional manner lends unmatched versatility to the process. In addition to an anti-receptor aptamer, for example, the hexamer could harbor up to five other components. These could include poly(amino ester)(n-PAE) (Lim et al., Bioconjug. Chem, 13:952- 957 (2002)), synthetic peptides (Mastrobattista et al., J Biol Chem, 277:27135- 27143 (2002); Plank et al., J Biol Chem, 269:12918-12924 (1994); and Van Rossenberg et al., J Biol Chem, 277:45803-45810 (2002)), virus-derived particles (Nicklin et al., Circulation, 102:231 -237 (2000)) for lysosome escape, adjuvants, drugs or toxins. Using the same principle, dimers or trimers could be utilized. Even the hexamer-bound empty procapsid could prove useful, serving as a nanocapsule to harbor DNA coding specific genes for delivery.
RNA is uniquely suitable for use in treating chronic diseases since it has a low or undetectable level of immunogenicity except when complexed with protein. ( Goldsby et al. In Immunology, 5th ed.; W. H. Freeman and Company: New York, 2002; pp 57-61 ; Madaio et al., J. Immunol. 1984;
132:872-876). The monomeric or multimeric pRNA chimera as described herein do not, in preferred embodiments, contain protein or peptides, and thus the use of protein-free nanoparticles formed from these artificial pRNA polynucleotides may be exploited advantageously to avoid immune responses, permitting long-term administration in the treatment of chronic diseases.
Therapeutic Methods. One or more RNA nanoparticles, such as a nanoparticle comprising the herein described artificial pRNA polynucleotide, for example a nanoparticle comprising one or more siRNA polynucleotides that are capable of interfering with target polypeptide expression, may also be used to modulate {e.g., inhibit or potentiate) target polypeptide activity in a patient. As used herein, a "patient" may be any mammal, including a human, and may be afflicted with a condition associated with undesired target polypeptide activity or may be free of detectable disease. Accordingly, the treatment may be of an existing disease or may be prophylactic. Non-limiting examples of conditions associated with inappropriate activity of specific siRNA target polypeptides may include disorders associated with cell proliferation, including cancer, graft- versus-host disease (GVHD), autoimmune diseases, allergy or other conditions in which immunosuppression may be involved, metabolic diseases, abnormal cell growth or proliferation, infectious diseases, obesity, impaired glucose tolerance and diabetes, and cell cycle abnormalities.
For administration to a patient, one or more RNA nanoparticles, such as (in certain preferred embodiments) a nanoparticle comprising the herein described artificial pRNA polynucleotide, or (in certain other
embodiments) comprised in an appropriate vector {e.g., including a vector which comprises a DNA sequence from which the subunits of the RNA nanoparticle can be transcribed and then self-assembled) are generally formulated as a pharmaceutical composition. A pharmaceutical composition may be a sterile aqueous or non-aqueous solution, suspension or emulsion, which additionally comprises a physiologically acceptable carrier (i.e., a nontoxic material that does not interfere with the activity of the active ingredient). Such compositions may be in the form of a solid, liquid or gas (aerosol).
Alternatively, compositions of the present embodiments may be formulated as a lyophilizate or compounds may be encapsulated within liposomes using well known technology. Pharmaceutical compositions within the scope of the present invention may also contain other components, which may be
biologically active or inactive. Such components include, but are not limited to, buffers (e.g., neutral buffered saline or phosphate buffered saline),
carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, chelating agents such as EDTA or glutathione, stabilizers, dyes, flavoring agents, and suspending agents and/or preservatives.
Any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of the present invention. Carriers for therapeutic use are well known, and are described, for example, in Remingtons Pharmaceutical Sciences, Mack Publishing Co. (A.R. Gennaro ed. 1985). In general, the type of carrier is selected based on the mode of administration. Pharmaceutical compositions may be formulated for any appropriate manner of administration, including, for example, topical, oral, nasal, intrathecal, rectal, vaginal, sublingual or parenteral administration, including subcutaneous, intravenous, intramuscular, intrasternal,
intracavernous, intrameatal or intraurethral injection or infusion. For parenteral administration, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, kaolin, glycerin, starch dextrins, sodium alginate, carboxymethylcellulose, ethyl cellulose, glucose, sucrose and/or magnesium carbonate, may be employed.
A pharmaceutical composition {e.g., for oral administration or delivery by injection) may be in the form of a liquid {e.g., an elixir, syrup, solution, emulsion or suspension). A liquid pharmaceutical composition may include, for example, one or more of the following: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium,
polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. A parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. The use of physiological saline is preferred, and an injectable pharmaceutical composition is preferably sterile.
The compositions described herein may be formulated for sustained release {i.e., a formulation such as a capsule or sponge that effects a slow release of compound following administration). Such compositions may generally be prepared using well known technology and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site. Sustained-release formulations may contain an agent dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane. Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.
Within a pharmaceutical composition, a therapeutic agent comprising an RNA nanoparticles comprising the herein described artificial pRNA polynucleotide as described herein (or, e.g., a recombinant nucleic acid construct comprising a polynucleotide encoding one or more of the RNA subunits of such a nanoparticle) may be linked to any of a variety of
compounds. For example, such an agent may be linked to a targeting moiety {e.g., a small molecule ligand, an aptamer, a monoclonal or polyclonal antibody, a protein or a liposome) that facilitates the delivery of the agent to the target site. As used herein, a "targeting moiety" may be any substance (such as a compound or cell) that, when linked to an agent enhances the transport of the agent to a target cell or tissue, thereby increasing the local concentration of the agent. Targeting moieties include small molecule ligands {e.g., folate), aptamers, antibodies or fragments thereof, receptors, ligands and other molecules that bind to cells of, or in the vicinity of, the target tissue. An antibody targeting agent may be an intact (whole) molecule, a fragment thereof, or a functional equivalent thereof. Examples of antibody fragments are F(ab')2, Fab', Fab and F[v] fragments, which may be produced by conventional methods or by genetic or protein engineering. Linkage is generally covalent and may be achieved by, for example, direct condensation or other reactions, or by way of bi- or multi-functional linkers. Targeting moieties may be selected based on the cell(s) or tissue(s) toward which the agent is expected to exert a therapeutic benefit. Pharmaceutical compositions may be administered in a manner appropriate to the disease to be treated (or prevented). An appropriate dosage and a suitable duration and frequency of administration will be determined by such factors as the condition of the patient, the type and severity of the patient's disease, the particular form of the active ingredient and the method of administration. In general, an appropriate dosage and treatment regimen provides the agent(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit {e.g., an improved clinical outcome, such as more frequent complete or partial remissions, or longer disease-free and/or overall survival, or a lessening of symptom severity). For prophylactic use, a dose should be sufficient to prevent, delay the onset of or diminish the severity of a disease associated with cell proliferation.
Optimal dosages may generally be determined using experimental models and/or clinical trials. In general, the amount of RNA nanoparticles (comprising the herein described artificial pRNA polynucleotide) that is present in a dose, or that is produced in situ by DNA present in a dose {e.g., from a recombinant nucleic acid construct comprising an encoding polynucleotide), ranges from about 0.01 μg to about 100 μg per kg of host, typically from about 0.1 μg to about 10 μg. The use of the minimum dosage that is sufficient to provide effective therapy is usually preferred. Patients may generally be monitored for therapeutic or prophylactic effectiveness using assays suitable for the condition being treated or prevented, which will be familiar to those having ordinary skill in the art. Suitable dose sizes will vary with the size of the patient, but will typically range from about 10 mL to about 500 mL for 10-60 kg animal.
Throughout this specification, unless the context requires otherwise, the word "comprise", or variations such as "comprises" or
"comprising", will be understood to imply the inclusion of a stated element or integer or group of elements or integers but not the exclusion of any other element or integer or group of elements or integers. As used herein the singular forms "a", "an" and "the" include plural aspects unless the context clearly dictates otherwise. Thus, for example, reference to "a cell" includes a single cell, as well as two or more cells;
reference to "an agent" includes one agent, as well as two or more agents; and so forth.
Each embodiment in this specification is to be applied mutatis mutandis to every other embodiment unless expressly stated otherwise.
Standard techniques may be used for recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation {e.g., electroporation, lipofection). Enzymatic reactions and purification techniques may be performed according to manufacturer's specifications or as commonly accomplished in the art or as described herein. These and related techniques and procedures may be generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification. See e.g., Sambrook et ai, 2001 , MOLECULAR CLONING: A LABORATORY MANUAL, 3d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Current Protocols in Molecular Biology (Greene Publ.
Assoc. Inc. & John Wiley & Sons, Inc., NY, NY); Current Protocols in
Immunology (Edited by: John E. Coligan, Ada M. Kruisbeek, David H.
Margulies, Ethan M. Shevach, Warren Strober, 2001 and 2010, John Wiley & Sons, NY, NY); or other relevant Current Protocol publications and other like references. Unless specific definitions are provided, the nomenclature utilized in connection with, and the laboratory procedures and techniques of, molecular biology, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well known and
commonly used in the art. Standard techniques may be used for recombinant technology, molecular biological, microbiological, chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients. The following Examples are presented by way of illustration and not limitation.
EXAMPLES
EXAMPLE 1
MATERIALS AND METHODS
Chemical synthesis of 2'-F-pRNA:
Chemical synthesis of two-piece pRNA. The 2'-F-pRNA monomer molecule was first chemically synthesized as two pieces with an approximate length of ~55nt of P1 and -60 nt of P2 (depending on the particular pRNA monomer) by Trilink Biotechnologies (San Diego, CA). The first oligonucleotide (P1 ) had a 3'-OH group. The second oligonucleotide (P2) had a 5'-phosphate group (Fig. 1A). To assemble the pRNA monomer, P1 and P2 were simply mixed and/or annealed at an equal molar ratio at the desired concentration. In order to obtain 5'-folate, 5'-Cy5, or 5'-AlexaFluor647 pRNA on P1 or P2, folate- CEP, Cy5-CEP, or AlexaFluor-CEP were synthesized and used in the last coupling step during synthesis of P1 and P2.
Enzymatic ligation of P1 and P2 to form a single full-length pRNA monomer . First, P1 and P2 oligonucleotides were dissolved in 1 X T4 RNA ligase buffer (New England BioLabs, Ipswich, MA) at 50 μΜ final concentration for each oligo. The oligonucleotides were annealed by heating to 90°C for 10 min followed by slow cooling to room temperature over the course of 45 minutes. To the annealed oligonucleotides solution, T4 RNA ligase I (1 .2 ΙΙ/μΙ_) (New England BioLabs, Ipswich, MA) was added and the reaction carried out at 37°C overnight to form the pRNA monomer. The ligated product was extracted using phenol :chloroform followed by ethanol precipitation and subsequent 10%/8M urea PAGE purification. The purified product was quantified by UV absorbance at 260 nm using a NanoDrop ND-1000 spectrophotometer. Cellular uptake ofpRNA nanoparticle by confocol
microscopy and flow cytometry:
Fluorescently-labeled pRNA nanoparticles were used for cellular uptake studies. Essentially, two labeling methods were used. First, direct coupling of fluorescence at 5' end of the oligonucleotides was used as described above. Second, the pRNA was labeled with fluorescein using the Label IT® kit and purified according to the manufacturer's instructions
(Invitrogen, Eugene, OR). KB cells were grown in a folate-free RPMI-1640 medium (Invitrogen, Eugene, OR) supplemented with 10% FBS. For the cellular uptake experiment, the cells were cultured in eight-well-chambered slides (LabTek®; Nunc, Roskilde, Denmark) at a density of 1x104 cells/well. Twenty-four hours later, the culture media was replaced with fresh 200 uL folate-free media, and the fluorescently labeled folate-pRNA nanoparticles were added at a final concentration of 200 nM, either in the absence or in the presence of 200-fold excess of free folic acid. After incubation of the cells at 37°C for 30 min, confocal microscopy was conducted. Images were recorded with an inverted Nikon A1 confocal microscope using a 40x objective. Images were processed using NIS software provided by Nikon.
IFN response assays in vitro:
Assess induction of IFN-response genes. To examine the induction of OAS1 &2, MX1 , and IFITM1 , KB cells were transfected with pRNAi (50nM) and poly l:C (1 g/mL) respectively using the FuGene HD transfection reagent (Roche). After 24 hours, total RNA was isolated using the RNeasy mini kit (Qiagen), and RT-PCR was conducted using the primer sets provided by the "IFNy qRTprimers" kit (InvivoGen) in conjunction with the One-step RT-PCR kit (Invitrogen) according to the manufacturer's instructions. Target gene expression was normalized to GAPDH expression. All reactions were done in triplicate and with no reverse transcriptase or no template as negative controls. To examine the expression of TLR-3, -7, and -9, human peripheral
mononuclear cells (PBMCs) were incubated for 24 hours with 2'-F modified pRNA and poly l:C as a positive control. The expression levels of human TLR receptors were analyzed by semi-quantitative RT-PCR using TLR RT-Primer Set (Invivogen, San Diego, CA), as described herein.
Examination of TNF-a induction in the mouse RAW-246 cell line. Mouse macrophage cell line, RAW-246 (ATCC, Manassas, VA), was plated at a density of 30,000 cells/well in 200 μΙ_ DMEM medium supplemented with 10% (v/v) FBS in 96 well plate. The cells were incubated with pRNA nanoparticles at final concentrations of 400, 100, 4 g/mL for 3 h at 37°C. Aliquots (20 μΙ_) from the culture medium were taken and analyzed using the ELISA kit for murine TNF-a, per the manufacturer's instruction (Antigenix America, NY).
Examination of human TLR3 pathway activation. HEK-Blue™- hTLR3 (Invivogen, San Diego, CA) cells were set up at a density of 300,000 cells/mL in a test medium containing DMEM, 4.5 g/L glucose, 100 g/mL Normocin™, 2 mM L-glutamine, 10% (v/v) heat inactivated FBS. The cell suspension (180 μΙ_) was mixed with a 20μΙ_ pRNA solution and plated in each well of a 96 well plate with final concentrations of 1000, 100, and 10 ng/mL, followed by overnight incubation at 37 °C. Aliquots (20 μΙ_) from the cell supernatant were mixed with a 180 μΙ_ QUANTI-Blue™ detection medium (Invivogen, San Diego, CA) and incubated at 37°C for 3 hours. The levels of SEAP were determined by measuring the UV absorbance at 620-655 nm.
Pharmacokinetic analysis in mice:
Balb/c nude male mice (3 mice total) were each injected with 600 μg of AlexaFluor647-labeled pRNA monomer (24 mg/kg) through the tail vein. Blood was collected (up to 20 μΙ_) through the lateral saphenous vein at 5 min, 30 min, 2hr, 5hr, and 24hr time points. Blood samples were collected in BD Vacutainer® SST™ Serum Separation Tubes. The tubes were inverted five times and left for 30 minutes at room temperature (to allow the blood to clot), followed by centrifugation at 1000-1300 g for 10 minutes. Two μΙ_ supernatant serums were mixed with 1 μΙ_ of proteinase-K and 37 μΙ_ of water. The mixture was incubated at 37°C for 30 minutes before loading onto the capillary gel electrophoresis (CGE) machine. The pRNA in the blood was quantified by CGE through measurement of the fluorescence intensity using a P/ACE MDQ capillary electrophoresis system with a 635 nm laser suitable for AlexaFluor647 fluorophores (Beckman Coulter, Inc., Fullerton, California). The capillaries used were 32 cm in length and 100 μιτι in diameter. Samples were loaded by voltage injection for 40 s at 4 kV and allowed to run for 25 min at 7.8 kV. The gel was replaced after every run. The buffer and the non-denaturing gel were purchased from Beckman Coulter (dsDNA 1000 Kit). The electropherograms produced were integrated using the software "32 Karat" version 7 provided by Beckman Coulter. The pRNA concentrations were calculated from a standard curve. The serum concentration profiles were fitted with an IV bolus non- compartmental model using the Kinetica program (Fisher Scientific, Inc.), and the key secondary pharmacokinetic parameters were deduced. The
pharmacokinetic studies were performed at Purdue animal facility per approved protocol.
Toxicological evaluation in mice:
For the cytokine induction study, 3 groups of 4 immunocompetent female C57B/6 mice (Harlan) aged 10 weeks were injected via tail vein with PBS, Ba'-2'-F-sur-pRNAi (KT-108) at 30mg/kg and KT- 108 at 10mg/kg. The blood was collected by cardiac puncture 3 hrs post injection. The plasma was prepared and analyzed for mouse TNF-a and IL-6 using ELISA assay
(Antigenix America, NY). For a 7-day repeat dose study, 4 groups of 5 mice were intravenously injected (tail vein) with: 1 ) PBS, 2) poly l:C at 30mg/kgm (Sigma, MO), 3) KT-108 at 30 mg/kg, and 4) KT-108 at 10 mg/kg. The mice were treated once every 48hr for 7 days (4 doses total). The mice were monitored for clinical signs and body weights. On day 7, 3 h post the fourth injection, the mice were euthanized per protocol and blood samples were collected by cardiac puncture for standard panel clinical chemistry (including PT, aPTT) and clinical pathology analysis. The gross pathology and organ weights were recorded (including spleen, lymph nodes, liver, and kidneys). The toxicology study was conducted at Explora BioLab Per approved protocol (San Diego, CA). Tumor targeting and biodistribution by imaging in xenograft tumor models:
For biodistribution and tumor targeting studies, 6-week-old male nude mice (nu/nu) were purchased from NCI/Frederick and maintained on a folate-free diet for a total of 2 weeks before the start of the experiment. The mice were injected with different cancer cells (KB cells ~3 x 106 cells per mouse, HeLa cells ~1 x 107 cells per mouse in 40 % matrigel in a folate free RPMI-1640 medium. When the tumors reached -500 mm3, the mice were injected intravenously through the tail vein with a single dose of 15 nmol (24 mg/kg) of KT-105 (FA-AlexaFluor647 labeled-pRNA). The control mice were injected with 10mg/kg of free foic acid intraperitoneally 10 min prior to the KT- 105 injection. The mice were euthanized by CO2 asphyxiation 24 hrs post injection, and whole-body imaging was conducted using an MS® Lumina station (Bindley Bioscience Center at Purdue). After whole-body imaging, the mice were dissected and the major organs and tumors were collected and laid out for organ imaging (tumors, liver, spleen, heart, lung, intestine, kidney, and skeletal muscle). The tumor targeting studies were performed at Purdue animal facility per approved protocol.
EXAMPLE 2
RESULTS
Chemical synthesis of two-piece 2'-fluoro-pyrimidine- modified pRNA molecules.
Since in vitro transcription cannot be scaled up for industrial production and cannot support the precise modifications, a scalable process of pRNA nanoparticles production was set out to develop by a total chemical synthesis to generate sufficient RNA for current animal studies and for industrial-scale manufacturing of pharmaceuticals in the future. However, the pRNA molecule (1 17 nt) is too long for current RNA chemical synthesis approach to produce reasonable yield and purity, particularly with the 2'-F- modification. Therefore, the two-piece strategy was adopted for the total synthesis of pRNA monomer, which was successfully shown using in vitro transcription and pRNA subunits, including subunits of distinct design (see Example 3). The full-length pRNA was divided into two pieces, P1 and P2, with a break point at 3' of nucleotide 55 located within the 53-58 single stranded loop region of the wild-type pRNA (see Example 3) (Fig. 1 , A). Each piece was approximately half the length (49-60 nt) of the full-length pRNA, rendering synthesis possible using conventional solid phase automated RNA synthetic chemistry, with a free hydroxyl on the 3'-end of P1 (P1 -OH-3') and 5'- phosphate group on P2 (5'-PO4-P2). This strategy created two new additional termini to facilitate functionalization. A chemical process to produce pRNA-P1 - and -P2 was developed using TBDMS chemistry. 2'-F-pyrimidine
phosphoramidites were used instead of the non-modified monomers along the entire length of the pRNA, or at specified positions as desired. A process was achieved that yielded P1 and P2 at subgram-scales with >80% purity as measured by HPLC, which was sufficient for in vivo small animal trials. The chemically synthesized pRNA components (P1/P2), even with functional modules (see below), self-assembled into a single non-covalently-bound two- molecule complex by simple 1 :1 molar ratio mixing (see Example 3) as shown by native gel analysis (Fig. 1 B). MFold analysis (http://dinamelt.bioinfo.rpi.edu/) confirmed the identical folding pattern of the two-piece and one-piece (full- length) pRNA (data not shown). To confirm the assumed equivalence of the chemically synthesized two-piece molecule to the one-piece molecule synthesized by in vitro transcription, two additional experiments were also performed: ligation and dimerization.
2 -F-P1 and -P2 are efficiently ligated by T4-RNA ligase into the full-length pRNA. The synthetic strategy produced two new termini (P1 -OH-3' and 5'-PO4-P2) that could be readily ligated to form a full-length molecule if desired. In principle, a correctly folded pRNA monomer would present the T4 RNA ligase with an intramolecular ligation step instead of the regular
intermolecular ligation between two separate single RNA strands, which in turn should increase the rate of this chemical step during enzyme catalysis (29-31 ). Also the presence of a preformed unligated monomer would result in the lack of circular RNAs, a common side product during RNA ligation using T4 RNA ligase (31 , 32). This concept was tested by incubating the annealed mixture (P1/P2) with T4-RNA ligase at 37°C, followed by denaturing PAGE analysis (Fig. 1 B). The results demonstrated that the two pieces were efficiently ligated almost to completion. The ligated full-length pRNA was indistinguishable from that generated by in vitro transcription as seen by gel electrophoresis. In addition, the absence of any circular side product that can be formed by ligation of the 3'-hydroxyl group and the 5'-phosphate group on P2 further confirmed the strategy.
The chemically synthesized P1/P2 complex with or without ligation formed a dimer with other pRNA. A correctly folded 2-piece pRNA monomer (Ba') or the 2-F modified pRNA monomer have been shown to form a dimer with a complementary (Ab') monomer (16, see Example 3). To test whether the pRNA monomer generated from the 2-F 2-piece folded correctly, a two-piece 2'-F-Sur-pRNAi Ba' monomer was mixed with a 2'F-pRNA Ab' monomer at a 1 :1 molar ratio, followed by native PAGE analysis. The results demonstrated that the two monomers, whether ligated or non-ligated, formed a dimer (Fig. 1 D). Fluorescent based capillary electrophoresis, a technique milder and more sensitive than regular slab gel, indicated that the efficiency of 2'-F-pRNA dimer formation was as high as 99% (Fig. 6).
The 2'-F-pRNA nanoparticle (two-piece) was stable. The stability of a pharmaceutical product is particularly important for manufacturing, storage, transportation, and potency maintenance (expiration date), etc.
Thermodynamically stability is also the foundation for diverse and robust modularizations. Furthermore, thermostability can also affect the behavior of nanoparticles inside the body upon administration. For a functional nucleic acid agent such as pRNA, the most important aspect of its stability lies in the stability of its folding, particularly the two-pieces folding together. Melting temperature (Tm) studies reveal that the nonligated 2'-F two-piece pRNA was stable. The 2'-F-pRNA was metabolically stable in the presence of serum or RNase A. The purpose of chemical modification was to make the pRNA nanoparticle metabolically stable in biological fluids (e.g. plasma). Previous data have shown that the 2'-F-modified pRNA generated by in vitro transcription was indeed significantly stabilized in the biological milieus (16). To test the chemically synthesized and self-assembled two-piece 2'-F-pRNA, this particle was incubated with culture media containing 10% and 50% human serum for various periods, followed by denaturing urea-PAGE analysis. A large proportion of the 2'-F-pRNAi remained intact for up to 24 hours (Fig. 7), in contrast to the non-modified RNA, which degraded rapidly. The enhanced stability was further confirmed by incubating the 2'-F pRNA with RNaseA, where the majority of full-length pRNAi remained intact (Fig. 7). These results demonstrated that the chemically synthesized 2'-F-pRNA was metabolically stable.
The pRNA nanoparticles did not induce IFN response in cultured ceiis in vitro. A safety profile is a key aspect of any nanodelivery system for systemic applications. A concern with a nucleic acid based system is the non-specific activation of interferon response (IFN) pathways. To this end, the potential induction of IFN responses was assessed in vitro using several cell-based systems. Since polyinosinic:polycytidylic acid (Poly l:C), a synthetic double-stranded RNA, is a ligand to Toll-like receptor (TLR)-3 and a potential inducer of cytokines (IFN, IL-6 and TNF-a, etc.) (33), it was used as a positive control in all tests. First, the gene expression profiles of several key interferon response genes were examined including OAS1 , 2 (2', 5'- oligoadenylate synthetase 1 , 2), MX1 , and IFITM1 (34) in KB cells upon transfection with pRNA. The data showed that the expression of these genes did not increase in KB cells transfected with either the non-modified or the 2'-F modified pRNAi (Fig. 2A). Second, double stranded RNA has been reported to stimulate the expression of tolllike receptors (TLRs) (35, 36). The effect of pRNAi on the expression of TLR-3, -7, and -9 genes was examined then in human PBMC. Again, the results indicated that 2'-F-pRNA did not induce these genes, as compared to the mock treatment, and in contrast to polyl:C (Fig. 2B). Third, we tested whether the exposure to the pRNA nanoparticles would cause cytokine induction in mouse macrophages. The RAW-264 mouse macrophage cell line was incubated with pRNA, at the concentrations indicated, for 3 hrs at 37°C. The TNF-a production in the culture media of the treated cells were then analyzed. The results demonstrated that the exposures to pRNA levels up-to 100ng/mL resulted in little induction, in contrast to that of poly l:C that caused dose-dependent induction of TNF-a (Fig. 2C). Fourth, HEK-Blue™-hTLR3 is a reporter 293-cell line that over-expresses the human TLR3 gene (hTLR3) and secretes reporter embryonic alkaline phosphatase (SEAP), whose gene is under the control of an NF-κΒ and AP-1 inducible promoter. Upon stimulation of the TLR3 receptor by dsRNA, the NF-κΒ and the AP-1 pathways are activated, which in turn activates the production and subsequent secretion of SEAP. The SEAP in the culture media provides a colorimetric readout of the activation of TLR3-induced pathways. pRNA was incubated with HEK-Blue™- hTLR3 overnight, and then quantified the SEAP production. We found that pRNA did not induce the TLR-3 pathway, in contrast to the poly l:C induced dose responsive induction of the TLR-3 pathway (Fig. 2D). In summary, pRNA nanoparticles did not induce interferon response in multiple cell types at all tested dose levels in vitro. Interestingly, pRNA with a longer double strand region (29bp long 573' duplex) did not cause any IFN response.
Functionalization of RNA nanoparticles: One important utility of nanoparticles for therapeutic or diagnostic applications is that different functional modules can be incorporated into a single nanoparticle. A robust nanodelivery system may in certain embodiments desirably have these features: 1 ) the incorporation should not change the structures and functions of either the nanoparticle core or the modules; 2) the modularization can still be achieved by a simple bottom-up self-assembly process using the same basic building blocks but with different pre-incorporated functional modules; 3) a chemical synthesis process can facilitate precisely controlled modulation of the building blocks. The herein described pRNA nanoparticles had these three features, exemplified by the following functional modularizatons.
Incorporation of fluorescent molecules at the 5'-end ofpRNA-P1 or P2. Fluorescence labeled nanoparticles can be used as imaging reporters for diagnostic application as well as for other imaging applications in research. RNA can be readily labeled by fluorescence using a commercially available kit, such as the one that uses a fluorescent platinum reagent that can non- specifically label any G base in a nucleic acid sequence (e.g. the Silencer® Labeling Kit from Ambion). However, this process is hardly stoichiometric, and the number of fluorescent tags per pRNA monomer is difficult to control, which in turn may affect folding, cause physical hindrance in intermolecular interaction, and/or disturb interaction with cell surface receptors. These difficulties can be more readily overcome during automated RNA synthesis by coupling the phosphoramidite of the desired fluorescent tag at a specific position within the RNA molecule.
Fluorescent tags were able to be introduced (such as Cy5, Cy3, FITC and AlexaFluor647) at the 5'-end as well as at the 3'-end or in the middle of the sequence of both P1 and P2. The fluorescence-labeled pRNA
nanoparticle was used in investigating the cellular uptake and intracellular trafficking (see below) and for in vivo targeting for diagnostic applications. Figure 1A shows examples of these fluorescent tags incorporated at the 5'- end of P1 and P2 using this method. These fluorescently labeled P1 or P2 were self-assembled with 5'-folate-P1 or P2 to form a fluorescently labeled folate- pRNA monomeric pRNA nanoparticle to be used for in vitro and in vivo imaging experiments.
Incorporation of folate at the 5'-end of P1 or P2 through direct coupling at the last step of chemical synthesis. Folate receptors (FR) are widely over-expressed in many cancer cell surfaces. Folate ligand binds to FR with high affinity (Kd of 0.1 -1 nM) (37). Recently, folate has been broadly tested as a targeting mechanism for delivering chemotherapeutic drugs, liposome, siRNA, or imaging reporters to tumors (38-42). Therefore, the folate- pRNA nanoparticle was tested for specific targeting to FR+ tumors.
Previously, it has been shown that 5'-folate-AMP can be incorporated into pRNA during in vitro transcription to generate 5'-folate-pRNA. However, this process is not quantitative (usually 10-30%), and ultimately, it is not a scalable procedure. Here, folate incorporation was achieved during the more reliable, scalable, and less labor-intensive automated (non-enzymatic) chemical synthesis. To introduce a folate moiety at the 5'-end, folate
phosphoramidite was first synthesized in collaboration with Berry & Associates, Inc. The folate phosphoramidite was then coupled into pRNA-P1 at the last step during regular automated chemical synthesis with coupling efficiencies > 90% (Fig. 1A). This efficiency is difficult to achieve by other methods.
Similarly, P2 could also be labeled with folate by a direct coupling method to create 5'-folate-pRNA P2. Again, the folate-pRNA P1 self-assembled with pRNA-P2 to form the folate-pRNA monomer, similar to the non-folate modified pRNA monomer (Fig. 1A).
Folate-pRNA monomeric and dimeric nanoparticles target FR+ cancer cells. Fluorescently labeled P1 or P2 and 5'-folate-P2 or P1 self- assembled to form a fluorescently labeled Cy5-pRNA-folate monomeric nanoparticle that was designed to specifically target the folate receptor (FR+) bearing cancer cells (Fig. 1A). This specific targeting was tested by incubating with KB cells followed by confocal microscopy and flow cytometry analysis. The fluorescence confocal microscopy results demonstrated that -100% KB cells were positive for Cy5 staining (see the Red Cy5 circle shown in Fig. 8 indicating cell surface staining at 30' incubation time), and inside cells
(internalized) with longer incubation time (4 h). This cell targeting was highly specific for the folate-receptor since the observed binding was effectively competed out by excess free folate (Fig. 8). There was no binding signal for incubation with the known folate receptor-negative (FR-) cell line, and no binding for a control pRNA nanoparticle without folatic acid (data not shown). Flow cytometry analysis also showed 100% staining (Fig. 8) that was competed out by excess folate. These results together confirmed specific in vitro uptake of the chemically synthesized folate-pRNA nanopartide by the FR+ cancer cells.
Since folate ligands, upon binding to FR, are internalized through receptor mediated endocytosis, the trafficking of folate-pRNA nanopartide (red) upon binding to receptors was then investigated. To help assess this, the Cy5- folate-pRNA nanopartide was incubated with the KB cells transfected with GFP-Rho-B fusion protein plasmid, followed by confocal examination. GFP- Rho-B is expressed exclusively in endosomes (early and mid-stage) and displays a green fluorescence. After 4 hr post incubation, the Cy5-pRNA nanopartide was found to be colocalized with GFP-Rho-B in endosomes in KB cells (yellow) (Fig. 8). Similarly, the Cy5-pRNA-Ba7folate-pRNA-Ab' dimeric nanopartide was also observed to bind and become internalized by FR+ cancer cells (not shown), as measured by the same method used for the monomer above.
Folate-pRNA nanoparticles specifically targeted FR+ human xenograft tumors in immunocompromised mice upon systemic exposure.
A ligand labeled pRNA nanopartide was tested for beneficial tissue distribution and the advantage of self-delivery to the disease tissues of interest upon systemic administration. The nanoparticles contained a specific ligand that could target only disease tissue; they were relatively small in size and hydrophilic, so as not to be trapped in the liver and spleen by the
reticuloendothelial system (RES); but they were sufficiently large not to be filtered out by or accumulated in the kidneys. To confirm these properties, the fluorescence-labeled folate-pRNA nanopartide (AlexaFluor647-folate-pRNA) was systemically delivered to nude mice bearing either HeLa or KB xenograft tumors. The Alexa Fluor-647 was chosen as a near infrared fluorescent dye for its brightness, photo-stability and far-red emission spectrum that did not overlap with autofluorescence levels in tissue to be conjugated to pRNA (5'-P2, see above) by direct coupling during the last step of P2 synthesis. Twenty-four hours post-administration, the animals were imaged using MS® Lumina station. Whole body imaging was first carried out, followed by ex vivo imaging of major organs in order to fully assess the fluorescence signals. The results demonstrated that the fluorescence was mostly concentrated in the tumors, in contrast to the small amount of fluorescence in other normal mouse tissues (Fig. 3A&B). This property signified important advantage of the herein described pRNA nanoparticle for more efficient delivery with fewer side effects, in contrast to other nanodelivery technologies (41 ). As a negative control, a group of mice was predosed with 10 mg/kg of folic acid administered
intraperitoneally 10 minutes before injection of Alexa Fluor 647-folate-pRNA through the tail vein. Both whole body and organ imaging analyses revealed significantly reduced fluorescence intensity in the tumors (Fig. 3A&B), compared to the mice that were not dosed with folic acid. These results clearly demonstrated the specific tumor targeting in vivo by folate-pRNA nanoparticles.
Next, the dose effect on the accumulation of pRNA in the tumor tissue was tested. The results demonstrated that a higher dose level caused increased fluorescence intensity in the tumor. The mean fluorescence increased 2.5 fold when the dose was increased from 6 mg/kg to 24 mg/kg (Fig. 3C). This dose-dependent accumulation of the fluorescent-pRNA nanoparticle suggested that the amount of pRNA nanoparticles delivered to target tissues was controllable by the amount of administrated dose and thus suitable for delivery of therapeutics and diagnostics, an important feature of pharmaceutical entities.
PK analysis of 2'-F-pRNA nanoparticle. Pharmacokinetic (PK) parameters describe the fate and/or behavior of a drug in the in vivo
environment after administration. Two of the key factors that may affect the PK profile are metabolic stability and clearance (e.g. renal filtration and elimination by RES). The 2'-F modified pRNA nanoparticles had significantly enhanced metabolic stability. The dimensions of the monomeric pRNA nanoparticles were > 1 1 nm, which was above the threshold of kidney filtration. The hydrophilic nature, in addition to the optimum size, reduced RES mediated clearance. These properties significantly improved the PK profiles of pRNA nanoparticles by extending T1/2 and reducing the elimination rate.
A PK analysis was carried out for the folate-2'-F-pRNA nanopartide in tumor bearing mice upon systemic administration (a single intravenous injection), in which P1 was fluorescently labeled (AlexaFluor647) at the 5'-end (Fig. 1A). Fluorescence labeling was to ensure sensitive detection and quantification of nanoparticles in plasma sample, as compared to the low sensitivity of UV detection/quantification. The labeled folate-2'-F-pRNA was injected via the tail vein at time 0, followed by blood collection at different time points post administration (5 min, 30 min, 2hrs, 5hrs, 24hrs). The fluorescent nanopartide concentration in serum was then determined using capillary gel electrophoresis (CGE). The choice of using CGE was to ensure the
quantification of the whole nanopartide at corresponding elution time, instead of fragmented/degraded pRNA molecules.
The Plasma concentration-time plot demonstrated a typical two- phase kinetics with an initial rapid distribution phase, followed by a relatively slow elimination phase (Fig. 4). The secondary PK parameters were calculated using a non-compartmental model, as shown in Table 1 . The results
demonstrated significantly extended terminal-phase T1/2 of 5-10 hrs and the increased systemic exposure of AUCIast of 2.0x105 hr*ng/ml_ when dosed at 24 mg/kg. The normalized volume of distribution Vd (1 .2 L/kg) suggested that a significant fraction seemed to be distributed to peripheral tissues (outside vascular or extravasation), particularly in tumor (as shown from bio-distribution results). The relatively small clearance (CI) value (significantly below the kidney filtration rate (43)) suggested that the nanoparticles were not efficiently filtered out by the kidneys. In addition, an apparent dose proportionality of exposure was also observed, suggesting no saturation of the elimination pathways.
In summary, pRNA was rapidly distributed and slowly eliminated, in contrast to the rapid elimination of siRNA (reported PK parameters in the literature are shown in Table 1 ) (44-48). Table 1. Secondar PK arameters of RNA nano articles
Figure imgf000056_0001
Note: **: (44, 45); (47); (6).
Toxicological evaluation of pRNA nanoparticles. Two toxicological assessments of pRNA were performed in mice. The rationale for choosing mice was to be consistent with both PK and tumor targeting studies. First, three groups of four immunocompetent C57B/6 mice each were injected via the tail-vein with PBS (group 1 ), pRNA at 30mg/kg (group 2), and pRNA at 10mg/kg (group 3) respectively. Three hours post administration, the plasma samples from the treated animals were analyzed for mouse TNF-a and IL-6 induction by ELISA. The results showed no induction of TNF-a and IL-6 at the tested dose levels. In the second study, four groups of five C57B/6 mice each were repeatedly administered pRNA nanoparticles once every 48 h by tail vein injection for one week (4 injections total). Each group was injected with PBS (group 1 ); 30 mg/kg polyl:C (group 2); 30 mg/kg pRNA (group 3); or 10 mg/kg pRNA (group 4), respectively. The animals were then examined for a variety of toxicological parameters. All the animals survived the entire dosing period without noticeable clinical signs or body weight changes. There were no gross pathology differences between the pRNA and PBS groups. There were slight enlargements in the spleen in the poly l:C treated group as compared to in the PBS group (Fig. 9). There were no enlargements in the liver, kidneys, and other organs for any of the treated groups as compared to the PBS control group (Fig. 9). Clinical pathology analysis indicated no apparent change in the pRNA-treated groups as compared to the PBS control group, while there were statistically significant increases in both the total number of white blood cells, monocytes, and neutrophils in the poly l:C treated group, along with an increase in the differentials of monocytes and neutrophils (Fig. 5) correlating to the enlarged spleen (see above). These changes in the poly l:C treated animals were consistent with the well-known immunostimulatory nature of poly l:C. Clinical chemistry results demonstrated normal parameters in all the treated animals. There was no change in the liver enzyme levels, correlating with the absence of liver enlargement in these animals (except that the ALT levels of animal # 1588 were above normal range, but this seems to be unrelated to pRNA because it was the only anomaly among all 10 animals and was without a dose correlation). All these data demonstrated that pRNA was safe, in contrast to poly l:C at the same dose level (30 mg/kg).
Discussion. RNA nanoparticles have several important features (for Review, see (5)). First, RNA base pairing is strong (AG of UC/AG: -2.4 kcal/mol vs. AG of dTdC/dAdG -1 .5 kcal/mol), enabling a more stable 2° structure. In contrast to DNA, RNA can fold into well-defined and stable 3° structures. For example, kissing-loop interactions can be 2-3 fold more stable than the RNA duplex of the same sequence (27,28). Second, RNA, as an informational molecule, can be fabricated in different sizes, structures and functions, which are all coded in its sequences. Consequently, there is a potential for rationally engineering of RNA 3° structures that can lead to useful functional modules (e.g. RNAi trigger and self-folding RNA scaffolds mimicking ribozymes and aptamers). Third, since RNA modularity is hierarchically manifested at chemical, structural, and supramolecular levels, a desired RNA nanostructure with multiple substructures and functions, in principle, can be predesigned and constructed by a bottom-up process using programmable basic building blocks. Fourth, scalable total synthetic chemistry procedures are now available for industrial manufacturing and precise modifications of these predesigned building blocks. In addition, two more attributes of RNA molecules make them potentially attractive pharmaceutical products: a) RNA is completely biocompatible, biodegradable and non-immunogenic, and b) modified RNA is resistant to degradation by ribonucleases without altering the original structure/functions in many cases (16).
Despite these important features in theory, RNA nanotechnology faces practical challenges because of its extreme flexibility and variability. Each RNA nucleotide has eight degrees of freedom, and there are competitions between the favorable stacking interaction and the non-favorable
conformational entropy. RNA folds in a complex process that involves divalent- ion mediated electrostatic interactions, conformational entropy, multistate RNA folding kinetics and non-canonical interactions (27, 28). A slight change in primary sequences can result in unpredictable new structures. Therefore, by the currently available tools, although it is theoretically possible to design RNA nanoparticles with the certain above features, it is very challenging to reliably predict how this nanoparticle might behave in reality. However, nature has provided us with RNA nanoscaffolds that are evolutionally selected to possess these features.
The pRNA secondary structure (1 , 4, 6, 21 ) has been demonstrated by the present studies to be retained in chemically synthesized two-piece pRNA monomers that were tightly folded and highly stable. These are believed to be the first RNA nanoparticles to have been comprehensively examined pharmacologically in vivo, and to be demonstrated to be safe with favorable PK and biodistribution profiles, as well as self delivery to tumor tissues by a specific targeting mechanism.
Another advantage of the present pRNA nanoparticle system is its robustness for precise functionalization. As demonstrated herein, folate and fluorescence dyes were stoichimetrically incorporated at the precise structural locations within the molecule as desired. Previous studies have also shown other types of ligand such as RNA aptamers could be incorporated into pRNA (50). Aptamers as functional modules can be produced using similar non- enzymatic chemical synthetic process and will have some similar
biocompartibility profiles as RNA nanoparticles. Aptamer attachment to herein described RNA nanoparticles did not disrupt the structures and/or functions of either the nanoparticle or the aptamer (data not shown).
The herein described pRNA nanoparticles thus will find advantageous use in therapeutic delivery, with synthetic uniformity, particle size, PK properties, and immunological/ toxicological properties that are superior to naked siRNA and to other polymeric or liposomal delivery platforms; these and other properties also provide advantages for imaging targeted disease tissues as demonstrated in this study. In addition to fluorescent dyes, other reporters such as radioactive isotopes or contrasting agents can also be incorporated for a variety of imaging applications, including PET and NMR.
References:
1 . Guo,P, Zhang,C, Chen,C, Trottier,M and Garver,K (1998) Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Mol. Cell., 2: 149-155.
2. Zhang, F, Lemieux,S, Wu,X, St.-Arnaud,S, McMurray,CT, Major,F et al. (1998) Function of hexameric RNA in packaging of bacteriophage phi29 DNA in vitro. Mol. Cell., 2: 141 -147.
3. Jaeger,L and Leontis,NB (2000) Tecto-RNA: One dimensional self-assembly through tertiary interactions. Angew. Chem Int. Ed Engl., 39: 2521 -2524.
4. Shu,D, Moll.WD, Deng,Z, Mao,C and Guo,P (2004) Bottom-up assembly of RNA arrays and superstructures as potential parts in
nanotechnology. Nano Lett, 4: 1717-1723.
5. Guo,P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol., 5: 833-842.
6. Guo P (2005) RNA Nanotechnology: Engineering, Assembly and Applications in Detection, Gene Delivery and Therapy. Journal of
Nanoscience and Nanotechnology, 5(12): 1964-1982.
7. Allen,TM and Cullis,PR (2004) Drug Delivery Systems:
Entering the Mainstream. Science, 303: 1818-1822. 8. Guo,P, Coban,O, Snead,NM, Trebley,J, Hoeprich,S, Guo,S et al. (2010) Engineering RNA for Targeted siRNA Delivery and Medical
Application. Advanced Drug Delivery Reviews, 62: 650-666.
9. Guo,P, Erickson,S and Anderson, D (1987) A small viral RNA is required for in vitro packaging of bacteriophage phi29 DNA. Science, 236: 690- 694.
10. Guo,P (2002) Structure and function of phi29 hexameric RNA that drive viral DNA packaging motor: Review. Prog in Nucl Acid Res & Mole Biol., 72: 415-472.
1 1 . Hoeprich,S and Guo,P (2002) Computer modeling of three- dimensional structure of DNA packaging RNA(pRNA) monomer, dimer, and hexamer of phi29 DNA Packaging motor. J Biol. Chem., 277(23): 20794-20803.
12. Chen,C, Sheng,S, Shao,Z and Guo,P (2000) A dimer as a building block in assembling RNA: A hexamer that gears bacterial virus phi29 DNA-translocating machinery. J Biol Chem, 275(23): 17510-17516.
13. Mat-Arip,Y, Garver,K, Chen,C, Sheng,S, Shao,Z and Guo,P (2001 ) Three-dimensional interaction of Phi29 pRNA dimer probed by chemical modification interference, cryo-AFM, and cross-linking. J. Biol. Chem., 276: 32575-32584.
14. Guo,S, Tschammer,N, Mohammed, S and Guo,P (2005) Specific delivery of therapeutic RNAs to cancer cells via the dimerization mechanism of phi29 motor pRNA. Hum Gene Ther., 16: 1097- 1 109.
15. KhaledA Guo,S, Li,F and Guo,P (2005) Controllable Self- Assembly of Nanopartides for Specific Delivery of Multiple Therapeutic
Molecules to Cancer Cells Using RNA Nanotechnology. Nano Letters, 5: 1797- 1808.
16. Liu J, Guo S, Cinier M, Shlyakhtenko L, Shu Y, Chen C et al. (2010) Fabrication of Stable and RNase- Resistant RNA Nanopartides Active in Gearing the Nanomotors for Viral DNA Packaging. ACS Nano, In Press. 17. Zhang,CL, Lee,C-S and Guo,P (1994) The proximate 5' and 3' ends of the 120-base viral RNA (pRNA) are crucial for the packaging of bacteriophage φ29 DNA. Virology, 201 : 77-85.
18. Garver,K and Guo,P (1997) Boundary of pRNA functional domains and minimum pRNA sequence requirement for specific connector binding and DNA packaging of phage phi29. RNA., 3: 1068-1079.
19. Reid,RJD, Bodley,JW and Anderson, D (1994) Characterization of the prohead-pRNA interaction of bacteriophage phi29. J Biol Chem, 269: 5157-5162.
20. Chen,C, Zhang,C and Guo,P (1999) Sequence requirement for hand-in-hand interaction in formation of pRNA dimers and hexamers to gear phi29 DNA translocation motor. RNA, 5: 805- 818.
21 . Shu,D, Huang, L, Hoeprich,S and Guo,P (2003) Construction of phi29 DNA-packaging RNA (pRNA) monomers, dimers and trimers with variable sizes and shapes as potential parts for nano-devices. J. Nanosci.
Nanotechnol., 3: 295-302.
22. Guo,S, Huang, F and Guo,P (2006) Construction of folate- conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells. Gene Ther, 13: 814-820.
23. Zhang,CL, Trottier,M and Guo,PX (1995) Circularly permuted viral pRNA active and specific in the packaging of bacteriophage φ29 DNA. Virology, 207: 442-451 .
24. Hoeprich,S, ZHou,Q, Guo,S, Qi,G, Wang,Y and Guo,P (2003) Bacterial virus phi29 pRNA as a hammerhead ribozyme escort to destroy hepatitis B virus. Gene Ther., 10: 1258-1267.
25. Li,L, Liu,J, Diao,Z, Guo,P and Shen,G (2009) Evaluation of specific delivery of chimeric phi29 pRNA siRNA nanoparticles to multiple tumor cells. Molecular BioSy stems, 5: 1361 -1368.
26. Shu Y, Cinier M and Guo P (2010) Bottom-up Assembly of Therapeutic pRNA-siRNA Nanoparticles Using Two RNA Fragments. Molecular Therapy, In Preparation. 27. Chen,SJ (2008) RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu. Rev. Biophys., 37: 197-214.
28. Hershkovitz E, Sapiro G, Tannenbaum A and Williams LD (2006) Statistical analysis of RNA backbone. IEEE/ACM Trans Comput Biol Bioimform, 3: 33-46.
29. Kurschat WC, Muller J, Wombacher R and Helm,M (2005) Optimizing splinted ligation of highly structured small RNAs. RNA, 11 : 1909- 1914.
30. Nishigaki K, Taguchi K, Kinoshita Y, Aita T and Husimi Y (1998) Y-ligation: an efficient method for ligating single-stranded DNAs and RNAs with T4 RNA ligase. Mol Divers., 4: 187-190.
31 . Stark MR, Pleiss JA, Deras M, Scaringe,SA and Rader SD (2006) An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs. RNA, 12: 2014-2019.
32. Gumport Rl and Uhlenbeck OC (1981 ) T4 RNA ligase as a nucleic acid synthesis and modification reagent. Gene Amplif Anal, 2: 313-345.
33. Kuhn R, Schwenk F, Aguet M and Rajewsky,K (1995) Inducible gene targeting in mice. Science, 269: 1427-1429.
34. Seon-Young,K, Jinliang,L, Galina,B, AndrewJB and David,J, V. Microarray analysis of changes in cellular gene expression induced by productive infection of primary human astrocytes: implications for HAD. Journal of Neuroimmunology 157: 17-26. 12-1 -2004. Ref Type: Abstract
35. Huang,S, Wei,W and Yun Y (2009) Upregulation of TLR7 and TLR3 gene expression in the lung of respiratory syncytial virus infected mice. Wei Sheng Wu Xue Bao, 49: 239-245.
36. Groskreutz,DJ, Monick,MM, Powers, LS, Yarovinsky,TO, Look,DC and Hunninghake,GW (2006) Respiratory Syncytial Virus Induces TLR3 Protein and Protein Kinase R, Leading to Increased Double-Stranded RNA Responsiveness in Airway Epithelial Cells. Journal of Immunology, 176: 1733-1740. 37. Kamen,BA and Caston,JD (1986) Properties of a Folate Binding Protein (FBP) isolated from porcine kidney. Biochemical Pharmacology, 35: 2323-2329.
38. Leamon CP (2007) Preclinical antitumor activity of a novel folate-targeted dual drug conjugate. Mol Pharmacol., 4: 659-667.
39. Reddy,JA, Westrick,E, Santhapuram,HKR, Howard,SJ, Miller,ML, Vetzel,M et al. (2007) Folate Receptor-Specific Antitumor Activity of EC131 , a Folate-Maytansinoid Conjugate. Cancer Research, 67: 6376-6382.
40. Reddy,JA, Dorton,R, Westrick,E, DawsonA Smith.T, Xu,LC et al. (2007) Preclinical Evaluation of EC145, a Folate-Vinca Alkaloid
Conjugate. Cancer Research, 67: 4434-4442.
41 . Turk,MJ, Waters,DJ and Low,PS (2004) Folate-conjugated liposomes preferentially target macrophages associated with ovarian
carcinoma. Cancer Letters, 213: 165-172.
42. Paulos,CM, Turk,MJ, Breur,GJ and Low,PS (2004) Folate receptor-mediated targeting of therapeutic and imaging agents to activated macrophages in rheumatoid arthritis. Advanced Drug Delivery Reviews, 56: 1205-1217.
43. Kwon Y (2001 ) Handbook of Essential Pharmacokinetics, Pharmacodynamics, and Drug Metabolism for Industrial Scientists.
44. Morrissey,DV, Lockridge,JA, Shaw,L, Blanchard,K, Jensen, K, Breen,W et al. (2005) Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs. Nat. Biotechnoi, 23: 1002-1007.
45. Morrissey,DV, Blanchard,K, Shaw,L, Jensen, K, Lockridge,JA, Dickinson, B et al. (2005) Activity of stabilized short interfering RNA in a mouse model of hepatitis B virus replication. Hepatology, 41 : 1349-1356.
46. Behlke,MA (2006) Progress towards in vivo use of siRNAs. Mol Ther, 13: 644-670.
47. Dassie,JP, Liu,XY, Thomas,GS, Whitaker,RM, Thiel.KW, Stockdale,KR et al. (2009) Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat Biotechnol., 27: 839-849.
48. Li,SD, Chen,YC, Hackett,MJ and Huang, L (2008) Tumor- targeted delivery of siRNA by selfassembled nanopartides. Mol. Ther., 16: 163- 169.
49. McNeil SE (2009) Nanoparticle therapeutics: a personal perspective. Wiley Interdiscip Rev Nanomed Nanobiotechnol, 1 : 264-271 .
50. Zhou J and Rossi JJ (2009) The therapeutic potential of cell- internalizing aptamers. Current Topics in Medicinal Chemistry, 9: 1 144-1 157.
EXAMPLE 3
ASSEMBLY OF THERAPEUTIC PRNA-SIRNA NANOPARTICLES USING
Two RNA FRAGMENTS
The 1 17-nucleotide RNA, called the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor, has been shown to be an efficient vector for the construction of RNA nanoparticles for the delivery of siRNA into specific cancer or viral infected cells. Currently, chemical synthesis of 1 17- nucleotide RNA is not feasible commercially. In addition, labeling at specific locations on pRNA requires the understanding of its modular organization. Here, we report multiple approaches for the construction of a functional 1 17- base pRNA using two synthetic RNA fragments with variable modifications. The resulting two-piece pRNA was fully competent in associating with other interacting pRNAs to form dimers, as demonstrated by the packaging of DNA via the nanomotor and the assembly of phi29 viruses in vitro. The pRNA subunit assembled from two-piece fragments harboring siRNA or receptor- binding ligands were equally competent in assembling into dimers. The subunits carrying different functionalities were able to bind cancer cells specifically, enter the cell, and silence specific genes of interest. The pRNA nanoparticles were subsequently processed by Dicer to release the siRNA embedded within the nanoparticle. These results indicate that the herein described synthetic pRNA siRNA chimeric nanopartides may be suitable for the treatment of diseases.
Introduction. Research in nanotechnology involves modification, engineering, and/or assembly of organized materials on the nanometer scale. RNA molecules can be designed and manipulated at a level of simplicity characteristic of DNA, while possessing the flexibility in structure and function or enzymatic activity similar to that of proteins. Thus, RNA is a suitable candidate for nanotechnological applications (1 -5). The concept of RNA nanotechnology has been proposed for more than a decade (2, 4, 6-9)(for review, see ref (1 , 10, 1 1 ). The first evidence was reported in 1998 showing that dimeric, trimeric, and hexameric RNA nanopartides can be assembled through self-assembly of multiple reengineered natural RNA molecules (2). The field of RNA nanotechnology becomes more and more popular due to the recognition of the potential of RNA nanopartides in the treatment of cancer, viral infection, genetics diseases and other human ailment (1 ).
Several RNA-based therapeutic approaches using small interfering RNA (siRNA) (12-15), and hbozymes(16-20) have been shown to down-regulate specific gene expression in cancerous or viral-infected cells. RNA aptamer has been shown to bear functions similar to that of antibodies in their ability to recognize specific ligands (organic compounds, nucleotides, or peptides) for targeted delivery through the formation of binding pockets(21 ,22). This has led to heightened interest in the scientific community and the rapid development of siRNA-based therapeutics. Specific delivery of siRNA to target cells has been achieved using the pRNA (packaging RNA) of bacteriophage phi29(23-25), which forms dimers and trimers via the interaction of the left (L- loop) and right (R-loop) interlocking loops(2,26,27). Phi29 DNA packaging motor uses six pRNAs that form a ring to gear the DNA packaging motor(2,27- 30). Each pRNA molecule contains two domains (Fig. 10a). One of the domains, bases 23-97, located at the central region of pRNA, is for
intermolecular interactions (27, 28, 31 , 32). The two interlocking loops reside within this domain. The second domain is for the binding of the DNA packaging enzyme gp16 (33). This domain is located at the 573' ends that pair to form a double-stranded helical region(34). Removal of this domain does not affect the formation of dimer, trimer and hexamer(27,32). Therefore, the pRNA 573' proximate double-stranded helical end(34) could serve to carry a therapeutic siRNA (Fig. 10a) (23,24).
Using this chimera technology, pRNA could escort the siRNA to silence genes and to destroy cancer cells of leukemia, lung, breast, head and neck, as well as others (23-25, 35-38). The pRNA system has several advantages including defined structure, controllable stoichiometry, multi- valency, targeted delivery, ideal nanoscale size (-20-40 nm), and minimal induction of antibody response to enable repeated treatments of chronic diseases (1 ). In addition, the pRNA is remarkably stable in a wide range of pH (-4-9), temperature, and organic solvents(3). These unique features of pRNA have great potential to be applied not only for gene delivery but also for nanomachine fabrication and pathogen detection.
However, one bottle neck in the RNA therapy and RNA
nanotechnology is the desirability of producing relatively large quantities of RNA. The pRNA subunit is about 1 17 nucleotides, which is beyond the limit of currently available commercial chemical RNA synthesis technologies
(maximum of 80 nucleotides with low yield). At this time, most of the pRNA or pRNA related chimeras are synthesized enzymatically using RNA polymerase. It has been reported that the pRNA can be dissected into a two-piece chimeric construct, in which two individual RNA oligonucleotides, one encompassing the R-loop and the other the L-loop, are clamped together via a six-nucleotide duplex(39). However, one of these pieces is located in the middle of the pRNA; this made the resulting RNA not suitable for the construction of therapeutic RNA nanoparticles harboring siRNA or other modules, and also not feasible for applications in drug delivery. In this study, we further develop the two-piece chimeric constructs to generate full-length functional pRNAs that are not only competent for driving the phi29 DNA packaging motor but also proficient for therapeutic and diagnostic purposes.
MATERIALS & METHODS
In vitro synthesis of RNA fragment and assembly of the pRNA complex using two RNA fragments. RNA fragments were transcribed by T7 RNA polymerase using dsDNA templates from PCR, as described previously (3). To construct two-piece pRNA siRNA(GFP),
pRNA siRNA(luciferase), and pRNA siRNA(survivin), the helical region at the 573' paired ends of pRNA was replaced with double-stranded siRNA that connects to bases 29 and 91 . The chimeric pRNA/siRNA two-piece assemblies were synthesized in vitro using the similar principle.
The intact two-piece RNA complex pRNA/siRNA(GFP), pRNA siRNA(luciferase), and pRNA siRNA(survivin) were assembled from the synthesized RNA fragments either by direct mixing of two fragments at 1 :1 molar ratio in TMS (10 mM Mg2+) buffer at room temperature for more than 30 mins or by annealing the two fragments in TMS through heating at 75 °C for 5 min, followed by slow cooling to room temperature. RNA complexes assembled from the two pieces were then purified from 10% native polyacrylamide gel(28).
Assay for pRNA dimer formation. The potential of dimer formation is one way to verify correct folding of the pRNA assembled from two pieces of RNA fragments. The pRNA construct Ab' monomer was mixed with their interacting partner pRNA Ba' in TBM buffer (89 mM Tris-HCI (pH 7.6), 0.2 M Boric Acid, and 5 mM MgCI2) at equal mole ratio, and incubated at room temperature for 30 min. The dimer formation was then assayed, followed by purification in 10% native polyacrylamide gel.
Assay for DNA packaging and virion assembly using the two- piece pRNA assemblies. Methods for the assay of pRNA activity in DNA- packaging(47) and in vitro virion assembly (41 ,42) have been reported previously. For DNA packaging assay, briefly, the synthesized and purified 10Ong two-piece pRNA assemblies and their dimer partner (1 -1 17) pRNA Ba', viral procapsid, gp16, and viral DNA-gp3, as well as the 10mM ATP (PH7.0) were mixed and incubated for 1 h at ambient temperature to let viral DNA translocate into preformed procapsid. Then the mixture was firstly treated with DNase I and followed by Protease K treatment. The treated mixture was separated by 0.8% Agarose gel and the procapsid protected DNA could be observed after ethidium bromide staining.
For in vitro virion assembly assay, the mature viral particles could be obtained by mixing two-piece pRNA Ab' monomer, (1 -1 17)pRNA Ba', viral procapsid, gp16, and DNA-gp3, 10mM ATP as well as other two components gp9 and gp1 1 -14 were incubated at room temperature. The mixture was plated on host Bacillus subtilis su+44. After 12-14hrs incubation at 37 °C, the plaque formation per plate was count and the viral assembly activity was calculated by PFU/mL.
Cell culture. Human nasopharyngeal carcinoma KB cells (American Type Culture Collection, ATCC, Manassas, VA) are routinely maintained in RPMI 1640 medium (Invitrogen, Carlsbad, CA) and
supplemented with 10% fetal bovine serum (FBS). Cultures were incubated at 37oC in a humidified 5% CO2 atmosphere.
GFP reporter assay to test the potential of the two-piece pRNA complex in escorting siRNA delivered into specific cells. For human nasopharyngeal epidermal carcinoma KB cells, 105 cells were seeded in 24- well plates. GFP-expressing plasmid pGFP-N2 (Clontech Laboratories, Inc., Mountain View, CA), two-piece pRNA AbVsiRNA(GFP) and different kind of mutant controls were co-transfected into cells by using lipofactamine 2000 (Invitrogen, Carlsbad, CA) 24 hours after seeding. The effect was measured at the level of eGFP expression, as observed by fluorescence microscopy(23,24).
Dual-Luciferase assays to test the potential of the two-piece pRNA complex in escorting siRNA delivered specifically into cells via folate receptors. For Dual- Luciferase assays(23), KB cells were seeded in 24-well plates. Gene silencing assays were performed by co-transfecting two- piece chimeric pRNA/siRNA(luciferase) with both plasmid pGL3 and pRL-TK (Promega, Madison, Wl) coding for firefly and renilla luciferase, respectively. The latter served as an internal control to normalize the luciferase data (Dual- Luciferase Reporter Assay System, Promega, Madison, Wl). Cells were washed once with PBS and lysed with passive lysis buffer. The plates were shaken for 15 minutes at room temperature. 20 μΙ_ of the lysate were added to 100 μΙ_ of luciferase assay reagent (LAR II) in a luminometer tube and firefly luciferase activity was measured. Upon addition of 20 μΙ_ of Stop & Glo
Reagent, control measurements of renilla Luciferase activity were then obtained. The previously obtained data was then normalized with respect to the renilla activity for determining the average ratio of firefly to renilla activity over several trials.
Cell Transfection assay and Western blot analysis to test the potential of the two-piece pRNA complex in escorting siRNA for gene silencing. KB Cells were seeded into 24-well plates overnight and transfected with 5nM, 20nM and 40nM two-piece pRNA siRNA(survivin) chimera as well as the scrambled control by Lipofectamine 2000. After 48 hrs, cells were rinsed and harvested in lysis buffer. Protein concentrations were determined and equal amounts of proteins were loaded onto a 15% polyacrylamide gel.
Membranes were blocked, incubated with primary antibody to survivin and β- actin (R&D Systems, Minneapolis, MN), and conjugated to a secondary antibody (Sigma-Aldrich Corp., St. Louis, MO). Membranes were then blotted by ECL kit (Millipore, Billerica, MA) and exposed to film for autoradiography.
Flow cytometry to test cell receptor binding of the two-piece pRNA complex harboring ligands. Cell binding studies were performed on KB cells maintained in folate-free RPMI-1640 medium (Invitrogen, Carlsbad, CA). The folate deficient KB cells were then trypsinized and rinsed with PBS. 500 nM two-piece RNA folate and control two-piece pRNA/NH2 were each incubated with the 2 x 105 KB cells at 37°C for 1 hr. After PBS wash, the cells were resuspended in PBS buffer. Flow Cytometry (Beckman Coulter, Brea, CA) was used to observe the cell binding efficacy of the pRNA folate complexes. Confocal microscopy to test cell binding and entry. For confocal microscopy, KB cells were grown on glass coverslides in folate-free RPMI-1640 medium overnight. Two-piece pRNA/folate and control two-piece pRNA/NH2 with siRNA were each incubated with the cells at 37°C for 2-3 hrs. After PBS wash, the cells were fixed by 4% paraformaldehyde and stained by Alexa Fluor® 488 phalloidin (Invitrogen, Carlsbad, CA) for cytoskeleton and TO- PRO®-3 iodide (642/661 ) (Invitrogen, Carlsbad, CA) for nucleus, staining as per the manufacturer's instructions. Cells were then assayed for binding and entry of the RNA complexes by the Zeiss LSM 510 laser scanning confocal microscope (Carl Zeiss).
Dicer processing of the two-piece pRNA/siRNA complex. The procedure for in vitro Dicer processing assay has been reported previously (23). The 5'-end [32P] labeled two-piece pRNA siRNA chimera or the intact pRNA siRNA chimera was treated with the recombinant Dicer (Genlantis/Gene Therapy Systems, San Diego, CA) and separated by 16% Urea/PAGE gel for subsequent autoradiography.
RESULTS
Nomenclature. The pRNA constructs used in this work are identified by: (i) the R-loop and/or L-loop sequence(s); and (ii) the started/ended nucleotide number. A particular R-loop sequence is assigned an upper case letter (i.e., A, B, ..), and a particular L-loop sequence is assigned a lower case letter with a prime (i.e., a', b', ..). The same set of letters (i.e., Aa') designates complementary sequences in the R/L loop, while different letters indicate lack of sequence complementarities. For example, Ab' indicates that the pRNA assemblies contain a right-hand loop A and the left hand loop b' for inter-RNA interaction with Ba' in the assembly of the pRNA dimer. Following the above rules, the 1 17-nt intact pRNA with various R-loop and L-loop is designated as (1 -1 17) Rl' (i.e., 1 -1 17 Ab').
Three two-piece pRNA assemblages (Fig. 10b) are designated as (1 -28)/(30-1 17) Ab', (1 -55)/(56-1 17) Ab' and (1 -71 )/(75-1 17) Ab'. Three two- piece pRNA chimeras (Fig. 10b) are designated as (1 -28)/(30-1 17) Ab' pRNA/siRNA (eGFP), (1 -55)/(56-1 17) Ab' pRNA/siRNA (eGFP) and (1 -71 )/(75- 1 17) Ab' pRNA/siRNA (eGFP). pRNA/siRNA(eGFP) represents a pRNA chimera that harbors a siRNA targeting the eGFP gene while pRNA/siRNA (luciferase) and pRNA/siRNA (survivin) represent pRNA chimeras that harbor siRNAs targeting the firefly luciferase gene and survivin gene respectively. (1 - 28) and (30-1 17) refer to start and stop of the RNA fragment one and fragment two, respectively, using phi29 pRNA seqAuence number as a reference.
Construction of pRNA assemblies by bottom-up approach using synthetic pRNA fragments. The goal of the construction of pRNA assemblies is two-fold: driving the DNA packaging motor of phi29 and harboring RNA moieties, functionalities, or chemical groups for therapeutic purposes. In each RNA chimeras, there are two important elements: the first one serves as the directing core to guide the folding and assembly of the resulting pRNA chimeras, whereas the second one functions to deliver these particles for medical applications. We constructed six pRNA assemblies using sets of RNA fragment pairs (P1 and P2) as building blocks shown in Fig. 10b by three different two-piece approaches including Ab'(1 -28)/(30-1 17), (1 -55)/(56-1 17), and (1 -71 )/(75-1 17). The six assemblies were categorized into two classes: three with wild-type pRNA sequences, and three with siRNA sequences replaced 573' helical regions (Fig. 10b, 10c). These three outlined two-piece approaches in pRNA construction overcome the size obstacle in RNA chemical synthesis, while maintaining the same bioactivity as the intact pRNA/siRNA particles. The design criteria for the two-piece assemblies were
1 ) each fragment of the two-piece RNAs should be smaller than 100nt and suitable for chemical synthesis.
2) The breaks on the pRNA chain to form functional two-piece particles basically followed the circular permutated pRNA (cpRNA) design which closes the proximity of the wild-type pRNA 573' end and has new 573' end opened at the different position along the pRNA chain. We adopted those new opening sites of functional cpRNAs which have viral DNA packaging ability and viral assembly activity (40) as the selected breaks for two-piece design to ensure the assembled two-piece pRNAs maintain their biological activities.
3) All the selected breaks are located at the less structural constraint and more flexible region. And the breaks should avoid the sequences involved in the intermolecular interaction, some important bulges responsible for viral packaging or the region which is for holding functional moieties such as siRNA insertion.
Assay for dimer formation to confirm the folding of the resulting two-piece RNA complex. Phi29 DNA packaging motor uses six pRNAs that form a ring to gear the DNA packaging motor (2, 27-30). It has been reported previously that dimers are the building blocks in the assembly of the phi29 DNA packaging motor (28). Also, this self-assembling property can be used for the fabrication of reengineered dimeric pRNA chimeras that can serve as polyvalent vehicles for specific targeting and delivery of siRNA or ribozyme to cancer cells(10,23-25,36). Thus, it is crucial to find out whether pRNA constructs can form dimers, which would provide direct evidence that pRNA monomeric subunits constructed by the two-piece approach retain the self- assembling property of the intact pRNA.
As shown in the 8% native PAGE gel (Fig. 10c), the two RNA fragments annealed to form three types of two-piece Ab' pRNA monomers, which migrated into the same position as wild-type monomer control ((1 - 1 17)Ab' and (1 -1 17)Ba'). The two-piece monomeric Ab' pRNA subsequently formed dimer, in the presence of its interacting partner (1 -1 17)Ba' pRNA and migrated into the upper dimer band which was at the same position as wild-type pRNA dimer Ab'-Ba'. The formation of dimers indicated that the two-piece pRNA assemblies folded into a conformation similar to that of the wild-type pRNA. Moreover, when the 573' paired helical region was replaced with a double-stranded siRNA, as with the three types of the two-piece pRNA siRNA assemblies, the dimer formation pattern did not change, as revealed by an 8% native PAGE gel (Fig. 10d) which also indicated the correct folding structure of the two-piece pRNA siRNA assemblies. DNA packaging and viral assembly activities of the two-piece pRNA assemblies. We used the phi29 system, with the known DNA
packaging and the viral assembly assays, to further investigate the biological activity of the two-piece assemblies. Considering that the retention of the biological activity can be directly correlated with the retention of the structure, we used these two assays to confirm whether the two-piece assemblies can fold as the wild-type pRNA. The phi29 DNA packaging assay (41 , 42) was carried out by replacing one of the subunits of the pRNA dimer with the two- piece pRNA assemblies. After in vitro assembly of the functional DNA packaging motor, the double-stranded viral genome was packaged into the viral prohead. The mixture was then treated by DNase I and separated by 0.8% agarose gel. The DNA successfully packaged was protected from DNase digestion and can be observed on the gel (Fig. 1 1 a). Although the two-piece assemblies showed less amount of packaged viral genome in the gel (Fig. 1 1 a, lane 10-12) as compare to intact pRNA (Fig. 1 1 a, lane 4), we still found that all three two-piece Ab' pRNA assemblies were proficient in driving the viral DNA packaging motor for packaging the viral genomic dsDNA (Fig. 1 1 a), suggesting that two-piece pRNA maintained the structure and functions of wild type pRNA.
The viral assembly assay also carried out by replacing one of the subunits of the dimer with the two-piece pRNA assemblies, the functional dimer will drive the DNA packaging motor to gear the viral genome into the procapsid and subsequently form the mature virons to infect the host bacteria and form plaques. The plaque forming units (PFU) per milliliter was used to reflect the RNA activity during the phi29 viral assembly. As shown in Fig 1 1 b, the control pRNA dimer showed 107 PFU/mL viral assembly activity while all three types of the two-piece Ab' pRNA assembled from two RNA fragments still exhibited around 106 PFU/mL viral assembly activity, thereby demonstrating that the chimeric dimers were indeed functional.
The gene silencing effect of the pRNA assemblies constructed by the two-piece approach. Three RNA complexes, which include (1 -28)7(30-1 17) Ab' pRNA/siRNA(eGFP), (1 -55)7(55-56) Ab' pRNA siRNA(eGFP), and (1 -71 )/(75-1 17) Ab' pRNA/siRNA(eGFP) containing a siRNA functionality targeting eGFP, were constructed (Fig. 12b) and shown competent in knocking down eGFP gene expression (Fig. 12a). To verify the specificity in gene silencing, these two-piece pRNA assemblies have been also constructed with a single mutation either in the sense strand, the anti-sense strand or both strands. Although the incorporation of a single mutation at the sense strand is not sufficient to inhibit the gene silencing function of the constructions (Fig. 12a), a single mutation on the complementary anti-sense strand resulted in a significant lost of the gene knock-down effects (Fig. 12a). As expected, the incorporation of the mutation on both strands also resulted in the lost of the gene knock-down effects.
To further investigate the ability of the two-piece pRNA to be used as a therapeutic module in the construction of multivalent nanoparticle, we constructed another set of three RNA complexes containing a siRNA
functionality targeting the experimental reporter, firefly luciferase gene (Fig. 13). This included the constructions (1 -28)/(30-1 17)Ab' pRNA/siRNA(firefly luciferase), (1 -55)/(55-56)Ab' pRNA/siRNA(firefly luciferase) and (1 -71 )/(75- 1 17)Ab' pRNA/siRNA(firefly luciferase). Compared to the eGFP gene knockdown assay, the dual-Luciferase report system can quantitatively measure the gene silencing effects of these three two-piece pRNA siRNA assemblies. The relative lucifrease activity was used to reflect the expression level of firefly luciferase gene by normalizing the firefly luciferase activity with the internal control, Renilla luciferase activity. The results indicated that all three constructs of the two-piece pRNA siRNA (firefly luciferase) displayed a dramatic decrease in firefly luciferase gene expression which is comparable to the intact
pRNA siRNA(firefly luciferase) after transfection.
Furthermore, the two-piece (1 -28)/(30-1 17) pRNA/siRNA(survivin) assembly showed similar silencing effects on the survivin gene expression as the intact pRNA siRNA(survivin) which is demonstrated by Western Blot assay; a two-piece pRNA siRNA assembly harboring scrambled survivin siRNA served as negative control (Fig. 14). This two-piece pRNA siRNA was processed efficiently by Dicer in vitro to release the end RNA fragment (23nt~27nt), as shown in Fig. 16. The processed small RNA fragments were confirmed to harbor the siRNA sequence by Northern Blot assay (data not shown).
Cell binding and entry of the two-piece pRNA/folate
therapeutic RNA nanoparticles. Many cancer cell lines, especially those of epithelial or myelocytic origin, overexpress the folate receptor (FR) on their surface(43). Folate has been used extensively as cancer cell delivery agent via folate receptor-mediated endocytosis(25, 37,44). Human nasopharyngeal epidermal carcinoma KB cells which have overexpressed FR on the cell surface(37) were used as the cell model and the fluorescently labeled two-piece pRNA folate was used to test its cell binding efficiency. A fluorescent two-piece pRNA NH2 that did not contain folate group was used as the negative control. Flow cytometry data showed that the binding efficiency of the fluorescent two- piece pRNA/folate was close to 100% (Fig. 15a). The binding specificity was also proved by free folate competitive assay. Free folate can competitively bind to the FR positive KB cells and reduce the fluorescent signal from two-piece pRNA folate binding. Confocal microscopy revealed strong binding of the fluorescent two-piece pRNA folate complex, as well as efficient entry of the RNA into the targeted cells. The entry was demonstrated by excellent co- localization and overlap of the fluorescent two-piece pRNA folate assembly (red) and cytoplasma (green) (Fig. 15b).
DISCUSSION
Rational design of two-piece RNA assemblies followed multiple cpRNA designs (40). All these cpRNAs showed comparable DNA packaging and viral assembly activity which indicated the new opening/break along the pRNA chain have no or less affects on the correct folding as well as the function of pRNA. Other criteria were also considered. The final assemblies generated by two-piece designs should: 1 ) still maintain the correct structure folding; and 2) maintain the similar function as intact particles. We
demonstrated that phi29 bacteriophage pRNA can be engineered to harbor therapeutic modules and efficiently assembled into higher order structures with defined stoichiometry using a two-piece construction approach. This method overcomes the current limitations in chemical synthesis of long RNA molecules, while retaining the structural and functional integraty and chemical stability of both wild type pRNAs and the therapeutic pRNA chimeras.
The two-piece pRNA constructs were structurally competent, evidenced by efficient dimer formation. However, the two-piece modules showed lower DNA packaging and viral assembly activity (-10 fold) compared to the wild type pRNA. The multivalent chimeric constructs harboring targeting, detection, and therapeutic moieties were functionally proficient, as
demonstrated by gene knock-down, and dual Luciferase assays. Moreover, the (1 -28)/(30-1 17) two-piece pRNA/siRNA chimera produced better silencing effects compared to the intact modules and the siRNA itself (Fig. 14).
Dicer in vitro processing results proved that the two-piece (1 - 28)/(30-1 17) pRNA siRNA can be processed by Dicer more efficiently and precisely than intact pRNA siRNA chimera. The intact pRNA/siRNA can only be processed to generate the RNA fragment larger than 23nt, while the two- piece module could be processed to generate -23 nt RNA fragment since the single nucleotide gap between nucleotide 28 and 30 within the two-piece pRNA siRNA molecule might facilitate the siRNA processing by Dicer.
Meanwhile, siRNA alone might be unstable in cytoplasm compared to the two- piece pRNA/siRNA chimera which folded into the strong secondary/tertiary structure resistant to various conditions (3) and might protect the embedded siRNA from fast degradation and resulting in an enhanced RNAi (RNA interference) function inside the cells. Furthermore, flow cytometry and confocal images demonstrated that the therapeutic two-piece pRNA modules were strongly bound to the target cells and subsequently internalized into cancer cells with high efficiency.
In summary, the results showed the feasibility of the two-piece approach in assembling functional RNA nanoparticles with high yield. The bottom-up self-assembly of pRNA using the two-piece approach demonstrated the addressable and programmable nature of pRNA. The constructed two- piece pRNA/siRNA and two-piece pRNA-folate chimera can further assemble into dimeric particles for targeted delivery of therapeutics into folate receptor positive cancer cells. This approach can be extended in the future to build more complex multifunctional nanoparticles for a wide range of therapeutic, detection, and diagnosis applications.
References-Example 3
1 . Guo,P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol., 5: 833-842.
2. Guo,P, Zhang,C, Chen,C, Trottier,M and Garver,K (1998) Inter- RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Mol. Cell., 2: 149-155.
3. Shu,D, Huang, L, Hoeprich,S and Guo,P (2003) Construction of phi29 DNA-packaging RNA (pRNA) monomers, dimers and trimers with variable sizes and shapes as potential parts for nano-devices. J. Nanosci.
Nanotechnol., 3: 295-302.
4. Shu,D, Moll.WD, Deng,Z, Mao,C and Guo,P (2004) Bottom-up assembly of RNA arrays and superstructures as potential parts in
nanotechnology. Nano Lett, 4: 1717-1723.
5. Hansma,HG, Oroudjev,E, Baudrey,S and Jaeger,L (2003) TectoRNA and 'kissing-loop' RNA: atomic force microscopy of self-assembling RNA structures. J Microsc, 212: 273-279.
6. Zhang, F, Lemieux,S, Wu,X, St.-Arnaud,S, McMurray,CT, Major,F et al. (1998) Function of hexameric RNA in packaging of bacteriophage phi29 DNA in vitro. Mol. Cell., 2: 141 -147.
7. Jaeger,L and Leontis,NB (2000) Tecto-RNA: One dimensional self-assembly through tertiary interactions. Angew. Chem Int. Ed Engl., 39: 2521 -2524.
8. Jaeger,L, Westhof,E and Leontis,NB (2001 ) TectoRNA:
modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res., 29: 455-463. 9. ChworosA SevercanJ, Koyfman,AY, Weinkam,P, Oroudjev,E, Hansma,HG et al. (2004) Building programmable jigsaw puzzles with RNA. Science, 306: 2068-2072.
10. Guo P (2005) RNA Nanotechnology: Engineering, Assembly and Applications in Detection, Gene Delivery and Therapy. Journal of
Nanoscience and Nanotechnology, 5(12): 1964-1982.
1 1 . Jaeger L and Chworos A (2006) The architectonics of programmable RNA and DNA nanostructures. Curr Opin Struct Biol., 16: 531 - 543.
12. Fire,A, Xu,S, Montgomery, MK, Kostas,SA, Driver,SE and Mello,CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391 : 806-81 1 .
13. Li,H, Li,WX and Ding,SW (2002) Induction and suppression of RNA silencing by an animal virus. Science, 296: 1319-1321 .
14. Brummelkamp,TR, Bernards, R and Agami,R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science, 296: 550-553.
15. Carmichael,GG (2002) Medicine: silencing viruses with RNA. Nature, 418: 379-380.
16. Kruger,K, Grabowski,PJ, Zaug,AJ, Sands,J, Gottschling,DE and Cech,TR (1982) Self-splicing RNA: autoexcision and autocydization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31 : 147-157.
17. Guerrier-Takada,C, Gardiner,K, Marsh,T, Pace,N and
Altman,S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35: 849-857.
18. Sarver,NA, Cantin,EM, Chang, PS, Zaia,JA, Ladne,PA, Stephens, DA et al. (1990) Ribozymes as potential anti-HIV-1 therapeutic agents. Science, 247: 1222-1225.
19. Chowrira,BM, Berzal-Herranz,A and Burke,JM (1991 ) Novel guanosine requirement for catalysis by the hairpin ribozyme. Nature, 354: 320- 322. 20. Nava Sarver, Edouard M.Cantin, Pairoj S.Chang, John A.Zaia, Paula A.Ladne, Delilah A.Stephens et al. (1990) Ribozymes as Potential Anti- HIV-1 Therapeutic Agents. Science, 24: 1222-1225.
21 . Ellington,AD and Szostak,JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346: 818-822.
22. Tuerk,C and Gold,L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA ploymerase. Science, 249: 505-510.
23. Guo,S, Tschammer,N, Mohammed, S and Guo,P (2005) Specific delivery of therapeutic RNAs to cancer cells via the dimerization mechanism of phi29 motor pRNA. Hum Gene Ther., 16: 1097-1 109.
24. KhaledA Guo,S, Li,F and Guo,P (2005) Controllable Self- Assembly of Nanoparticles for Specific Delivery of Multiple Therapeutic
Molecules to Cancer Cells Using RNA Nanotechnology. Nano Letters, 5: 1797- 1808.
25. Guo,S, Huang, F and Guo,P (2006) Construction of folate- conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells. Gene Ther, 13: 814-820.
26. Guo,P, Erickson,S and Anderson, D (1987) A small viral RNA is required for in vitro packaging of bacteriophage phi29 DNA. Science, 236: 690-694.
27. Chen,C, Zhang, C and Guo,P (1999) Sequence requirement for hand-in-hand interaction in formation of pRNA dimers and hexamers to gear phi29 DNA translocation motor. RNA, 5: 805-818.
28. Chen,C, Sheng,S, Shao,Z and Guo,P (2000) A dimer as a building block in assembling RNA: A hexamer that gears bacterial virus phi29 DNA-translocating machinery. J Biol Chem, 275(23): 17510-17516.
29. Chen,C and Guo,P (1997) Sequential action of six virus- encoded DNA-packaging RNAs during phage phi29 genomic DNA
translocation. J. Virol., 71 : 3864-3871 . 30. Shu,D, Zhang, H, Jin,J and Guo,P (2007) Counting of six pRNAs of phi29 DNA-packaging motor with customized single molecule dual- view system. EMBO J., 26: 527-537.
31 . Reid,RJD, Bodley,JW and Anderson, D (1994)
Characterization of the prohead-pRNA interaction of bacteriophage phi29. J Biol Chem, 269: 5157-5162.
32. Garver,K and Guo,P (1997) Boundary of pRNA functional domains and minimum pRNA sequence requirement for specific connector binding and DNA packaging of phage phi29. RNA., 3: 1068-1079.
33. Lee,TJ and Guo,P (2006) Interaction of gp16 with pRNA and DNA for genome packaging by the motor of bacterial virus phi29. J. Mol Biol., 356: 589-599.
34. Zhang, CL, Tellinghuisen,T and Guo,P (1995) Confirmation of the helical structure of the 573' termini of the essential DNA packaging pRNA of phage q>29. RNA, 1 : 1041 -1050.
35. Hoeprich,S, ZHou,Q, Guo,S, Qi,G, Wang,Y and Guo,P (2003) Bacterial virus phi29 pRNA as a hammerhead ribozyme escort to destroy hepatitis B virus. Gene Ther., 10: 1258-1267.
36. Liu,H, Guo,S, Roll,R, Li,J, Diao,Z, Shao,N et al. (2007) Phi29 pRNA Vector for Efficient Escort of Hammerhead Ribozyme Targeting Survivin in Multiple Cancer Cells. Cancer Biol. Ther., 6: 697-704.
37. Li,L, Liu,J, Diao,Z, Guo,P and Shen,G (2009) Evaluation of specific delivery of chimeric phi29 pRNA siRNA nanoparticles to multiple tumor cells. Molecular BioSy stems, 5: 1361 -1368.
38. Zhang, HM, Su,Y, Guo,S, Yuan,J, Lim,T, Liu,J et al. (2009) Targeted delivery of anti-coxsackievirus siRNAs using ligand-conjugated packaging RNAs. Antiviral Res., 83: 307-316.
39. Fang,Y, Shu,D, Xiao,F, Guo,P and Qin,PZ (2008) Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging. Biochemical and Biophysical Research Communications, 372: 589-594. 40. Zhang,CL, Trottier,M and Guo,PX (1995) Circularly permuted viral pRNA active and specific in the packaging of bacteriophage φ29 DNA. Virology, 207: 442-451 .
41 . Lee,CS and Guo,P (1994) A highly sensitive system for the in vitro assembly of bacteriophage phi29 of Bacillus subtilis. Virology, 202: 1039- 1042.
42. Lee,CS and Guo,P (1995) In vitro assembly of infectious virions of ds-DNA phage φ29 from cloned gene products and synthetic nucleic acids. J. Virol., 69: 5018-5023.
43. Lu,Y and Low,PS (2003) Immunotherapy of folate receptor- expressing tumors: review of recent advances and future prospects. J. Control Release, 91 : 17-29.
44. Lu,Y and Low, PS (2002) Folate-mediated delivery of macromolecular anticancer therapeutic agents. Adv. Drug Deliv. Rev., 54: 675- 693.
45. Chen,SJ (2008) RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu. Rev. Biophys., 37: 197-214.
46. Mitra,S, Shcherbakova V, Altman,RB, Brenowitz,M and Laederach,A (2008) High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res., 36: e63.
47. Guo,P, Grimes, S and Anderson, D (1986) A defined system for in vitro packaging of DNA-gp3 of the Bacillus subtilis bacteriophage phi29.
Proc. Natl. Acad. Sci. USA, 83: 3505-3509.
The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent
applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, applications and publications to provide yet further embodiments.
These and other changes can be made to the embodiments in light of the above-detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.

Claims

CLAIMS What is claimed is:
1 . An artificial pRNA polynucleotide, comprising a first pRNA piece P1 , and a second pRNA piece P2, wherein:
P1 and P2 self-assemble non-covalently to form a two- piece pRNA monomer having a wild-type pRNA secondary structure and a break between a P1 3'-end and a P2 5'-end, said break being situated in a single-stranded loop formed by nucleotides corresponding to nucleotide positions 53-58 in a wild-type pRNA sequence;
P1 comprises a RNA polynucleotide of at least 29-57 nucleotides and includes a P1 intermolecular interaction domain of about 29 nucleotides comprising the P1 3'-end;
P2 comprises a RNA polynucleotide of at least 39-62 nucleotides and includes a P2 intermolecular interaction domain of about 39 nucleotides comprising the P2 5'-end; and
the P1 intermolecular interaction domain and the P2 intermolecular interaction domain interact non-covalently to form the artificial pRNA polynucleotide.
2. The artificial pRNA polynucleotide of claim 1 which is produced by non-enzymatic chemical synthesis.
3. The artificial pRNA polynucleotide of claim 1 which is capable of forming a pRNA dimer.
4. The artificial pRNA polynucleotide of claim 1 which is capable of mediating double-stranded DNA phage motor-driven DNA packaging and virion assembly.
5. The artificial pRNA polynucleotide of claim 1 which further comprises at least one heterologous component.
6. The artificial pRNA polynucleotide of claim 1 which further comprises at least two heterologous components.
7. The artificial pRNA polynucleotide of either claim 6 or claim 7 wherein at least one heterologous component is selected from (i) a
heterologous component that is covalently attached to a P1 5'-end, (ii) a heterologous component that is covalently attached to the P1 3'-end, (iii) a heterologous component that is covalently attached to the P2 5'-end, and (iv) a heterologous component that is covalently attached to a P2 3'-end.
8. The artificial pRNA polynucleotide of claim 7 wherein the heterologous component is selected from the group consisting of an siRNA, a targeting moiety, a ribozyme, an RNA aptamer, an antisense RNA, a peptide nucleic acid, a detectable label, a therapeutic agent and an endosome- disrupting agent.
9. The artificial pRNA polynucleotide of claim 1 which comprises one or a plurality of modified nucleotides.
10. The artificial pRNA polynucleotide of claim 9 in which the modified polynucleotide is selected from a 2'-fluoro-2'-deoxy nucleotide or a derivative thereof, a phosphorothioate , a 2'-O-methyl ribonucleotide or a derivative thereof, a 2'-NH2-2'-deoxy nucleotide or a derivative thereof, and a 2'- CH3-2'-deoxy nucleotide or a derivative thereof.
1 1 . The artificial pRNA polynucleotide of claim 1 which does not elicit a TLR-mediated response when administered to a mammal.
12. The artificial pRNA polynucleotide of claim 8 in which the heterologous component comprises a Dicer substrate that is processed by a Dicer pathway to yield a siRNA that is capable of specifically interfering with expression of a gene.
13. The artificial pRNA polynucleotide of claim 8 in which P1 and P2 self-assemble to form a substantially full-length pRNA.
14. A method of delivering a biologically active moiety to a cell, comprising contacting the cell with the artificial pRNA polynucleotide of claim 8, under conditions and for a time sufficient for uptake by the cell of the artificial pRNA polynucleotide, wherein the heterologous component comprises the biologically active moiety.
PCT/US2012/020469 2011-01-07 2012-01-06 Synthetic non-covalently self-assembling bipartite prna chimeras WO2012094586A2 (en)

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US10982210B2 (en) 2018-03-02 2021-04-20 Sixfold Bioscience Ltd. Compositions for delivery of cargo to cells
US11357865B2 (en) 2020-04-27 2022-06-14 Sixfold Bioscience Ltd. Compositions containing nucleic acid nanoparticles with modular functionality

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN106367420B (en) * 2016-10-17 2018-11-20 阜阳职业技术学院 Specifically bind the single-strand DNA aptamer of (1,3)-callose in Candida albicans

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080064647A1 (en) * 2000-08-23 2008-03-13 Peixuan Guo Prna Chimera
US20100003753A1 (en) * 2005-08-01 2010-01-07 Purdue Research Foundation Multivalent rna nanoparticles for delivery of active agents to a cell

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080064647A1 (en) * 2000-08-23 2008-03-13 Peixuan Guo Prna Chimera
US20100003753A1 (en) * 2005-08-01 2010-01-07 Purdue Research Foundation Multivalent rna nanoparticles for delivery of active agents to a cell

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
ABDELMAWILA, S. ET AL.: 'Pharmacological characterization of chemically synthesized monomeric phi29 pRNA nanoparticles for systemic delivery' MOLECULAR THERAPY vol. 19, no. 7, 05 April 2011, pages 1312 - 1322 *
LIU, H. ET AL.: 'Phi29 pRNA vector for efficient escort of hammerhead ribozyme targeting survivin in multiple cancer cells' CANCER BIOLOGY AND THERAPY vol. 6, no. 5, 03 February 2007, pages 697 - 704 *
SHU, Y. ET AL.: 'Assembly of therapeutic pRNA-siRNA nanoparticles using bipartite approach' MOLECULAR THERAPY vol. 19, no. 7, 05 April 2011, pages 1304 - 1311 *

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