WO1998000435A9 - Segment de liaison pour oligonucleotide et techniques comprenant des oligonucleotides immobilises et lies - Google Patents

Segment de liaison pour oligonucleotide et techniques comprenant des oligonucleotides immobilises et lies

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Publication number
WO1998000435A9
WO1998000435A9 PCT/US1997/011496 US9711496W WO9800435A9 WO 1998000435 A9 WO1998000435 A9 WO 1998000435A9 US 9711496 W US9711496 W US 9711496W WO 9800435 A9 WO9800435 A9 WO 9800435A9
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species
metal ion
coordinate
moiety
strand
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PCT/US1997/011496
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English (en)
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WO1998000435A2 (fr
WO1998000435A3 (fr
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Priority to JP10504429A priority Critical patent/JP2000514799A/ja
Priority to AU40389/97A priority patent/AU739391B2/en
Priority to EP97937951A priority patent/EP0917533A2/fr
Publication of WO1998000435A2 publication Critical patent/WO1998000435A2/fr
Publication of WO1998000435A3 publication Critical patent/WO1998000435A3/fr
Publication of WO1998000435A9 publication Critical patent/WO1998000435A9/fr

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  • the present invention relates generally to the production of single-stranded DNA molecules, and more particularly to the production of single-stranded DNA using immobilized metal affinity chromatography.
  • the avidin/biotin combination adds enough mass to the surface that the technique, when used to detect binding of a single strand of DNA to the immobilized strand, can lack precision.
  • a object of the present invention to provide improved techniques for linking an oligonucleotide such as DNA, or a single strand of DNA, to another moiety or a surface, and to resolve a desired strand of DNA from its complement.
  • the present invention provides a nucleotide coupled to a linking moiety that can coordinate a metal ion, namely, a species having a formula L n -N y , where N represents the nucleotide and L represents the moiety which can coordinate a metal ion.
  • n is at least 1
  • y is at least 1.
  • N ⁇ is DNA
  • L can be histaminylpurine where n is approximately 6.
  • the invention provides a species having a formula R-Ch-M-
  • R represents a chemical moiety that can be linked to a surface, or linked to a chemical or biological species.
  • Ch represents a chelating agent that can coordinate a metal ion
  • M represents a metal ion coordinated by the chelating agent
  • N represents a nucleotide
  • L represents a moiety that can coordinate a metal ion
  • n and y each is at least 1.
  • the chelating agent is, according to one embodiment, a quadradentate chelating agent, for example nitrilotriacetic acid.
  • the invention also provides a single stranded oligonucleotide immobilized on a surface and free of hybridization to any complimentary strand that is also immobilized on the surface to the extent that the complimentary strand cannot be removed under conditions that cause denaturization of oligonucleotide strand from its complimentary strand.
  • the single-stranded immobilized oligonucleotide also will withstand conditions, while remaining immobilized, harsher than 2 molar urea.
  • the strand can be a strand of DNA.
  • the invention provides a method.
  • the method involves providing first and second complementary strands of oligonucleotide, contacting a surface of a solid phase with the first and second strands, and allowing the first strand to be immobilized at the surface.
  • the second strand is allowed to be carried away from the surface without immobilization at the surface.
  • this aspect involves providing first and second complementary strands of DNA in a fluid medium, passing the fluid medium across a surface of a solid phase, and allowing the first strand to be immobilized at the surface while the second strand is allowed to be carried by the fluid medium away from the surface without immobilization.
  • the various aspects of the invention can be combined in a variety of ways.
  • the single stranded oligonucleotide immobilized on a surface and free of hybridization to any complimentary strand that is also immobilized on the surface to the extent that the complimentary strand cannot be removed under conditions that cause denaturization can be immobilized via linkages such as L n -N y or R-Ch-M-L n -N y , above.
  • the methods can be practiced using any of the species that can facilitate immobilization of an oligonucleotide.
  • Fig. 1 is a schematic representation of double-stranded DNA immobilized, via an attached linking moiety coordinated to a metal ion, to a solid phase surface;
  • Fig. 2 illustrates, schematically, primers and double-stranded PCR template used in one set of examples; and Fig. 3 is a photocopy of a denaturing polyacrylamide gel electrophoresis analysis of DNA strand resolution using a technique of the present invention.
  • Min, C Cushing, T. Verdine, G., "Template-Directed Interference Footprinting of Protein- Adenine Contacts,", J. Am. Chem. Soc. 1996, 118, 6116-6120; and Min, C. Verdine, G., “Immobilized Metal Affinity Chromatography of DNA,” Nucleic Acids Res. 1996, 24, 3806-3810, both are incorporated herein by reference.
  • the present invention provides a linking functionality for attachment of an oligonucleotide to another moiety or to a surface of a solid phase, where solid phase is defined as any material insoluble in a medium used in conjunction with a procedure involving the oligonucleotide.
  • the technique can be used, for example, to link an oligonucleotide to a solid phase surface such as a chromatography solid phase, or to a surface of a biosensor element such as a surface plasmon resonance (SPR) chip (for a discussion of SPR see, for example, Sternberg, et al, "Quantitative Determination of Surface Concentration of Protein with Surface Plasmon Resonance Using Radiolabeled Proteins", Journal of Colloid and Interface Science, 43:2 513- 526, 1991, and references therein).
  • SPR surface plasmon resonance
  • the technique also can be used, for example, to link an oligonucleotide to a surface of a bead or plate used in a bioassay, to a label such as a fluorescent label, or another molecule or solid entity.
  • the invention involves providing a species having the generalized formula L n -N y , where N y represents a natural or synthetic, single or multiple-strand oligonucleotide typified in DNA or a strand of DNA, and L n represents a linking functionality where L represents a ligating moiety that can coordinate a metal ion, and n is at least 1, preferably at least 2, and more preferably at least 5. According to preferred embodiments, n is from 2 to 10, and most preferably is about 6.
  • L is a molecule that can be chemically attached to an oligonucleotide via, for example, the ester bond of the oligonucleotide backbone, and L n has a generalized formula I, below.
  • Z is an organic moiety and Y is a ligand having the ability to coordinate a metal ion, Z and Y together allowing incorporation of L n into or on an oligonucleotide sequence.
  • Z and Y can be a single moiety in that a single organic moiety can provide functionality compatible with an oligonucleotide sequence and also coordinate a metal ion.
  • Z is a hydrocarbon chain or a cyclic hydrocarbon group, optionally interrupted by hetero groups, of a length of from about 1 to about 10 carbon atoms.
  • hydrocarbon is meant to include alkyl, alkenyl, alkynyl, cycloalkyl, aryl, alkaryl, aralkyl, and the like.
  • Y (or Y and Z together) is a ligand that can coordinate free coordination sites on a metal ion, such as a metal ion immobilized on a metal affinity chromatography solid phase without complete coordination of the ion by the solid phase (see, for example, Hochuli et al., "New Metal Chelate Adsorbent Selective for Proteins and Peptides Containing Neighboring Histidine
  • Y can be as defined above for Z, and preferably includes groups such as -N-, alcohols, thiols, carboxylates (including carboxylic acid), and the like which can address a vacant coordination site on a metal ion.
  • Cyclic and heterocyclic organic compounds including -N- such as imidazoles, phenanthroline, adenine, cytosine, and thymine are suitable.
  • amino acids satisfying these criteria such as histidine, lysine, cysteine, methionine, asparagine, tyrosine, glutamine, glutamate, and aspartate are suitable.
  • Species such as hydroxamic acid also are suitable.
  • the above moieties can serve as Z, with a different one of the above or another moiety serving as Y and satisfying the criterion of coordination to a metal ion.
  • purine, thymine, adenine, cytosine, or a combination could serve as Z, with another nucleic acid, amino acid, or nitrogen- containing cyclic, multi-cyclic, or heterocyclic compound serving as Y.
  • the available -NH 2 - group can be used to couple Y defined by, for example, histamine.
  • 6-histaminyl purine defines Y
  • Z is a cyclic ether (II, below).
  • Species L n -N y finds use in conjunction with a metal ion partially coordinated by a chelating agent that is linked, or can be linked, to a moiety or surface of interest. That is, the species finds use in a combination of the formula:
  • R represents a chemical or physical moiety
  • Ch represents a chelating agent that can coordinate a metal ion
  • M represents a metal ion coordinated by the chelating agent.
  • R can be a particulate species such as gold sol, a label such as a fluorescent label, a biological molecule of interest such as a binding partner for interaction with another species, a chromatography solid phase, or a linking or linkable moiety that can effect coupling of species III to any desired surface or species.
  • the particular species or surface to which species III is coupled is not important, but the invention lies in the ability to coordinate N y to R via L n .
  • the metal ion is preferably selected from those that have at least four coordination sites, preferably six coordination sites.
  • a non-limiting list of metal ions suitable includes Co + , Cr 3+ , Hg 2+ , Pd 2+ , Pt 2+ , Pd 4+ , Pt 4+ , Rh 3+ , Ir 3+ , Ru 3+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , Cd 2+ , Pb 2 ⁇ Mn 2+ .
  • the chelating agent is preferably selected from bidentate, tridentate, and quadradentate, chelating agents, and is selected in conjunction with the metal ion so that when the chelating agent coordinates the metal ion, at least two free coordination sites of the metal remain.
  • the chelating agent and metal are selected so that the chelating agent can coordinate the metal ion with a degree of stability great enough that the metal ion will remain immobilized at the surface by the chelating agent.
  • the chelating agent is selected as one that has a chelating moiety and a non-chelating linker moiety, such that it can be covalently linked via its linker moiety to the moiety R while leaving the chelating moiety undisturbed by the covalent linkage and free to coordinate a metal ion.
  • the chelating agent can be selected as one that can be modified via routine organic synthesis to include a non-chelating linker moiety, if such synthesis leaves undisturbed the chelating moiety.
  • non-chelating linker moiety should provide functionality suitable for chemical linkage such as, for example, an amine, alcohol, carbamate, carboxylic acid, thiol, aldehyde, olefin. etc., for formation of an ester linkage, formation of an amide linkage, thiol displacement and thiol ether formation, and the like.
  • chelating agents and corresponding metal ions can be selected by those of ordinary skill in the art.
  • selection reference can be made to "Chelating Agents and Metal Chelates", Dwyer, F. P.; Mellor, D. P., Academic Press, and "Critical Stability Constants", Martell, A. E.; Smith, R. M., Plenum Press, New York. These works describe a variety of chelating agents, and discuss the stability of coordination between chelating agents and metal ions.
  • a chelating agent and metal ion is selected such that the dissociation constant of the combination in aqueous solution is better than 10 nM at physiological pH, that is, such that at least one half of the metal ions are coordinated by chelating agent at a concentration of 10 nM.
  • a non-limiting exemplary list of suitable chelating agents includes nitrilotriacetic acid, 2,2'-bis(salicylideneamino)-6,6'-demethyldiphenyl, and 1 ,8-bis(a-pyridyl)-3 ,6-dithiaoctane.
  • nitrilotriacetic acid 2,2'-bis(salicylideneamino)-6,6'-demethyldiphenyl
  • 1 ,8-bis(a-pyridyl)-3 ,6-dithiaoctane As an example of one, preferred arrangement using species III, reference is made to Fig.
  • a species 25 linked to a solid phase surface includes an oligonucleotide, in particular DNA 10 including a first strand 12 and a second, complementary strand 14 including a linking functionality (L n ) 16 defined by 6 histaminyl purines, two of which (18 and 20, respectively) are coordinated to a metal ion 22.
  • Metal ion 22 also is coordinated by chelating agent 24 (a nitrilotriacetic acid derivative, as illustrated) which coordinates four of the six coordination sites of the metal ion, leaving two free coordination sites addressable by linking functionality 16.
  • Chelating agent 24 is attached, via linker 26 (a hydrocarbon chain, as illustrated), to a surface 28 of a solid phase 30. Linkage of chelating agent 24 to surface 28 via linker 26 can be accomplished by any means such as covalent attachment, or the like.
  • linker 26 is selected as one that promotes formation of a self-assembled monolayer of a plurality of linkers 26 at surface 28, and linker 26 terminates at its end opposite the chelating agent in a functionality that is attracted to surface 28 and thereby promotes formation of a self-assembled monolayer.
  • a metal-coordinating chelating agent immobilized at a surface as part of a self-assembled monolayer is described in commonly-owned co-pending U.S. patent application serial number 08/312,388, now U.S. Patent No. 5,620,850, referenced above.
  • Self-assembled monolayer- forming species also are described in U.S. Patent No. 5,512,131, issued April 30, 1996 to Kumar and Whitesides, incorporated herein by reference.
  • a self-assembled monolayer containing a chelating agent 24 is provided for use with species L n -N y such as DNA 10 including linking functionality 16
  • L n -N y such as DNA 10 including linking functionality 16
  • it can be advantageous to form a self-assembled mixed monolayer as defined in application serial number 08/312,388, and U.S. Patent No. 5,620,850 referenced above
  • a heterogeneous self-assembled monolayer including an ordered assembly of at least another self- assembled monolayer- forming species other than species 25.
  • a heterogeneous monolayer defined by less than about 50% of species 25 and greater than about 50% of another species such as one terminating in a moiety that does not interact with L n or N y can be formulated, as well as one with a ratio of less than about 30% species 25, or less than about 20%> species 25, etc. It is to be understood that coordination of linking functionality 16 to M may involve linkage via two neighboring ligating moieties L (H, for histaminyl purine, as illustrated in FIG. 1), or another arrangement.
  • linking functionality 16 may include neighboring ligating moieties L and/or ligating moieties L separated by one or more intermediate moieties - o - that do not have ligating capacity, so long as linking functionality 16 possesses the ability to coordinate free coordination sites at M.
  • Y (and Y in combination with Z if Z has coordinating capacity) and n should be selected to provide the oligonucleotide with coordinating capacity sufficient to link the oligonucleotide to a metal ion to the extent that the oligonucleotide does not become detached from the metal ion during the course of a procedure involving the oligonucleotide coordinated to the metal ion so as, for example, to immobilize the oligonucleotide at a solid phase.
  • Coordination should not, however, be so strong that L n will compete with coordination of the metal ion by the chelating agent to the extent that the metal ion is stripped from the chelating agent (thus, e.g., stripped from a solid phase, label, or other moiety).
  • L n will compete with coordination of the metal ion by the chelating agent to the extent that the metal ion is stripped from the chelating agent (thus, e.g., stripped from a solid phase, label, or other moiety).
  • ligands such as ethylenediamine tetra acetic acid would be unsuitable.
  • the test oligonucleotide then can be labeled radioactively at the 5' end by mixing with T 4 polynucleotide kinase, then with ⁇ 32 P-ATP. Then the oligonucleotide can be mixed with beads of resin containing immobilized, coordinated metal ion, the beads rinsed, and determination can be made as to whether radioactivity is present at the beads. If radioactivity is present, then the selection of L (i.e. Y or Y and R together) and n is appropriate to provide coordination capacity sufficient to immobilize the oligonucleotide, but not to the extent that the metal ion is stripped from the chelating agent.
  • L i.e. Y or Y and R together
  • beads can be flushed with an eluting fluid such as 200mM imidazole and determination made as to whether the radioactivity is still present at the beads.
  • the present invention also represents an improvement over immobilization of single- stranded oligonucleotide at a surface via biotin/avidin or biotin/streptavidin linkage. That linkage will withstand conditions only up to 2 molar urea, or less.
  • the present invention involves immobilization that withstands conditions harsher than 2 molar urea.
  • Example 1 Synthesis Of A Nucleotide Including A Moiety That Can Coordinate A Metal Ion
  • the 6-histaminylpurine moiety was introduced through the convertible nucleotide approach by analogy to reported procedures (Ferentz, A.E.; Verdine, G.L., J. Am. Chem. Soc. 1991. 113, 4000-4002; Ferentz, A.E.; Verdine, G.L.
  • the crude oligonucleotides were purified by denaturing polyacrylamide gel electrophoresis. An additional dG residue was added at the 5'-end to ensure efficient end-labeling using polynucleotide kinase.
  • the present IMAC-based strategy must be capable of resolving PCR-amplified duplex DNA into its two component strands.
  • we used one H 6 -tagged primer plus one unmodified primer to amplify a 183 base-pair segment of the plasmid pUC18-mARRE2, thereby to furnish a duplex product with an H 6 -tag on only one strand.
  • the DNA template for PCR amplification was derived from the commercial cloning vector pUC18 by inserting a segment of the murine interleukin-2 enhancer into the BamHl site (Chen, L.; Jain, J.; Oakley, M.G.; glover, J.N.M.: Dervan, P.B.: Hogan, P.G.: Rao, A.; Verdine, G.L. Curr. Biol. 1995, 5, 882-889).
  • pUC18 and close relatives are more widely used in bacterial cloning than each of the unbound and bound fractions was added 900 ⁇ l absolute ethanol (stored at 20 °C), then the tubes were vortexed briefly and chilled for 30 min on dry powdered CO 2 . The tubes were microcentrifuged for 30 min at 16,000 x g. The supernatant was removed and the pellet washed with 200 ⁇ l 80% aqueous EtOH (-20 °C). Following removal of the ethanol solution, the tubes were dried by centrifugal lyophilization (SpeedVac, Savant). To each dry tube was added 50 ⁇ l TE buffer. The DNA concentration was determined by UV spectrophotometry.
  • top and bottom strands refers to the sequence as mapped in Figure 2.
  • the "top” strand also corresponds to the coding strand of the lacZ' ⁇ peptide, part of which was encoded within the polylinker region of pUCl 8. That is, the PCR product generated using primers la + 2b will bear the H 6 -tag on the "top” strand only, whereas that generated using 2a + lb will bear the H 6 -tag on the "bottom” strand only.
  • the yield of PCR product formed in these reactions was no less than that observed in parallel reactions with only unmodified primers (data not shown), thus indicating that the H 6 -tag does not affect PCR amplification adversely.
  • Primers la/lb contain a sequence that is identical to a stretch (shaded) of the "top" strand of the plasmic pUC18-mARRE2; they are extended in the rightward direction (5'-3') during PCR.
  • Primers 2a/2b contain a sequence that is identical to a stretch (shaded) of the "bottom” strand of pUC18-mARRE2; they are extended in the leftward direction.
  • the shaded sequence in primers la and 2a denotes the H 6 -tag.
  • E and H denote the EcoR I and Hnd III sites, respectively, of the pUC18 polylinker; a stretch of the murine IL-2 enhancer (mARR ⁇ 2, batched) was inserted to the BamH I site to generate pUC18-mARRE2.
  • mARR ⁇ 2 murine IL-2 enhancer
  • the nucleotide including a moiety that can coordinate a metal ion was immobilized at a surface.
  • the H 6 -tagged oligonucleotides (2a/2b) and their unmodified counterparts (lb/2b) were 5'-end-labeled with 32 P, then passed in parallel through a Ni +2 - nitrilotriactic acid (NTA)-agarose resin.
  • NTA Ni +2 - nitrilotriactic acid
  • the PCR products were denatured in 6- M guanidinum-HCl, then incubated batch wise with Ni 2+ -NTA-agarose.
  • Example 3 Immobilization of a First Strand of First and Second Complementary Strands of DNA at a Surface with Selective Removal of the Second Strand, and Quantitative Determination of Bound Versus Unbound Strands
  • H 6 -tag confers, upon an oligonucleotide, the ability to be selectively and reversibly retained on a surface, specifically
  • Ni 2+ -NTA-agarose Ni 2+ -NTA-agarose.
  • the technique results in single- stranded oligonucleotide immobilized on a surface and free of hybridization to any complimentary strand that is also immobilized on the surface to the extent that the complimentary strand cannot be removed under conditions that cause denaturization of oligonucleotide strand from its complimentary strand.
  • the retarded mobility of the H 6 -tagged strand relative to the unmodified strand may arise from the partial positive charge of its 6 pendant imidazole moieties at pH 8 and a greater length, due to incomplete polymerization of the T 6 -stretch opposite H 6 during PCR.
  • the identities of the strands were independently verified by PAGE analysis of PCR reactions that employed one 32 P-labeled primer and one nonradioactive primer. Although this slight difference in mobility provides a convenient means of assaying the strand resolution by IMAC, it is not sufficiently large to permit preparative strand resolution by gel electrophoresis and extraction.
  • Fig. 3 is a photocopy of the results of denaturing PAGE of DNA strand resolution using IMAC.
  • Each panel of three lanes represents the results obtained using a pair of PCR primers, one of which (la or 2a) contains an H6-tag and the other of which (2b or lb, respectively) is unmodified.
  • C (lanes 1 and 4): controls showing the mixture of strands obtained directly by PCR, prior to IMAC resolution; U (lanes 2 and 5): unbound fractions from IMAC; B (lanes 3 and 6): bound fraction from IMAC, after elution with 200 mM imidazole. The unbound fractions from IMAC in Fig.
  • Example 4 Template-Directed Polymerization Using Surface-Immobilized N n -N, To assay the biological activity of single-stranded DNA generated through the PCR-
  • IMAC sequence we employed the resolved strands as templates in Sanger dideoxy sequencing runs.
  • the experiment was carried out using oligonucleotide strands that had been synthesized so as to be attachable to a surface, in accordance with the invention, but were not attached to the surface during the experiment.
  • the experiment proves the concept that the single-stranded oligonucleotide, immobilized at a surface in accordance with the invention, retains its biological activity.
  • single-stranded DNA was immobilized at a surface of a column, as described above, and then the surface-immobilized DNA was flushed from the column, and a chelating agent was used to complex any remaining or free nickel ion in solution.
  • a chelating agent was used to complex any remaining or free nickel ion in solution.
  • the unmodified strands were found to be excellent sequencing templates, but the H 6 -tagged strands failed to support template-directed polymerization.
  • the H 6 - tagged DNA solutions contain adventitious Ni 2+ in amounts sufficient to cause profound inhibition of the DNA polymerase enzyme. This problem was overcome simply by adding 1,10- phenanthroline to the imidazole-containing eluate prior to precipitation with ethanol.

Abstract

On décrit une technique permettant de lier un oligonucléotide, tel qu'un brin unique d'ADN, à une autre fraction ou phase solide. On utilise un oligonucléotide possédant une fonctionnalité de liaison qui peut être définie par six purines hystaminyales voisines qui peuvent être coordonnées à un ion métal qui est également coordonné par un agent de chélation lié à une phase solide ou une autre fraction. Cette invention est tout particulièrement utile pour effectuer la résolution d'un brin d'ADN de son complément; pour ce faire on donne au premier brin d'ADN la fonctionnalité de liaison puis on envoie l'ADN à travers une phase solide de chromatographie à affinité pour les métaux.
PCT/US1997/011496 1996-07-03 1997-06-30 Segment de liaison pour oligonucleotide et techniques comprenant des oligonucleotides immobilises et lies WO1998000435A2 (fr)

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JP10504429A JP2000514799A (ja) 1996-07-03 1997-06-30 オリゴヌクレオチドリンカーおよび固定化および結合オリゴヌクレオチドを用いる技術
AU40389/97A AU739391B2 (en) 1996-07-03 1997-06-30 Oligonucleotide linker and techniques involving immobilized and linked oligonucleotides
EP97937951A EP0917533A2 (fr) 1996-07-03 1997-06-30 Segment de liaison pour oligonucleotide et techniques comprenant des oligonucleotides immobilises et lies

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US60/021,195 1996-07-03

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US7893222B2 (en) * 2002-12-20 2011-02-22 University Of Houston Introduction of structural affinity handles as a tool in selective nucleic acid separations
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