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Definitions

• the present invention provides compositions and methods for modulating the expression of Type III sodium channel (Navl.3).
• this invention relates to antisense compounds, particularly oligonucleotides, specifically hybridizable with nucleic acids encoding Type III sodium channel (Navl.3). Such oligonucleotides have been shown to modulate the expression of Type III sodium channel (Navl.3).
• Voltage-dependent sodium channels play a fundamental role in controlling neuronal membrane excitability. They are responsible for the upstroke of the action potential in neurons. Neuropathic pain is considered to be the result of injured and/or remodeled neurons, which exhibit an increase in excitability in both primary afferent fibers and synaptic contacts within the central pain processing pathway.
• sodium channel blockers include carbamazepine, lamotrigine, and phenytoin.
• lidocaine another sodium channel blocker, was recently approved for treatment of certain types of neuropathic pain.
• sodium channel blockers are currently the treatment of choice for neuropathic pain, they have been only moderately successful in treating these conditions.
• a primary factor in the weak efficacy of these compounds is their lack of selectivity and low affinity for the various sodium channels resulting in numerous side effects including emesis, dizziness, ataxia, and cardiotoxicity.
• Many recent efforts have been focused on defining and describing which sodium channels are actively involved in the development and maintenance of neuropathic pain.
• the alpha subunit is the pore forming subunit and to date, 11 alpha subunits have been identified including 7 neuronal, 2 glial, 1 muscular, 1 cardiac subunit.
• the alpha subunits can be divided into three classes based on their sensitivity to tetrodotoxin (TTX): TTX sensitive (TTXs), TTX resistant (TTXr), and TTX insensitive (TTXi).
• TTXs channels are sensitive to TTX in the nanomolar range, have a low threshold for activation and rapid inactivation kinetics. These channels include the skeletal muscle channel, two channels that are found primarily in peripheral neurons and all brain type channels described thus far. [004] Recent reports have suggested that the type III sodium channel
• Navl.3 may also be involved in neuropathic pain development and maintenance. This particular channel is found in brain, peripheral nerve and, neuroendocrine cells. Critically, it is absent from heart and many other peripheral organs.
• the mRNA for Navl .3 increases in small and large DRG neurons following axotomy in animal models (Dib-Hajj S, et al, Proc.Natl. Acad. Sci. 1996; 93:14950-14954), suggesting its involvement in neuropathic pain.
• peripheral nerve damage produced a large increase in the expression of a tetrodotoxin (TTX)- sensitive Navl .3 sodium channel (Boucher TJ, et al, Science 2000; 290: 124- 127) They also replicated past experiments from several labs establishing that the development of neuropathic pain is linked to increased spontaneous activity following nerve damage and that this ectopic activity is sensitive to TTX. Finally, the study from Wood's group also found that glial-derived neurotrophic factor (GDNF) prevented the induction of Navl .3, reduced the spontaneous activity of the injured nerve, thus preventing the resulting neuropathic pain.
• GDNF glial-derived neurotrophic factor
• TTX- sensitive sodium channels and in particular Navl.3, as having a role in the development and maintenance of neuropathic pain that follows nerve damage.
• Navl.3 Type III sodium channel
• antisense technology could specifically target neonatal vs. adult forms of Navl .3.
• Exon 6 of the Navl .3 gene is alternatively spliced in humans (Lu C-M, Brown GB. J. Mol. Neurosci. 1988; 10:67-70) and rodents (Gustafson TA, et al. J. Biol. Chem.
• exon 6 sequences are very similar, differing by only a single amino acid at the protein level, but they could be targeted individually by sequence-specific antisense oligonucleotides. This could be useful in the treatment of certain pediatric disorders, such as neonatal, infantile, or childhood epilepsies.
• Antisense technology is emerging as an effective means for reducing the expression of specific gene products and may therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications for the modulation of Navl.3 expression.
• the present invention is directed to antisense compounds, particularly oligonucleotides, which are targeted to a nucleic acid encoding Navl.3, and which modulate the expression of Navl.3.
• Pharmaceutical and other compositions comprising the antisense compounds of the invention are also provided. Further provided are methods of modulating the expression of Navl .3 in cells or tissues comprising contacting said cells or tissues with one or more of the antisense compounds or compositions of the invention. Further provided are methods of treating an animal, particularly a human, suspected of having or being prone to a disease or condition associated with expression of Navl.3 by administering a therapeutically or prophylactically effective amount of one or more of the antisense compounds or compositions of the invention.
• the present invention employs oligomeric antisense compounds, particularly oligonucleotides, for use in modulating the function of nucleic acid molecules encoding Navl.3, ultimately modulating the amount of Navl .3 produced. This is accomplished by providing antisense compounds, which specifically hybridize with one or more nucleic acids encoding Navl.3.
• target nucleic acid and “nucleic acid encoding Navl .3” encompass DNA encoding Navl .3, RNA (including pre- mRNA and mRNA) transcribed from such DNA, and also cDNA derived from such RNA.
• the specific hybridization of an oligomeric compound with its target nucleic acid interferes with the normal function of the nucleic acid.
• This modulation of function of a target nucleic acid by compounds, which specifically hybridize to it, is generally referred to as "antisense".
• the functions of DNA to be interfered with include replication and transcription.
• the functions of RNA to be interfered with include all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA.
• the overall effect of such interference with target nucleic acid function is modulation of the expression of Navl.3.
• modulation means either an increase (stimulation) or a decrease (inhibition) in the expression of a gene.
• inhibition is the preferred form of modulation, of gene expression and mRNA is a preferred target.
• Targeting an antisense compound to a particular nucleic acid is a multistep process.
• the process usually begins with the identification of a nucleic acid sequence whose function is to be modulated. This may be, for example, a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent.
• the target is a nucleic acid molecule encoding Navl.3.
• the targeting process also includes determination of a site or sites within this gene for the antisense interaction to occur such that the desired effect, e.g., detection or modulation of expression of the protein, will result.
• a preferred intragenic site is the region encompassing the translation initiation or termination codon of the open reading frame (ORF) of the gene. Since, as is known in the art, the translation initiation codon is typically 5'-AUG (in transcribed mRNA molecules; 5'-ATG in the corresponding DNA molecule), the translation initiation codon is also referred to as the "AUG codon,” the “start codon” or the “AUG start codon”. A minority of genes have a translation initiation codon having the RNA sequence 5 '-GUG, 5 '-UUG or 5 '-CUG, and 5 '-
• translation initiation codon and “start codon” can encompass many codon sequences, even though the initiator amino acid in each instance is typically methionine (in eukaryotes) or formylmethionine (in prokaryotes). It is also known in the art that eukaryotic and prokaryotic genes may have two or more alternative start codons, any one of which may be preferentially utilized for translation initiation in a particular cell type or tissue, or under a particular set of conditions.
• start codon and “translation initiation codon” refer to the codon or codons that are used in vivo to initiate translation of an mRNA molecule transcribed from a gene encoding Navl.3, regardless of the sequence(s) of such codons.
• a translation termination codon or "stop codon" of a gene may have one of three sequences, i.e. 5'-UAA, 5'- UAG and 5 '-UGA (the corresponding DNA sequences are 5 '-TAA, 5 '-TAG and 5'-TGA, respectively).
• start codon region and “translation initiation codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5' or 3') from a translation initiation codon.
• stop codon region and “translation termination codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5' or 3') from a translation termination codon.
• Other target regions include the 5 ' untranslated region (5 'UTR), known in the art to refer to the portion of an mRNA in the 5 ' direction from the translation initiation codon, and thus including nucleotides between the 5 ' cap site and the translation initiation codon of an mRNA or corresponding nucleotides on the gene, and the 3' untranslated region (3'UTR), known in the art to refer to the portion of an mRNA in the 3' direction from the translation termination codon, and thus including nucleotides between the translation termination codon and 3' end of an mRNA or corresponding nucleotides on the gene.
• 5 ' untranslated region 5 'UTR
• 3' untranslated region known in the art to refer to the portion of an mRNA in the 3' direction from the translation termination
• the 5' cap of an mRNA comprises an N7-methylated guanosine residue joined to the 5'-most residue of the mRNA via a 5 '-5' triphosphate linkage.
• the 5' cap region of an mRNA is considered to include the 5' cap structure itself as well as the first 50 nucleotides adjacent to the cap.
• the 5' cap region may also be a preferred target region.
• mRNA splice sites i.e., intron-exon junctions
• intron-exon junctions may also be preferred target regions, and are particularly useful in situations where aberrant splicing is implicated in disease, or where an overproduction of a particular mRNA splice product is implicated in disease. Aberrant fusion junctions due to rearrangements or deletions are also preferred targets.
• introns can also be effective, and therefore preferred, target regions for antisense compounds targeted, for example, to DNA or pre-mRNA.
• oligonucleotides are chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect.
• hybridization means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases.
• adenine and thymine are complementary nucleobases, which pair through the formation of hydrogen bonds.
• “Complementary,” as used herein, refers to the capacity for precise pairing between two nucleotides.
• oligonucleotide and the DNA or RNA are considered to be complementary to each other at that position.
• the oligonucleotide and the DNA or RNA are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides which can hydrogen bond with each other.
• “specifically hybridizable” and “complementary” are terms which are used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between the oligonucleotide and the DNA or RNA target.
• an antisense compound need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable.
• An antisense compound is specifically hybridizable when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.
• Antisense compounds are commonly used as research reagents and diagnostics.
• antisense oligonucleotides which are able to inhibit gene expression with dazzling specificity, are often used by those of ordinary skill to elucidate the function of particular genes.
• Antisense compounds are also used, for example, to distinguish between functions of various members of a biological pathway. Antisense modulation has, therefore, been harnessed for research use.
• oligonucleotide refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof.
• oligonucleotides composed of naturally occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally occurring portions which function similarly.
• modified or substituted oligonucleotides are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases.
• antisense oligonucleotides are a preferred form of antisense compound, the present invention comprehends other oligomeric antisense compounds, including but not limited to oligonucleotide mimetics such as are described below.
• the antisense compounds in accordance with this invention preferably comprise from about 8 to about 30 nucleobases (i.e. from about 8 to about 30 linked nucleo sides).
• Particularly preferred antisense compounds are antisense oligonucleotides, even more preferably those comprising from about 12 to about 25 nucleobases.
• a nucleoside is a base-sugar combination.
• the base portion of the nucleoside is normally a heterocyclic base.
• the two most common classes of such heterocyclic bases are the purines and the pyrimidines.
• Nucleotides are nucleosides that further include a phosphate group covalently linked to the sugar portion of the nucleoside.
• the phosphate group can be linked to either the 2', 3' or 5' hydroxyl moiety of the sugar.
• the phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound.
• the respective ends of this linear polymeric structure can be further joined to form a circular structure, however, open linear structures are generally preferred.
• the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide.
• the normal I linkage or backbone of RNA and DNA is a 3' to 5' phosphodiester linkage.
• oligonucleotides containing modified backbones or non-natural internucleoside linkages include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone.
• modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
• Preferred modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3 'alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3 '-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3 '-5' linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'.
• Preferred modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
• morpholino linkages formed in part from the sugar portion of a nucleoside
• siloxane backbones sulfide, sulfoxide and sulfone backbones
• formacetyl and thioformacetyl backbones methylene formacetyl and thioformacetyl backbones
• alkene containing backbones sulfamate backbones
• sulfonate and sulfonamide backbones amide backbones; and others having mixed N, O, S and CH 2 component parts.
• both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups.
• the base units are maintained for hybridization with an appropriate nucleic acid target compound.
• an oligomeric compound an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA).
• PNA peptide nucleic acid
• the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone.
• nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
• Representative United States patents that teach the preparation of PNA compounds include, but are not limited to, U.S. 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science, 1991, 254, 1497-1500.
• Most preferred embodiments of the invention are oligonucleotides with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular -CH -NH-O-CH -, -CH -N (CH 3 ) -O-CH 2 - [known as a methylene (methylimino) or MMI backbone] , - CH 2 -O-N (CH 3 ) -CH 2 -, -CH 2 N(CH 3 )-N(CH 3 )-CH 2 - and -O-N(CH 3 )-CH 2 - CH - [wherein the native phosphodiester backbone is represented as -O-P- O-CH -] of the above referenced U.S.
• Modified oligonucleotides may also contain one or more substituted sugar moieties.
• Preferred oligonucleotides comprise one of the following at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C] to C ]0 alkyl or C 2 to do alkenyl and alkynyl.
• oligonucleotides comprise one of the following at the 2' position: Ci to Cio, ( lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, CI, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ON0 , NO , N 3 , NH 2 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties.
• a preferred modification includes 2' -methoxyethoxy (T -O-CH 2 CH 2 OCH 3 , also known as 2'-O- (2- methoxyethyl) or 2'-MOE) (Martin et al., Helv. Chim. Ada, 1995, 78, 486- 504) i.e., an alkoxyalkoxy group.
• a further preferred modification includes 2'-dimethylaminooxyethoxy, i.e., a O(CH ) ON(CH 3 ) 2 group, also known as 2'-DMAOE, as described in examples herein below, and 2'- dimethylaminoethoxyethoxy (also known in the art as 2'-O- dimethylaminoethoxyethyl or 2'-DMAEOE), i.e., 2'-O-CH 2 -O-CH 2 -N (CH ) , also described in examples herein below.
• 2'-dimethylaminooxyethoxy i.e., a O(CH ) ON(CH 3 ) 2 group, also known as 2'-DMAOE, as described in examples herein below
• 2'- dimethylaminoethoxyethoxy also known in the art as 2'-O- dimethylaminoethoxyethyl or 2'-DMAEOE
• Oligonucleotides may also include nucleobase (often referred to in the art simply as "base”) modifications or substitutions.
• unmodified or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
• Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5 -hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5- halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5- substitute
• nucleobases include those disclosed in United States Patent No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858- 859, Kroschwitz, J.I., ed. John Wiley & Sons, 1990, those disclosed by Englisch et al, Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y.S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S.T. and Lebleu, B. ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention.
• 5-substituted pyrimidines include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine.
• 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2°C (Sanghvi, Y.S., Crooke, S.T. and Lebleu, B., eds, Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are presently preferred base substitutions, even more particularly when combined with 2 '-O- methoxy ethyl sugar modifications.
• Representative United States patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. 3,687,808, as well as U.S. 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,750,692; and 5,681,941, each of which is herein inco ⁇ orated by reference.
• oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates, which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide.
• moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem.
• a thioether e.g., hexyl-S- tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al, Nucl.
• Acids Res., 1990, 18, 3777-3783 a polyamine or a polyethylene glycol chain (Mancharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 365'-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Ada, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937).
• antisense compounds which are chimeric compounds.
• Chimeric antisense compounds or “chimeras,” in the context of this invention are antisense compounds, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound.
• oligonucleotides typically contain at least one region wherem the oligonucleotide is modified so as to confer upon the oligonucleotide increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid.
• An additional region of the oligonucleotide may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids.
• RNase H is a cellular endonuclease, which cleaves the RNA strand of RNA:DNA duplex.
• RNA target Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of oligonucleotide inhibition of gene expression. Consequently, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligonucleotides hybridizing to the same target region.
• Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.
• Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as described above. Such compounds have also been referred to in the art as hybrids or gapmers. Representative United States patents that teach the preparation of such hybrid structures include, but are not limited to, U.S.
• the antisense compounds used in accordance with this invention may be conveniently, and routinely made tlirough the well-known technique of solid phase synthesis.
• Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, CA). Any other means for such synthesis known in the art may additionally or alternatively be employed.
• the antisense compounds of the invention are synthesized in vitro and do not include antisense compositions of biological origin, or genetic vector constructs designed to direct the in vivo synthesis of antisense molecules.
• the compounds of the invention may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as for example, liposomes, receptor targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption.
• the antisense compounds of the invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to prodrags and pharmaceutically acceptable salts of the compounds of the invention, pharmaceutically acceptable salts of such prodrags, and other bioequivalents.
• prodrug indicates a therapeutic agent that is prepared in an inactive form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes or other chemicals and/or conditions.
• prodrug versions of the oligonucleotides of the invention are prepared as SATE [(S-acetyl-2- thioethyl) phosphate] derivatives according to the methods disclosed in WO 93/24510 to Gosselin et al., published December 9, 1993 or in WO 94/26764 to Imbach et al.
• pharmaceutically acceptable salts refers to physiologically and pharmaceutically acceptable salts of the compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.
• Pharmaceutically acceptable base addition salts are formed with metals or amines, such as alkali and alkaline earth metals or organic amines. Examples of metals used as cations are sodium, potassium, magnesium, calcium, and the like.
• Suitable amines are N, N'- dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, dicyclohexylamine, ethylenediamine, N-methylglucamine, and procaine (see, for example, Berge et al., "Pharmaceutical Salts," J. ofPharma Sci., 1911, 66, 119).
• the base addition salts of said acidic compounds are prepared by contacting the free acid form with a sufficient amount of the desired base to produce the salt in the conventional manner.
• the free acid form may be regenerated by contacting the salt form with an acid and isolating the free acid in the conventional manner.
• a "pharmaceutical addition salt” includes a pharmaceutically acceptable salt of an acid form of one of the components of the compositions of the invention. These include organic or inorganic acid salts of the amines. Preferred acid salts are the hydrochlorides, acetates, salicylates, nitrates and phosphates.
• Suitable pharmaceutically acceptable salts include basic salts of a variety of inorganic and organic acids, such as, for example, with inorganic acids, such as for example hydrochloric acid, hydrobromic acid, sulfuric acid or phosphoric acid; with organic carboxylic, sulfonic, sulfo or phospho acids or N-substituted sulfamic acids, for example acetic acid, propionic acid, glycolic acid, succinic acid, maleic acid, hydroxymaleic acid, methylmaleic acid, fumaric acid, malic acid, tartaric acid, lactic acid, oxalic acid, gluconic acid, glucaric acid, glucuronic acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, salicylic acid, 4-aminosalicylic acid, 2- phenoxybenzoic acid, 2-acetoxybenzoic acid, embonic acid, nicotinic acid or isonicot
• Pharmaceutically acceptable salts of compounds may also be prepared with a pharmaceutically acceptable cation.
• Suitable pharmaceutically acceptable cations are well known to those skilled in the art and include alkaline, alkaline earth, ammonium and quaternary ammonium cations. Carbonates or hydrogen carbonates are also possible.
• salts formed with cations such as sodium, potassium, ammonium, magnesium, calcium, polyamines such as spermine and spermidine, etc.
• acid addition salts formed with inorganic acids for example hydrochloric acid, hydrobromic acid, sulfliric acid, phosphoric acid, nitric acid and the like
• salts formed with organic acids such as, for example, acetic acid, oxalic acid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconic acid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p- toluenesulfonic acid, naphthalenedisulf
• the antisense compounds of the present invention can be utilized for diagnostics, therapeutics, prophylaxis, and as research reagents and kits.
• an animal preferably a human, suspected of having a disease or disorder, which can be treated by modulating the expression of Navl .3, is treated by administering antisense compounds in accordance with this invention.
• the compounds of the invention can be utilized in pharmaceutical compositions by adding an effective amount of an antisense compound to a suitable pharmaceutically acceptable diluent or carrier.
• Use of the antisense compounds and methods of the invention may also be useful prophylactically, e.g., to prevent or delay infection, inflammation or tumor formation, for example.
• the antisense compounds of the invention are useful for research and diagnostics, because these compounds hybridize to nucleic acids encoding Navl.3, enabling sandwich and other assays to easily be constructed to exploit this fact.
• Hybridization of the antisense oligonucleotides of the invention with a nucleic acid encoding Navl .3 can be detected by means known in the art. Such means may include conjugation of an enzyme to the oligonucleotide, radiolabelling of the oligonucleotide or any other suitable detection means. Kits using such detection means for detecting the level of Navl.3 in a sample may also be prepared.
• the present invention also includes pharmaceutical compositions and formulations, which include the antisense compounds of the invention.
• the pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral.
• Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration.
• Oligonucleotides with at least one 2'-O- methoxyethyl modification are believed to be particularly useful for oral administration.
• Intraventricular drug administration for the direct delivery of drug to the brain of a patient, may be desired for the treatment of patients with diseases or conditions afflicting the brain.
• a silicon catheter is surgically introduced into a ventricle of the brain of a human patient, and is connected to a subcutaneous infusion pump
• the pump is used to inject the oligonucleotides and allows precise dosage adjustments and variation in dosage schedules with the aid of an external programming device.
• the reservoir capacity of the pump is 18-20 mL and infusion rates may range from 0.1 mL/h to 1 mL/h.
• the pump reservoir may be refilled at 3 -10 week intervals. Refilling of the pump is accomplished by percutaneous puncture of the self-sealing septum of the pump.
• the pump is used to inject the oligonucleotides and allows precise dosage adjustments and variations in dose schedules with the aid of an external programming device.
• the reservoir capacity of the pump is 18-20 mL, and infusion rates may vary from 0. 1 mL/h to 1 mL& Depending on the frequency of drug administration, ranging from daily to monthly, and dosage of drug to be administered, ranging from 0.01 micro g to 100 g per kg of body weight, the pump reservoir may be refilled at 3 -10 week intervals. Refilling of the pump is accomplished by a single percutaneous puncture to the self-sealing septum of the pump. The distribution, stability and pharmacokinetics of oligonucleotides within the central nervous system may be followed according to known methods. Subdural administration is also envisioned other by a pump mechanism or direct injection.
• the silicon catheter is configured to connect the subcutaneous infusion pump to, e.g., the hepatic artery, for delivery to the liver.
• Infusion pumps may also be used to effect systemic delivery of oligonucleotides (Ewel et al., Cancer Research, 1992, 52, 3005; Rubenstein et al., J. Surg. Oncol., 1996, 62, 194).
• compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders.
• Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
• Coated condoms, gloves and the like may also be useful.
• compositions and formulations for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets or tablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders may be desirable.
• Compositions and formulations for parenteral, intrathecal or intraventricular administration may mclude sterile aqueous solutions, which may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.
• compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions may be generated from a variety of components that mclude, but are not limited to, preformed liquids, self- emulsifying solids and self-emulsifying semisolids.
• the pharmaceutical formulations of the present invention may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques mclude the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.
• compositions of the present invention may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, liquid syrups, soft gels, suppositories, and enemas.
• the compositions of the present invention may also be formulated as suspensions in aqueous, non-aqueous or mixed media.
• Aqueous suspensions may further contain substances, which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran.
• the suspension may also contain stabilizers.
• the pharmaceutical compositions may be formulated and used as foams.
• Emulsions are often biphasic systems comprising of two immiscible liquid phases intimately mixed and dispersed with each other.
• emulsions may be either water-in-oil (w/o) or of the oil-in-water (o/w) variety.
• Emulsions may contain additional components in addition to the dispersed phases and the active drug, which may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase. Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants may also be present in emulsions as needed.
• compositions may also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil- in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions.
• Such complex formulations often provide certain advantages that simple binary emulsions do not.
• Multiple emulsions in which individual oil droplets of an o/w emulsion enclose small water droplets constitute a w/o/w emulsion.
• a system of oil droplets enclosed in globules of water stabilized in an oily continuous provides an o/w/o emulsion.
• Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion may be a semisolid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that may be incorporated into either phase of the emulsion.
• Emulsifiers may broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N. Y., volume 1 , p. 199).
• Synthetic surfactants also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N. Y., volume 1 , p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199).
• Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion.
• HLB hydrophile/lipophile balance
• surfactants may be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).
• Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia.
• Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations.
• non-emulsifying materials are also included in emulsion formulations and contribute to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives, and antioxidants (Block, in
• Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed phase droplets and by increasing the viscosity of the external phase.
• polysaccharides for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth
• cellulose derivatives for example, carboxymethylcellulose and carboxypropylcellulose
• synthetic polymers for example, carbomers, cellulose ethers, and carb
• emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that may readily support the growth of microbes
• these formulations often incorporate preservatives.
• preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid.
• Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation.
• Antioxidants used may be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulf ⁇ te, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.
• free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulf ⁇ te
• antioxidant synergists such as citric acid, tartaric acid, and lecithin.
• compositions of oligonucleotides and nucleic acids are formulated as microemulsions.
• a microemulsion may be defined as a system of water, oil and amphiphile, which is a single optically isofropic, and thermodynamically stable liquid solution (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N ., volume 1, p. 245).
• microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain- length alcohol to form a transparent system.
• microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 1852-5).
• Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte.
• microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington 's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA, 1985, p. 271).
• microemulsions offer the advantage of solubilizing water-insoluble drags in a formulation of thermodynamically stable droplets that are formed spontaneously.
• Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (S0750), decaglycerol decaoleate (DAO750), alone or in combination with cosurfactants.
• ionic surfactants non-ionic surfactants
• Brij 96 polyoxyethylene oleyl ethers
• polyglycerol fatty acid esters tetraglycerol monolaurate (ML310
• the cosurfactant usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules.
• Microemulsions may, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art.
• the aqueous phase may typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol.
• the oil phase may include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and triglycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.
• materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and triglycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.
• Microemulsions are particularly of interest from the standpoint of drag solubilization and the enhanced absorption of drags.
• Lipid based microemulsions have been proposed to enhance the oral bioavailability of drags, including peptides (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol, 1993, 13, 205).
• Microemulsions afford advantages of improved drag solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm.
• microemulsions may form spontaneously when their components are brought together at ambient temperature. This may be particularly advantageous when formulating thermolabile drugs, peptides or oligonucleotides.
• Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications. It is expected that the microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of oligonucleotides and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of oligonucleotides and nucleic acids within the gastrointestinal tract, vagina, buccal cavity and other areas of administration.
• Liposomes There are many organized surfactant stractures besides microemulsions that have been studied and used for the formulation of drugs. These include monolayers, micelles, bilayers and vesicles. Vesicles, such as liposomes, have attracted great interest because of their specificity and the duration of action they offer from the standpoint of drug delivery. As used in the present invention, the term "liposome” means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers. [0067] Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior.
• the aqueous portion contains the composition to be delivered.
• Cationic liposomes possess the advantage of being able to fuse to the cell wall.
• Noncationic liposomes although not able to fuse as efficiently with the cell wall, are taken up by macrophages in vivo.
• lipid vesicles In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. Therefore, it is desirable to use a liposome, which is highly deformable and able to pass through such fine pores.
• liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can inco ⁇ orate a wide range of water and lipid soluble drags; liposomes can protect encapsulated drags in their internal compartments from metabolism and degradation (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, P. 245).
• Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.
• Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomes start to merge with the cellular membranes. As the merging of the liposome and cell progresses, the liposomal contents are emptied into the cell where the active agent may act. [0071] Liposomal formulations have been the focus of extensive investigation as the mode of delivery for many drags. There is growing evidence that for topical administration, liposomes present several advantages over other formulations. Such advantages mclude reduced side- effects related to high systemic abso ⁇ tion of the administered drug, increased accumulation of the administered drag at the desired target, and the ability to administer a wide variety of drags, both hydrophilic and hydrophobic, into the skin.
• liposomes to deliver agents including high-molecular weight DNA into the skin.
• Compounds including analgesics, antibodies, hormones and high-molecular weight DNAs have been administered to the skin. The majority of applications resulted in the targeting of the upper epidermis.
• Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes, which interact with the negatively charged DNA molecules to form a stable complex. The positively charged DNA/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al, Biochem. Biophys. Res. Commun., 1987, 147, 980 - 985) [0074] Liposomes, which are pH-sensitive or negatively charged, entrap DNA rather than complex with it. Since both the DNA and the lipid are similarly charged, repulsion rather than complex formation occurs.
• One maj or type of liposomal composition includes phospholipids other than naturally derived phosphatidylcholine.
• Neutral liposome compositions for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC).
• Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamme (DOPE).
• DOPE dioleoyl phosphatidylethanolamme
• Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC.
• PC phosphatidylcholine
• Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.
• Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drags to the skin, in particular systems comprising non-ionic surfactant and cholesterol.
• Non-ionic liposomal formulations comprising Novasome TM I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and NovasomeTM II (glyceryl distearate/ cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporin-A into different layers of the skin (Hu et al. S. T.P.Pharma. Sci., 1994, 4, 6, 466).
• Liposomes also include "sterically stabilized" liposomes, a term, which, as used herein, refers to liposomes comprising one or more specialized lipids that, when inco ⁇ orated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such, specialized lipids.
• sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside GM I , or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety.
• PEG polyethylene glycol
• Patent No. 5,213,804 and European Patent No. EP 0 496 813 Bl Liposomes comprising a number of other lipid-polymer conjugates are disclosed in WO 91/05545 and U.S. Patent No. 5,225,212 (both to Martin et al.) and in WO 94/20073 (Zalipsky et al.) Liposomes comprising PEG-modified ceramide lipids are described in WO 96/10391 (Choi et al.).
• U.S. Patent Nos. 5,540,935 (Miyazaki et al.) and 5,556,948 (Tagawa et al.) describe PEG- containing liposomes that can be further derivatized with functional moieties on their surfaces.
• a limited number of liposomes comprising nucleic acids are known in the art.
• WO 96/40062 to Thierry et al. discloses methods for encapsulating high molecular weight nucleic acids in liposomes.
• U.S. Patent No. 5,264,221 to Tagawa et al. discloses protein-bonded liposomes and asserts that the contents of such liposomes may include an antisense RNA.
• U.S. Patent No. 5,665,710 to Rahman et al. describes certain methods of encapsulating oligodeoxynucleotides in liposomes.
• Transfersomes are yet another type of liposomes, and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transfersomes may be described as lipid droplets, which are so highly deformable that they are easily able to penetrate through pores, which are smaller than the droplet. Transfersomes are adaptable to the environment in which they are used, e.g. they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transfersomes it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transfersomes have been used to deliver serum albumin to the skin. The transfersome-mediated delivery of seram albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.
• Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes.
• HLB hydrophile/lipophile balance
• the nature of the hydrophilic group also known as the "head" provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, NY, 1988, p. 285)
• the surfactant molecule is not ionized, it is classified as a nonionic surfactant.
• Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about ⁇ 8 depending on their structure.
• Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters.
• Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class.
• the polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.
• Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates.
• the most important members of the anionic surfactant class are the alkyl sulfates and the soaps.
• Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.
• the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric.
• Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N- alkylbetaines and phosphatides.
• the use of surfactants in drag products, formulations and in emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, NY, 1988, p. 285).
• Penetration Enhancers [0089] In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids particularly oligonucleotides, to the skin of animals.
• Penetration enhancers may be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chelating nonsurfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92). Each of the above mentioned classes of penetration enhancers are described below in greater detail.
• surfactants In connection with the present invention, surfactants
• these penetration enhancers include, for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92); and perfluorochemical emulsions, such as FC-43. Takahashi et al., J. Pharm.
• Fatty acids Narious fatty acids and their derivatives which act as penetration enhancers include, for example, oleic acid, lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein (l-monooleoyl-.rac- glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate, l-dodecylazacycloheptan-2-one, acylcarnitines, acylchohnes, C,- ⁇ o alkyl esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di- glycerides thereof (i.e., oleate, laurate, caprate, myristate, palm
• Bile salts The physiological role of bile includes the facilitation of dispersion and abso ⁇ tion of lipids and fat-soluble vitamins (Branton, Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds. McGraw-Hill, New York, 1996, pp. 934-935). Narious natural bile salts, and their synthetic derivatives, act as penetration enhancers. Thus the term "bile salts" includes any of the naturally occurring components of bile as well as any of their synthetic derivatives.
• the bile salts of the invention include, for example, cholic acid (or its pharmaceutically acceptable sodium salt, sodium cholate), dehydrocholic acid (sodium dehydrocholate), deoxy cholic acid (sodium deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium glycocholate), glycodeoxychohc acid (sodium gly codeoxy cholate), taurocholic acid (sodium taurocholate), taurodeoxychohc acid (sodium taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodium glycodihydrofusidate'and polyoxyethylene-9-lauryl ether (POE) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In:
• Chelating agents as used in connection with the present invention, can be defined as compounds that remove metallic ions from solution by forming complexes therewith, with the result that abso ⁇ tion of oligonucleotides through the mucosa is enhanced. With regards to their use as penetration enhancers in the present invention, chelating agents have the added advantage of also serving as DNase inhibitors, as most characterized DNA nucleases require a divalent metal ion for catalysis and are thus inhibited by chelating agents (Jarrett, J.
• Chelating agents of the invention include but are not limited to disodium. ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino acyl derivatives of beta-diketones (enamines)(Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi, Critical
• Non-chelating non-surfactants can be defined as compounds that demonstrate insignificant activity as chelating agents or as surfactants but that nonetheless enhance abso ⁇ tion of oligonucleotides through the alimentary mucosa (Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33).
• This class of penetration enhancers include, for example, unsaturated cyclic ureas, 1 -alkyl- and 1- alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews in
• oligonucleotides may also be added to the pharmaceutical and other compositions of the present invention.
• cationic lipids such as lipofectin (Junichi et al, U.S. Patent No.
• cationic glycerol derivatives include cationic glycerol derivatives, and polycationic molecules, such as polylysine (Lollo et al, PCT Application WO 97/30731), are also known to enhance the cellular uptake of oligonucleotides.
• nucleic acids include glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and te ⁇ enes such as limonene and menthone.
• glycols such as ethylene glycol and propylene glycol
• pyrrols such as 2-pyrrol
• azones such as 2-pyrrol
• te ⁇ enes such as limonene and menthone.
• compositions of the present invention also inco ⁇ orate carrier compounds in the formulation.
• carrier compound or “carrier” can refer to a nucleic acid, or analog thereof, which is inert (i.e., does not possess biological activity per se) but is recognized as a nucleic acid by in vivo processes that reduce the bioavailability of a nucleic acid having biological activity by, for example, degrading the biologically active nucleic acid or promoting its removal from circulation.
• a nucleic acid and a carrier compound can result in a substantial reduction of the amount of nucleic acid recovered in the liver, kidney or other extracirculatory reservoirs, presumably due to competition between the carrier compound and the nucleic acid for a common receptor.
• the recovery of a partially phosphorothioate oligonucleotide in hepatic tissue can be reduced when it is coadministered with polyinosinic acid, dexfran sulfate, polycytidic acid or 4-acetamido-4'isothiocyano-stilbene-2,2' disulfonic acid (Miyao et al., Antisense Res.
• a "pharmaceutical carrier” or “excipient” is a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal.
• the excipient may be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with a nucleic acid and the other components of a given pharmaceutical composition.
• Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodium starch glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc.).
• binding agents e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxyprop
• compositions of the present invention can also be used to formulate the compositions of the present invention.
• suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.
• Formulations for topical administration of nucleic acids may include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases.
• the solutions may also contain buffers, diluents and other suitable additives.
• Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration, which do not deleteriously react with nucleic acids, can be used.
• Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.
• Other Components [00103]
• the compositions of the present invention may additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels.
• Aqueous suspensions may contain substances, which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol, and/or dexfran.
• the suspension may also contain stabilizers.
• compositions containing (a) one or more antisense compounds and (b) one or more other chemotherapeutic agents which function by a non-antisense mechanism.
• chemotherapeutic agents include, but are not limited to, anticancer drags such as daunorabicin, dactinomycin, doxorubicin, bleomycin, mitomycin, nitrogen mustard, chlorambucil, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine (CA), 5-fluorouracil (5-FU), floxuridine (5-FUdR), methotrexate (MTX), colchicine, vincristine, vinblastine, etoposide, teniposide, cisplatin and diethylstilbestrol (DES).
• anticancer drags such as daunorabicin, dactinomycin, doxorubicin, bleomycin, mitomycin, nitrogen mustard, chloramb
• Anti-inflammatory drags including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drags, including but not limited to ribivirin, vidarabine, acyclovir and ganciclovir, may also be combined in compositions of the invention.
• compositions of the invention may contain one or more antisense compounds, particularly oligonucleotides, targeted to a first nucleic acid and one or more additional antisense compounds targeted to a second nucleic acid target.
• antisense compounds are known in the art. Two or more combined compounds may be used together or sequentially.
• the formulation of therapeutic compositions and their subsequent administration is believed to be within the skill of those in the art. Dosing is dependent on severity and responsiveness of the disease state to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of the disease state is achieved. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient.
• Optimum dosages may vary depending on the relative potency of individual oligonucleotides, and can generally be estimated based on EC 50 S found to be effective in in vitro and in vivo animal models. In general, dosage is from 0.01 ⁇ g to 100 g per kg of body weight, and may be given once or more daily, weekly, monthly or yearly, or even once every 2 to 20 years. Persons of ordinary skill in the art can easily estimate repetition rates for dosing based on measured residence times and concentrations of the drug in bodily fluids or tissues.
• the oligonucleotide is administered in maintenance doses, ranging from 0.01 ⁇ g to 100 g per kg of body weight, once or more daily, to once every 20 years.
• 2'-Deoxy and 2'-methoxy beta-cyanoethyldiisopropyl phosphoramidites are available from commercial sources (e.g. Chemgenes, Needham MA or Glen Research, Inc. Sterling VA).
• Other 2'-O-alkoxy substituted nucleoside amidites are prepared as described in U.S. Patent 5,506,351, herein inco ⁇ orated by reference.
• the standard cycle for unmodified oligonucleotides is utilized, except the wait step after pulse delivery of tetrazole and base is increased to 360 seconds.
• Oligonucleotides containing 5-methyl-2'-deoxycytidine (5-Me- C) nucleotides are synthesized according to published methods [Sanghvi, et. al, Nucleic Acids Research, 1993, 21, 3197-3203] using commercially available phosphoramidites (Glen Research, Sterling NA or ChemGenes, ⁇ eedham MA). 2'-FIuoro amidites
• 2'-fluoro oligonucleotides are synthesized as described previously [Kawasaki, et. al., J. Med. Chem., 1993, 36, 831-841] and United States patent 5,670,633, herein inco ⁇ orated by reference. Briefly, the protected nucleoside ⁇ 6-benzoyl-2'-deoxy-2'-fluoroadenosine is synthesized utilizing commercially available 9-beta-D- arabinofuranosyladenine as starting material and by modifying literature procedures whereby the 2'-alpha-fluoro atom is introduced by a S N 2- displacement of a 2'-beta-trityl group.
• N6-benzoyl-9-beta-D- arabinofuranosylademne is selectively protected in moderate yield as the 3',5'-ditetrahydropyranyl (THP) intermediate.
• THP 3',5'-ditetrahydropyranyl
• Deprotection of the THP and N6-benzoyl groups is accomplished using standard methodologies and standard methods are used to obtain the 5'-dimethoxytrityl-(DMT) and 5'- DMT-3 '-phosphoramidite intermediates.
• 2'-O-Methoxyethyl-substituted nucleoside amidites are prepared as follows, or alternatively, as per the methods of Martin, P., Helvetica Chimica Acta, 1995, 78, 486-504. 2,2'-Anhydro[l-(beta-D-arabinofuranosyl)-5-methyluridinel
• the solution is poured into fresh ether (2.5 L) to yield a stiff gum.
• the ether is decanted and the gum is dried in a vacuum oven (60°C at 1 mm Hg for 24 h) to give a solid that is crashed to a light tan powder.
• the material is used as is for further reactions (or it can be purified further by column chromatography using a gradient of methanol in ethyl acetate (10-25%) to give a white solid.
• 2'-O-Methoxyethyl-5'-O-dimethoxytrityl-5-methyluridine 160 g, 0.506 M is co- evaporated with pyridine (250 mL) and the dried residue dissolved in pyridine (1.3 L). A first aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) is added and the mixture stirred at room temperature for one hour. A second aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) is added and the reaction stirred for an additional one hour. Methanol (170 mL) is then added to stop the reaction.
• a first solution is prepared by dissolving 3 '-O-acetyl-2'-O- methoxyethyl-5'-O-dimethoxytrityl-5-methyluridine (96 g, 0.144 M) in
• N4-Benzoyl-2'-O-methoxyethyl-5'-O-dimethoxytrityl-5-methylcytidine (85 g, 0.134 M) is dissolved in DMF (800 mL) and benzoic anhydride (37.2 g, 0.165 M) is added with stirring. After stirring for 3 hours, TLC showed the reaction to be approximately 95% complete. The solvent-'is evaporated and the residue azeotroped with MeOH (200 mL).
• 2'-O-(Aminooxyethyl) nucleoside amidites and 2'-O- (dimethylaminooxyethyl) nucleoside amidites 2'-(Dimethylaminooxyethoxy) nucleoside amidites [00124] 2'-(Dimethylaminooxyethoxy) nucleoside amidites [also known in the art as 2'-O-(dimethylaminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs.
• O 2 -2'-anhydro-5-methyluridine (Pro. Bio. Sint, Narese, Italy, lOO.Og, 0.4'6 mmol), dimethylaminopyridine (0.66g, 0.013eq, 0.0054mmol) are dissolved in dry pyridine (500 ml) at ambient temperature under an argon atmosphere and with mechanical stirring, tert- Butyldiphenylchlorosilane (125.8g, 119.0mL, l.leq, 0.458mmol) is added in one portion. The reaction is stirred for 16 h at ambient temperature. TLC (Rf 0.22, ethyl acetate) indicated a complete reaction.
• the solution is concentrated under reduced pressure to a thick oil. This is partitioned between dichloromethane (1 L) and saturated sodium bicarbonate (2x1 L) and brine (1 L). The organic layer is dried over sodium sulfate and concentrated under reduced pressure to a thick oil.
• the oil is dissolved in a 1 :1 mixture of ethyl acetate and ethyl ether (600mL) and the solution is cooled to -10°C.
• the resulting crystalline product is collected by filtration, washed with ethyl ether (3x200 mL), and dried (40°C, 1mm Hg, 24 h) to a white solid
• 5'-O-tert-Butyldiphenylsilyl-2'-O-(2-hydroxyethyl)-5-methyluridine [00126] In a 2 L stainless steel, unstirred pressure reactor is added borane in tetrahydrofuran (1.0 M, 2.0 eq, 622 mL). In the fume hood and with manual stirring, ethylene glycol (350 mL, excess) is added cautiously at first until the evolution of hydrogen gas subsides. 5'-O-tert-Butyldiphenylsilyl- O 2 -2'anhydro-5-methyluridine (149 g, 0.3'1 mol) and sodium bicarbonate (0.074 g, 0.003 eq) are added with manual stirring.
• the reactor is sealed and heated in an oil bath until an internal temperature of 160°C is reached and then maintained for 16 h (pressure ⁇ 100 psig).
• the reaction vessel is cooled to ambient and opened.
• TLC Rf 0.67 for desired product and Rf 0.82 for ara-T side product, ethyl acetate
• the reaction is stopped, concentrated under reduced pressure (10 to 1mm, Hg) in a warm water bath (40-100°C) with the more extreme conditions used to remove the ethylene glycol. [Alternatively, once the low boiling solvent is gone, the remaining solution can be partitioned between ethyl acetate and water.
• Aqueous NaHCO 3 solution (5%, lOmL) is added and extracted with ethyl acetate (2x20mL). Ethyl acetate phase is dried over anhydrous Na 2 SO , evaporated to dryness. Residue is dissolved in a solution of IM PPTS in MeOH (30.6mL). Formaldehyde (20% w/w, 30mL, 3.37mmol) is added and the reaction mixture is stirred at room temperature for 10 minutes. Reaction mixture cooled to 10°C in an ice bath, sodium cyanoborohydride (0.39g, 6.13mmol) is added, and reaction mixture stirred at 10°C for 10 minutes.
• reaction mixture is removed from the ice bath and stirred at room temperature for 2 hrs.
• 5% NaHCO 3 (25mL) solution is added and extracted with ethyl acetate (2x25mL).
• Ethyl acetate layer is dried over anhydrous Na 2 SO and evaporated to dryness.
• the residue obtained is purified by flash column chromatography and eluted with 5% MeOH in CH 2 C1 2 to get 5'-O- tertbutyldiphenylsilyl-2'-O-[N,N-dimethylaminooxyethyl]-5- methyluridine as a white foam.
• Triethylamine trihydrofluoride (3.91mL, 24.0mmol) is dissolved in dry THF and triethylamine (1.67mL, 12mmol, dry, kept over KOH). This mixture of triethylamine- 2HF is then added to 5'-O-tert-butyldiphenylsilyl- 2'-O-[N,N-dimethylaminooxyethyl]-5-methyluridine (1.40g, 2.4mmol) and stirred at room temperature for 24 hrs. Reaction is monitored by TLC (5% MeOH in CH 2 C1 2 ). Solvent is removed under vacuum and the residue placed on a flash column and eluted with 10% MeOH in CH 2 C1 2 to get 2'-O-
• 5 '-O-DMT-2 '-O-(dimethylaminooxyethyl)-5-methyluridine (1.08g, 1.67mmol) is co-evaporated with toluene (20mL).
• N,N-diisopropylamine tetrazonide (0.29g, 1.67mmol) is added and dried over P20, under high vacuum overnight at 40°C.
• the reaction mixture is dissolved in anhydrous acetonitrile (8.4mL) and 2-cyanoethyl-N,N,N 1 ,N 1 - tetraisopropylphosphoramidite (2.12mL, 6.08mmol) is added.
• reaction mixture is stirred at ambient temperature for 4 hrs under inert atmosphere.
• the progress of the reaction is monitored by TLC (hexane: ethyl acetate 1:1).
• the solvent is evaporated, then the residue is dissolved in ethyl acetate (70mL) and washed with 5% aqueous NaHCO 3 (40mL). Ethyl acetate layer is dried over anhydrous Na 2 SO and concentrated.
• Residue obtained is chromatographed (ethyl acetate as eluent) to get 5'-O-DMT-2'-O-(2-N,N- dimethylaminooxyethyl)-5-methyluridine-3'-[(2-cyanoethyl)-N,N- diisopropylphosphoramidite] as a foam.
• 2'-(Aminooxyethoxy) nucleoside amidites [also known in the art as 2'-O-(aminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs. Adenosine, cytidine and thymidine nucleoside amidites are prepared similarly. N2-isobutyryl-6-O-diphenylcarbamoyl-2'-O-(2-ethylacetyl)-5'-O-(4,4'- dimethoxytrityl)guanosine-3'-[(2-cyanoethyl)-N,N- diisopr opylph osph or amidite]
• the 2'-O-aminooxyethyl guanosine analog may be obtained by selective 2'-O-alkylation of diaminopurine riboside.
• Multigram quantities of diaminopurine riboside may be purchased from Schering AG (Berlin) to provide 2'-O-(2-ethylacetyl) diaminopurine riboside along with a minor amount of the 3'-O-isomer.
• 2'-O-(2-ethylacetyl) diaminopurine riboside may be resolved and converted to 2'-O-(2ethylacetyl)guanosine by treatment with adenosine deaminase.
• Standard protection procedures should afford 2'-O-(2-ethylacetyl)-5 '-O-(4,4'-dimethoxytrityl)guanosine and 2-N-isobutyryl-6-O-diphenylcarbamoyl-2 ' -O-(2-ethylacetyl)-5 ' -O- (4,4'-dimethoxytrityl)guanosine which may be reduced to provide 2-N- isobutyryl-6-O-diphenylcarbamoyl-2 ' -O-(2-ethylacetyl)-5 ' -O-(4,4 ' - dimethoxvtrityl)guanosine.
• the hydroxyl group may be displaced by N-hydroxyphthalimide via a Mitsunobu reaction, and the protected nucleoside may phosphitylated as usual to yield 2-N-isobutyryl-6-O- di ⁇ henylcarbamoyl-2 ' -O-(2-ethylacetyl)-5 '-O-(4,4 ' - dimethoxytrityl)guanosine-3'-[(2-cyanoethyl)-N,N- diisopropylphosphoramiditel.
• 2'-dimethylaminoethoxyethoxy (2'-DMAEOE) nucleoside amidites [00135] 2' -dimethylammoethoxyethoxy nucleoside amidites (also known in the art as 2'-O-dimethylaminoethoxyethyl, i.e., 2'O-CH 2 -O-CH 2 - N(CH 2 ) 2 , or 2'-DMAEOE nucleoside amidites) are prepared as follows. Other nucleoside amidites are prepared similarly.
• the bomb is cooled to room temperature and opened.
• the crade solution is concentrated and the residue partitioned between water (200 mL) and hexanes (200 mL).
• the excess phenol is extracted into the hexane layer.
• the aqueous layer is extracted with ethyl acetate (3x200 mL) and the combined organic layers are washed once with water, dried over anhydrous sodium sulfate and concentrated.
• the residue is columned on silica gel using methanol/methylene chloride 1 :20 (which has 2% triethylamine) as the eluent. As the column fractions are concentrated a colorless solid forms which is collected to give the title compound as a white solid.
• the thiation wait step is increased to 68 sec and is followed by the capping step.
• the oligonucleotides are purified by precipitating twice with 2.5 volumes of ethanol from a 0.5 M NaCl solution.
• Phosphinate oligonucleotides are prepared as described in U.S. Patent 5,508,270, herein inco ⁇ orated by reference.
• Alkyl phosphonate oligonucleotides are prepared as described in U.S. Patent 4,469,863, herein inco ⁇ orated by reference.
• 3 '-Deoxy-3 '-methylene phosphonate oligonucleotides are prepared as described in U.S. Patents 5,610,289 or 5,625,050, herein inco ⁇ orated by reference.
• Phosphoramidite oligonucleotides are prepared as described in U.S. Patent, 5,256,775 or U.S. Patent 5,366,878, herein inco ⁇ orated by reference.
• Alkylphosphonothioate oligonucleotides are prepared as described in WO 94/17093 and WO 94/02499 herein inco ⁇ orated by reference.
• 3 '-Deoxy-3 '-amino phosphoramidate oligonucleotides are prepared as described in U.S. Patent 5,476,925, herein inco ⁇ orated by reference.
• Phosphotriester oligonucleotides are prepared as described in U.S. Patent 5,023,243, herein inco ⁇ orated by reference.
• Borano phosphate oligonucleotides are prepared as described in U.S. Patents 5,130,302 and 5,177,198, both herein inco ⁇ orated by reference.
• Formacetal and thioformacetal linked oligonucleosides are prepared as described in U.S. Patents 5,264,562 and 5,264,564, herein inco ⁇ orated by reference.
• Ethylene oxide linked oligonucleosides are prepared as described in U.S. Patent 5,223,618, herein inco ⁇ orated by reference.
• PNAs Peptide nucleic acids
• PNA Peptide Nucleic Acids
• Chimeric oligonucleotides, oligonucleosides or mixed oligonucleotides/oligonucleosides of the invention can be of several different types. These include a first type wherein the "gap" segment of linked nucleosides is positioned between 5 ' and 3 ' "wing" segments of linked nucleosides and a second "open end” type wherein the "gap” segment is located at either the 3' or the 5' terminus of the oligomeric compound. Oligonucleotides of the first type are also known in the art as “gapmers” or gapped oligonucleotides.
• oligonucleotides or oligonucleosides are purified by precipitation twice out of 0.5 M NaCl with 2.5 volumes ethanol. Synthesized oligonucleotides are analyzed by polyacrylamide gel electrophoresis on denaturing gels and judged to be at least 85% full-length material.
• Non-standard nucleosides are synthesized as per known literature or patented methods. They are utilized as base protected betacyanoethyldiisopropyl phosphoramidites.
• Oligonucleotides are cleaved from support and deprotected with concentrated NH OH at elevated temperature (55-60°C) for 12-16 hours and the released product then dried in vacuo. The dried product is then resuspended in sterile water to afford a master plate from which all analytical and test plate samples are then diluted utilizing robotic pipettors.
• the concentration of oligonucleotide in each well is assessed by dilution of samples and UN abso ⁇ tion spectroscopy.
• the full-length integrity of the individual products is evaluated by capillary electrophoresis (CE) in either the 96 well format (Beckman P/ACETM MDQ) or, for individually prepared samples, on a commercial CE apparatus (e.g., Beckman P/ACETM 5000, ABI 270).
• Base and backbone composition is confirmed by mass analysis of the compounds utilizing electrospray-mass spectroscopy. All assay test plates are diluted from the master plate using single and multi-channel robotic pipettors. Plates are judged to be acceptable if at least 85% of the compounds on the plate are at least 85% full length.
• cells may be seeded onto 100 mm or other standard tissue culture plates and treated similarly, using appropriate volumes of medium and oligonucleotide.
• A549 cells A549 cells:
• the human lung carcinoma cell line A549 can be obtained from the American Type Culture Collection (ATCC) (Manassas, VA).
• A549 cells are routinely cultured in DMEM basal media (Gibco/Life Technologies, Gaithersburg, MD) supplemented with 10% fetal calf serum (Gibco/Life Technologies, Gaithersburg, MD), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Gibco/Life Technologies, Gaithersburg, MD). Cells are routinely passaged by trypsinization and dilution when they reached 90% confluence.
• NHDF cells are routinely passaged by trypsinization and dilution when they reached 90% confluence.
• Human neonatal dermal fibroblast can be obtained from the Clonetics Co ⁇ oration (Walkersville MD). NHDFs are routinely maintained in Fibroblast Growth Medium (Clonetics Co ⁇ oration, Walkersville MD) supplemented as recommended by the supplier. Cells are maintained for up to 10 passages as recommended by the supplier.
• HEK cells can be obtained from the Clonetics Co ⁇ oration (Walkersville MD). NHDFs are routinely maintained in Fibroblast Growth Medium (Clonetics Co ⁇ oration, Walkersville MD) supplemented as recommended by the supplier. Cells are maintained for up to 10 passages as recommended by the supplier. HEK cells:
• HEK Human embryonic keratmocytes
• Clonetics Co ⁇ oration Walkersville MD
• HEKs are routinely maintained in Keratinocyte Growth Medium (Clonetics Co ⁇ oration, Walkersville MD) formulated as recommended by the supplier.
• Cells are routinely maintained for up to 10 passages as recommended by the supplier.
• MCF-7 cells
• the human breast carcinoma cell line MCF-7 is obtained from the American Type Culture Collection (Manassas, VA). MCF-7 cells are routinely cultured in DMEM low glucose (Gibco/Life Technologies,
• LA4 cells [00169] The mouse lung epithelial cell line LA4 is obtained from the American Type Culture Collection (Manassas, VA).
• LA4 cells are routinely cultured in F12K medium (Gibco/Life Technologies, Gaithersburg, MD) supplemented with 15% fetal calf serum (Gibco/Life Technologies, Gaithersburg, MD). Cells are routinely passaged by trypsinization and dilution when they reached 90% confluence. Cells are seeded into 96-well plates (Falcon-Primaria #3872) at a density of 3000-6000 cells/ well for use in RT-PCR analysis.
• cells may be seeded onto 100 mm or other standard tissue culture plates and treated similarly, using appropriate volumes of medium and oligonucleotide. Treatment with antisense compounds:
• oligonucleotide When cells reached 80% confluence, they are treated with oligonucleotide. For cells grown in 96-well plates, wells are washed once with 200 ⁇ L OPTI-MEM tm -l reduced-seram medium (Gibco BRL) and then treated with 130 ⁇ L of OPTI-MEMTMTM-l containing 3.75 ⁇ g/mL LIPOFECTINTM (Gibco BRL) and the desired concentration of oligonucleotide. After 4-7 hours of treatment, the medium is replaced with fresh medium. Cells are harvested 16-24 hours after oligonucleotide treatment. [00172] The concentration of oligonucleotide used varies from cell line to cell line. To determine the optimal oligonucleotide concentration for a particular cell line, the cells are treated with a positive control oligonucleotide at a range of concentrations.
• Buffer RW1 1 mL of Buffer RW1 is added to each well of the RNEASY 96 TM plate and the vacuum again applied for 15 seconds.
• 1 mL of Buffer RPE is then added to each well of the RNEASY 96 TM plate and the vacuum applied for a period of 15 seconds.
• the Buffer RPE wash is then repeated and the vacuum is applied for an additional 10 minutes.
• the plate is then removed from the QIAVACTM manifold and blotted dry on paper towels. The plate is then re-attached to the QIAVACTM manifold fitted with a collection tube rack containing 1.2 mL collection tubes. RNA is then diluted by pipetting 60 ⁇ L water into each well, incubating one minute, and then applying the vacuum for 30 seconds.
• Quantitation of Navl .3 mRNA levels is determined by real-time quantitative PCR using the ABI PRISM 7700 Sequence Detection System (PE-Applied Biosystems, Foster City, CA) according to manufacturer's instructions.
• ABI PRISM 7700 Sequence Detection System PE-Applied Biosystems, Foster City, CA
• PCR polymerase chain reaction
• amplification products are quantitated after the PCR is completed
• products in real-time quantitative PCR are quantitated as they accumulate. This is accomplished by including in the PCR reaction an oligonucleotide probe that amieals specifically between the forward and reverse PCR primers, and contains two fluorescent dyes.
• a reporter dye e.g., JOE, FAMTM, or VIC, obtained from either Operon Technologies Inc., Alameda, CA or PE- Applied Biosystems, Foster City, CA
• a quencher dye e.g., TAMRA, obtained from either Operon Technologies Inc., Alameda, CA or PE-Applied Biosystems, Foster City, CA
• reporter dye emission is quenched by the proximity of the 3' quencher dye.
• annealing of the probe to the target sequence creates a substrate that can be cleaved by the 5 '-exonuclease activity of Taq polymerase.
• cleavage of the probe by Taq polymerase releases the reporter dye from the remainder of the probe (and hence from the quencher moiety) and a sequence-specific fluorescent signal is generated.
• additional reporter dye molecules are cleaved from their respective probes, and the fluorescence intensity is monitored at regular intervals by laser optics built into the ABI PRISMTM 7700 Sequence Detection System.
• a series of parallel reactions containing serial dilutions of mRNA from untreated control samples generates a standard curve that is used to quantitate the percent inhibition after antisense oligonucleotide treatment of test samples .
• PCR reagents can be obtained from PE-Applied Biosystems, Foster City, CA.
• RT-PCR reactions are carried out by adding 25 ⁇ L PCR cocktail (lx TAQMANTM buffer A, 5.5 MM MgCl 2 , 300 ⁇ M each of dATP, dCTP and dGTP, 600 ⁇ M of dUTP, 100 nM each of forward primer, reverse primer, and probe, 20 Units RNAse inhibitor, 1.25 Units AMPLITAQ GOLDTM, and 12.5 Units MuLV reverse franscriptase) to 96 well plates containing 25 ⁇ L poly(A) mRNA solution.
• the RT reaction is carried out by incubation for 30 minutes at 48 °C.
• Probes and primers to human Navl .3 were designed to hybridize to a human Navl .3 sequence, using published sequence, information (GenBank accession number NM_006922, inco ⁇ orated herein as Figure 1.
• the PCR primers were: forward primer: TTGACTTTGTGGTGGTGATTCTCT SEQ ID NO : 9097
• PCR probe is: FAM- ACCTTGTTCCGAGTGATCCGTCTTGC SEQ ID NO:
• the PCR probe is: 5' JOE- CGCGTCTCCTTTGAGCTGTTTGCA SEQ ID NO: 1
• oligonucleotides are designed to target different regions of the human Navl.3 RNA, using published sequences (NM_006922, incorporated herein as Figure 1.
• the oligonucleotides are shown in Table 1. "Position" indicates the first (5 '-most) nucleotide number on the particular target sequence to which the oligonucleotide binds.
• the indicated parameters for each oligo were predicted using RNAstructure 3.7 by David H. Mathews, Michael Zuker, and Douglas H. Turner.
• All compounds in Table 1 are chimeric oligonucleotides ("gapmers") 20 nucleotides in length, composed of a central "gap" region consisting often 2'deoxynucleotides, which is flanked on both sides (5' and 3' directions) by four-nucleotide "wings".
• the wings are composed of 2 '-methoxyethyl (2'-MOE) nucleotides.
• Cytidine residues in the 2' -MOE wings are 5- methylcytidines. All cytidine residues are 5-methylcytidines.
• TGCTTTTAATTTGCCTTTGT 8650 SEQ ID NO:58 -21.9 -22.3 66.3 0.3 0 -3.6
• GGGTAGTGCTCCATGGCCAT 2800 SEQ ID NO: 61 -21.5 -30 83.5 -7.4 -0.4 -10 AATTTGCCTTTGTTCTGTAG
• TTGTTCTGTAGTACTGCTTG 8634 SEQ ID NO: 74 -21 -22.4 69.5 -0.7 0 -7.8
• TTTTCTCTGACCTCTTTTCC 6445 SEQ ID NO: 86 -20.5 -24.6 73.4 -4.1 0 -2.2
• TCCCCACGGTCTCCCTTAAC 5680 SEQ ID NO: 91 -20.4 -30.4 79.6 -9.4 -0.3 -3.5
• AAAGTAGGAAGTGGTGTTGG 1337 SEQ ID NO: 94 -20.3 -20.7 63.1 1.7 0 -1.3
• ATCCTTTGCCCGACCTCTGA 2210 SEQ ID NO: 112 -19.7 -29.7 78.8 -10 0 -3
• GATTTCTATAACTTTTGGCT 3569 SEQ ID NO: 114 -19.7 -20.1 61.9 0 0 -3.7 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• AATAGGTTTTGTCAGTAGGC 7784 SEQ ID NO: 116 -19.7 -21.9 67.8 -2.2 0 -2.8
• CTTGTTCCTTTTTGGGCTTC 576 SEQ ID NO:121 -19.5 -25.6 75.8 -5.6 -0.2 -3.8
• ATGTTTTCCCAGCAGCACGT 1650 SEQ ID NO: 122 -19.5 -27.8 77.3 -8.3 0 -5.4
• CCCACGGTCTCCCTTAACTG 5678 SEQ ID NO: 124 -19.5 -28.9 76.4 -9.4 0.2 -3.5
• ATCTTTTCATCCTGCACATT 454 SEQ ID NO:125 -19.4 -23.5 69.5 -4.1 0 -4.8
• GCATCTGAGCCATTTCCACA 1480 SEQ ID NO: 130 -19.3 -27.1 76 -7.8 0 -3.8
• ACCTACTCCACTGAAATCTC 1880 SEQ ID NO: 131 -19.3 -23 66.6 -3.7 0 -2.5
• CAGTAGCAGCAAGGTTGTCT 3438 SEQ ID NO: 138 -19.2 -24.9 74.5 -5.7 0 -4.6
• TTTTTCTGGTTTGTCTTTCT 6416 SEQ ID NO: 262 -18 -22.3 70.2 -4.3 0 -1.5
• CTTCTCTTTCTGACTTCCGT 2506 SEQ ID NO: 272 -17.8 -25.3 74.3 -7.5 0 -2.6
• TTCGAAGATTCCACCAGATC 4041 SEQ ID NO: 283 -17.7 -22.9 65.8 -4.5 -0.4 -6.2
• CTTTTTCTGCTGGTTGAAGT 4880 SEQ ID NO:285 -17.7 -22.9 69.2 -5.2 0 -3.7
• ACGTTTCAAAGTGGTTGTAA 6143 SEQ ID NO:288 -17.7 -20 60.6 -1.6 -0.4 -5.2 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• TAAGCTGTTCGAGCATCTGC 1809 SEQ ID NO:291 -17.6 -24.4 71.1 -4.5 -2.3 -7.6
• CTCACGGCTCTTTGCCTTCC 2572 SEQ ID NO:304 -17.5 -29.6 81.4 -9.9 -2.2 -5.7
• TTCCCATCTCTAAGATAATT 3655 SEQ ID NO:309 -17.5 -20.5 61.5 -2.4 ⁇ -0.3 -4.3
• TTTTCGAAGATTCCACCAGA 4043 SEQ ID NO: 311 -17.5 -22.7 65.1 -4.5 -0.4 -6.8
• TAGCCAGCGCCAACATTATC 4672 SEQ ID NO:312 -17.5 -25.7 70.8 -7.5 -0.5 -7.6
• GCAACTGCCTGAGCTTCTTC 1840 SEQ ID NO: 323 -17.4 -26.8 76.8 -8.2 -1.1 -5.2
• CAGTACAGACAATCCCTCCA 3002 SEQ ID NO:327 -17.4 -25.7 71.8 -7.6 -0.4 -5.3
• TTTCGAAGATTCCACCAGAT 4042 SEQ ID NO:328 -17.4 -22.6 64.7 -4.5 -0.4 -6.8
• TCTAGCATGGTTTTGATAGT 4174 SEQ ID NO: 329 -17.4 -21.7 67.1 -3.4 -0.7 -4.3
• GCCATTAAAGTAGGAAGTGG 1343 SEQ ID NO: 340 -17.3 -21.3 63 -4 0 -3.7
• AGAATAGGTTTTGTCAGTAG 7786 SEQ ID NO: 350 -17.3 -19.5 62.1 -2.2 0 -2.7 TTGCCACTTTGTTCATGGCT
• ATGTGCTGTGTTCATCATCA 2253 SEQ ID NO: 356 -17.2 -23.7 71.9 -6.5 0 -3.6
• TCAGGGGCTCTGCACTTTCT 5808 SEQ ID NO:369 -17.2 -27.8 81.1 -9.6 -0.9 -4.8
• TGTTCCTTTTTGGGCTTCTT 574 SEQ ID NO: 373 -17.1 -25.6 75.8 -8 -0.2 -3.8
• TACAGACAATCCCTCCACAT 2999 SEQ ID NO:375 -17.1 -24.7 68.9 -7.6 0 -2.1 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• ATAGCCAGCGCCAACATTAT 4673 SEQ ID NO:377 -17.1 -25.3 69.3 -7.5 -0.5 -7.6
• AAGATTTTCCCAATAGTCTT 1616 SEQ ID NO: 383 -17 -20.9 62.8 -3.9 0 -3.5
• TTCCTGTTGCTTTTTAAGCT 1823 SEQ ID NO:385 -17 -23.5 69.9 -3.9 -2.6 -7.1
• CAGTCATGGGGTAGTGCTCC 2808 SEQ ID NO:390 -17 -27.8 81.4 -10.3 -0.1 -6.7
• TTCTTTTTCTGCTGGTTGAA 4882 SEQ ID NO:396 -17 -22.2 67.5 -5.2 0 -3.7
• ATTTGAATCCATTGTGCCAT 1358 SEQ ID NO:408 -16.9 -23 66.2 -6.1 0 -3.1
• AGTACAGACAATCCCTCCAC 3001 SEQ ID NO:414 -16.9 -25.2 71.2 -7.6 -0.4 -5.3
• TTTTGTCAGTAGGCAGTATC 7778 SEQ ID NO: 425 -16.9 -22.5 70.6 -5.1 -0.1 -4
• CCAAACTTCTTTTTCTGCTG 4888 SEQ ID NO:430 -16.8 -22.2 65.3 -5.4 0 -3.6
• AATAATCATGTCTTGTTTTA 6290 SEQ ID NO:433 -16.8 -17.2 55.6 1.3 0 -4.7 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• CTTTTCATCCTGCACATTTA 452 SEQ ID NO: 435 -16.7 -22.9 67.7 -6.2 0 -4.8
• AATTGCCTTTCCTTTATTCA 749 SEQ ID NO: 436 -16.7 -22.7 66.6 -6 0 -3
• TTTAAGCTGTTCGAGCATCT 1811 SEQ ID NO: 441 -16.7 -22.8 67.6 -4.5 -1.5 -7.4
• ATCAGTAGCAGCAAGGTTGT 3440 SEQ ID NO: 445 -16.7 -24 72.3 -7.3 0 -5.4
• TTCTGCTGGTTGAAGTTATC 4876 SEQ ID NO: 48 -16.7 -21.9 67.4 -5.2 0 -3.7
• TGTATTCGAAGGGCATCCAT 6070 SEQ ID NO: 450 -16.7 -24.1 68.5 -6.2 -1.1 -8.2
• GGTATCTCATCCCTGTCAAA 266 SEQ ID NO:455 -16.6 -24.7 71.4 -8.1 0 -2.4
• TTGAATCCATTGTGCCATTA 1356 SEQ ID NO:456 -16.6 -22.7 65.7 -6.1 0 -3.1
• AAAGTGGTTGTAATAGGCTC 6136 SEQ ID NO: 463 -16.6 -20.5 62.9 -3.9 0 -3.7
• TATCTCATTTATTCTTACAA 348 SEQ ID NO: 472 -16.5 -17.4 56.2 -0.7 0 -0.9
• ATCATTATCTTGTTCCTTTT 584 SEQ ID NO: 473 -16.5 -21.2 65.6 -4.7 0 -1.9
• TTTTCTGCTGGTTGAAGTTA 4878 SEQ ID NO:480 -16.5 -21.7 66.5 -5.2 0 -3.7
• TTCCTTGGAATTTGTTTGCT 5004 SEQ ID NO:481 -16.5 -22.9 67.7 -5.6 -0.6 -6.3
• ATCCATTGTGCCATTAAAGT 1352 SEQ ID NO: 491 -16.4 -22.5 65.3 -6.1 0 -3.1 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• CCACCAGATCTTCCCTTTGC 4031 SEQ ID NO:498 -16.4 -28.9 78.9 -12.5 0 -5.6
• CCTGTCTTCCATCTGTATTC 6083 SEQ ID NO: 501 -16.4 -25.3 75.2 -8.9 0 -1.6
• ACCCTGCTTCACAGAGTTGC 6638 SEQ ID NO:502 -16.4 -27.6 78.4 -9.9 -1.2 -4.8
• AAATGATCTAGGTTTGAGTG 8100 SEQ ID NO:507 -16.4 -18.6 58.5 -2.2 0 -4.9
• GGTGGTTACTACTATTATTA 8731 SEQ ID NO:510 -16.4 -19.8 62.1 -2.9 -0.1 -3.9
• TTCCTTTTTGGGCTTCTTGG 572 SEQ ID NO: 511 -16.3 -25.6 74.9 -8.8 -0.2 -3.8
• TTTCCCAATAGTCTTGAGTC 1611 SEQ ID NO: 512 -16.3 -23.1 69.4 -6.8 0.3 -3.3
• CTTCCTGTTGCTTTTTAAGC 1824 SEQ ID NO: 513 -16.3 -23.5 69.9 -5.4 -1.8 -6.1
• GAAGATTCCACCAGATCTTC 4038 SEQ ID NO:518 -16.3 -23 67.5 -4.5 -2.2 -6.8
• ATTCCTTGGAATTTGTTTGC 5005 SEQ ID NO: 520 -16.3 -22 65.7 -4.1 -1.5 -8.1 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• GCAGCATAGGCAATATTAAC 7562 SEQ ID NO: 525 -16.3 -20.7 61.8 -2.7 -1.6 -6.7
• TGAATCATGCACTAGTTTGT 8613 SEQ ID NO: 529 -16.3 -20.9 63.7 -4.6 0 -5.7
• ATCTGAGCCATTTCCACAGA 1478 SEQ ID NO: 535 -16.2 -25.2 72.2 -7.8 -1.1 -4.9
• ATCGCAGTACAGACAATCCC 3006 SEQ ID NO: 543 -16.2 -24.7 69.4 -7.8 -0.4 -5.3
• GATACCCTGCTTCACAGAGT 6641 SEQ ID NO:549 -16.2 -26 74.4 -8.5 -1.2 -5.1 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• TTGTCAGTAGGCAGTATCCA 7776 SEQ ID NO:551 -16.2 -25 75.1 -8.3 -0.2 -4
• GAAGAATAGGTTTTGTCAGT 7788 SEQ ID NO:552 -16.2 -19.7 61.7 -3.5 0 -2.7
• TGCTTGTTTTGCTATTGCGT 2181 SEQ ID NO: 564 -16.1 -24.6 71.7 -6.9 -1.5 -5.8
• GTTCCATTCCCATCTCTAAG 3661 SEQ ID NO:567 -16.1 -25.2 72.6 -9.1 0 -1.6
• TTAATACACCCTTCAGTAAA 3976 SEQ ID NO:568 -16.1 -19.5 58.5 -3.4 0 -3.6
• ATACCCTGCTTCACAGAGTT 6640 SEQ ID NO: 570 -16.1 -25.5 73.5 -8.5 -0.7 -5.1
• TTTATTCTTACAATATCCCT 341 SEQ ID NO: 571 -16 -20.3 61.4 -4.3 0 -2.6
• TCCCATCTCTAAGATAATTA 3654 SEQ ID NO:578 -16 -20.1 60.7 -3.4 -0.5 -4.7 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• ATCATGCACTAGTTTGTTGT 8610 SEQ ID NO:586 -16 -22.3 68.5 -6.3 0 -5.7
• TTAAGCTGTTCGAGCATCTG 1810 SEQ ID NO:587 -15.9 -22.7 67.1 -4.5 -2.3 -7.3
• TATTTCAATTCCAGTATTAT 3623 SEQ ID NO:590 -15.9 -18.2 57.6 -2.3 0 -2.5
• TTGCTTATTTCAATTCCAGT 3628 SEQ ID NO: 591 -15.9 -21.6 65.2 -5.7 0 -3.6
• TCATCCTCACTCAGGGGCTC 5818 SEQ ID NO: 594 -15.9 -28.4 82.4 -11.6 -0.8 -7.6
• GCAGCACGTTTTTCGATAGC 541 SEQ ID NO: 600 -15.8 -24.9 71.1 -8.1 -0.9 -5.8
• AATGTGCTGTGTTCATCATC 2254 SEQ ID NO: 602 -15.8 -22.3 68.1 -6.5 0 -3.1
• CTGTTGCGTCGCTCTCCATG 2320 SEQ ID NO: 603 -15.8 -28.3 78.2 -12.5 0.4 -6.2
• AGTTTACTTTCACGTTTTTC 4650 SEQ ID NO: 607 -15.8 -20.5 64 -4.7 0 -4.7 kcal/ mol kcal/mol deg C kcal/mol kcal/mol kcal/mol kcal/mol
• TAAACATGACCAGGAAGAGC 5454 SEQ ID NO: 610 -15.8 -20.2 59.6 -4.4 0 -5.2
• CGGTCTCCCTTAACTGAGCT 5674 SEQ ID NO: 611 -15.8 -27.3 75.6 -10.9 -0.3 -6.2
• GACAGGGTTCTTGTATACTG 6933 SEQ ID NO: 616 -15.8 -22.3 68 -5.8 -0.4 -6.5
• TTAATAGAAGTTGTTTATCA 7441 SEQ ID NO: 618 -15.8 -16.2 53.4 0.4 0 -2.9
• GGTAGAAAATGATCTAGGTT 8106 SEQ ID NO: 622 -15.8 -18.7 58.3 -2.2 -0.4 -4.9
• TTTTTTTTTTTCCACCTTAT 9086 SEQ ID NO: 624 -15.8 -21 63.7 -5.2 0 -0.5
• CATGGATCACGAAGAAACGT 1021 SEQ ID NO: 625 -15.7 -19.9 57.7 -3.4 -0.6 -6
• AGCAGCACGTAATGTCAACT 1640 SEQ ID NO: 628 -15.7 -22.9 66.3 -7.2 0 -5.4
• CTTTGCTTATTTCAATTCCA 3630 SEQ ID NO: 633 -15.7 -21.4 64.1 -5.7 0 -3.6

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