Modified polynucleotides and uses thereof

Abstract

Provided is a polynucleotide comprising mRNA, rRNA or viral RNA, comprising ribose rings that are covalently modified at the 2′-OH position. Further provided are methods for producing a double-stranded oligo- or polynucleotide from a template comprising an oligo- or polyribonucleotide, a proportion of the ribose rings of which are covalently modified at the 2′-OH position to bear a substituent which enables replication of the template by the nucleic acid polymerase. Also provided is use of a poly-nucleotide comprising mRNA, rRNA or viral RNA, a proportion of the ribose rings of which are covalently modified at the 2′-OH position, in a hybridisation reaction

1 . A composition comprising an oligo- or polynucleotide, wherein said oligo- or polynucleotide comprises mRNA, rRNA or viral RNA and a proportion of the ribose rings of said oligo- or polynucleotide are covalently modified at the 2′-OH position.  
     
     
         2 . The composition of  claim 1  wherein: 
 a) said oligo- or polynucleotide is at least any one integer between 1% and 100%, inclusive, of said ribose rings are covalently modified at the 2′-OH position;    b) said oligo- or polynucleotide is at least 10% of said ribose rings are covalently modified at the 2′-OH position;    c) said oligo- or polynucleotide is at least 25% of said ribose rings are covalently modified at the 2′-OH position;    d) said oligo- or polynucleotide is at least 50% of said ribose rings are covalently modified at the 2′-OH position;    e) said oligo- or polynucleotide is at least 75% of said ribose rings are covalently modified at the 2′-OH position;    f) said oligo- or polynucleotide is at least 80% of said ribose rings are covalently modified at the 2′-OH position;    g) said oligo- or polynucleotide is at least 85% of said ribose rings are covalently modified at the 2′-OH position;    h) said oligo- or polynucleotide is at least 90% of said ribose rings are covalently modified at the 2′-OH position;    i) said oligo- or polynucleotide is at least 95% of said ribose rings are covalently modified at the 2′-OH position;    j) said oligo- or polynucleotide is at least 99% of said ribose rings are covalently modified at the 2′-OH position;    k) said 2′-OH position of said ribose rings is covalently modified so that a single strand of the polynucleotide is replicable by a nucleic acid polymerase to generate a second strand of polynucleotide complementary to the single strand;    l) at least some of said ribose rings bear at the 2′-OH position a substituent which is labeled with a label, and optionally wherein said label comprises a fluorescent label, a radioactive label, an enzyme, a ligand or an affinant for a label;    m) said ribose rings bear at the 2′-OH position a substituent, OR, wherein R comprises a moiety selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, C1-C10 haloalkoxyalkyl, C1-C10 aminoalkoxyalkyl, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 arylalkyl, C6-C14 arylalkenyl, C1-C10 alkanoyl, C1-C10 alkenoyl, C1-C10 haloalkanoyl, C1-C10 dihaloalkanoyl, C1-C10 trihaloalkanoyl, C2-C10 haloformylalkanoyl, C1-C10 aminoalkanoyl, C6-C14 arylalkanoyl, C6-C14 arylalkenoyl, C1-C10 alkoxyalkanoyl, C6-C14 aryloxyalkanoyl, C6-C14 alkylarylalkanoyl, C1-C10 azidoalkanoyl, C1-C10 carboxyalkanoyl, C1-C10 carboxyalkenoyl, C1-C10 carboxyalkynoyl, C6-C14 haloarylalkanoyl, C6-C14 aminoarylalkanoyl, C7-C15 alkylaminoarylalkanoyl, C1-C10 haloalkenoyl, C1-C10 haloalkynoyl, C1-C10 alkylsilanyl, C3-C10 trialkylsilanyl C1-C10 alkoxycarbonyl, C3-C18 alkylthioalkoxyalkoxycarbonyl, C1-C10 alkenyloxycarbonyl, C3-C18 alkoxyalkoxyalkyl, C2-C12 alkoxyalkyl, C2-C12 alkylthioalkyl, C1-C10 alkylsulfonyl, and C12-C28 diarylphosphone; or a substituent R′, wherein R′ is selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, halo, amino, C1-C10 alkylamino, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 and arylalkyl; or more specifically wherein R is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, methoxymethyl, methylthiomethyl, methoxyethoxymethyl, (2-chloroethyl)oxyethyl, (2-aminoethyl) oxyethyl, phenyl, 4-methylphenyl, benzyl, cinnamyl, formyl, acetyl, propanoyl, butanoyl, pentanoyl, hexanoyl, heptanoyl, octanoyl, nonanoyl, pivaloyl, isobutanoyl, isopentanoyl, carboxyacetyl, chloroformylnonanoyl, 3-carboxypropanoyl, 4-aminobutanoyl, 4-chlorobutanoyl chloroacetyl, dichloroacetyl, trifluoroacetyl, trichloroacetyl, 3-azidopropanoyl, 4-azidobutyryl acryloyl, propioloyl, crotonoyl, benzoyl, diphenylacetyl, phenoxyacetyl, methoxyacetyl, methoxycarbonyl, 2-(methylthiomethoxy)ethoxycarbonyl, vinyloxycarbonyl, 4-methylbenzoyl, 4-chlorobenzoyl, 2-methylaminobenzoyl, 2-aminobenzoyl, 4-aminobenzoyl, 4-nitrobenzoyl, cinnamoyl, silanyl, trimethylsilanyl, triethylsilanyl, tripropylsilanyl, triisopropylsilanyl, t-butyldimethylsilanyl, 2-chlorophenyl (4-nitrophenyl)phosphono, and methylsulfonyl; or a substituent R′, wherein R′ is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, t-butyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, phenyl, benzyl, fluoro, chloro, bromo, iodo, and amino;    n) said mRNA, rRNA or viral RNA is naturally-occurring;    o) said mRNA, rRNA or viral RNA comprises cellular RNA; or    p) said composition comprises a mixture of polynucleotides, wherein said mixture comprises cellular mRNA, rRNA or viral RNA.    
     
     
         3 . A method of using a modified oligo- or polynucleotide wherein a proportion of the ribose rings of said polynucleotide are covalently modified at the 2′-OH position for: 
 a) producing the modified oligo- or polynucleotide comprising the steps of: 
 (1) contacting in a reaction medium RNA comprising an oligo- or poly-ribonucleotide with a reaction system comprising a reactant capable of covalently modifying the 2′-OH position of the ribose rings of the RNA;  
 (2) reacting the RNA with the reaction system to produce modified oligo- or polynucleotide under conditions to achieve covalent modification of greater than 25% of the 2′-OH positions of the ribose rings; and  
 (3) optionally separating the modified oligo- or polynucleotide from the reaction medium, wherein the reaction medium comprises at least 20% v/v organic solvent and the reaction system is capable of achieving the covalent modification in one hour or less;  
   b) replicating a modified RNA comprising: obtaining the modified RNA of  claim 1;  and replicating the modified RNA to form a complementary polynucleotide using a nucleic acid polymerase; and optionally wherein said complementary polynucleotide comprises a cDNA and said nucleic acid polymerase comprises a DNA polymerase, or wherein said method further comprises a step of ligating said complementary polynucleotide, either a single or double stranded, to a vector polynucleotide;    c) protecting and deprotecting RNA comprising: obtaining the RNA of  claim 1;  reacting the modified oligo- or polynucleotide with a reactant capable of removing the substituent under conditions to reinstate an —OH group at the 2′-OH position;    d) a nucleic acid sequencing method or for the preparation of a medicament for binding specifically to an in vivo target to achieve a therapeutic, prophylactic or diagnostic effect;    e) producing a double-stranded oligo- or polynucleotide from a template, which comprises contacting the template with a plurality of mononucleotides comprising UTP, dTTP and/or dUTP, ATP and/or dATP, GTP and/or dGTP, and CTP and/or dCTP, in the presence of a nucleic acid polymerase, and optionally a template primer under conditions to polymerize the mononucleotides to form a nucleic acid strand complementary to the template, wherein the template comprises an oligo- or polyribonucleotide, a proportion of the ribose rings of which are covalently modified at the 2′-OH position to bear a substituent which enables replication of the template by the nucleic acid polymerase, and further optionally wherein; 
 (1) at least 25% of the ribose rings are covalently modified at the 2′-OH position;  
 (2) at least 90% of the ribose rings are covalently modified at the 2′-OH position;  
 (3) said ribose rings bear at the 2′-OH position a substituent, OR, wherein R comprises a moiety selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, C1-C10 haloalkoxyalkyl, C1-C10 aminoalkoxyalkyl, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 -arylalkyl, C6-C14 arylalkenyl, C1-C10 alkanoyl, C1-C10 alkenoyl, C1-C10 haloalkanoyl, C1-C10 dihaloalkanoyl, C1-C10 trihaloalkanoyl, C2-C10 haloformylalkanoyl, C1-C10 aminoalkanoyl, C6-C14 arylalkanoyl, C6-C14 arylalkenoyl, C1-C10 alkoxyalkanoyl, C6-C14 aryloxyalkanoyl, C6-C14 alkylarylalkanoyl, C1-C10 azidoalkanoyl, C1-C10 carboxyalkanoyl, C1-C10 carboxyalkenoyl, C1-C10 carboxyalkynoyl, C6-C14 haloarylalkanoyl, C6-C14 aminoarylalkanoyl, C7-C15 alkylaminoarylalkanoyl, C1-C10 haloalkenoyl, C1-C10 haloalkynoyl, C1-C10 alkylsilanyl, C3-C10 trialkylsilanyl C1-C10 alkoxycarbonyl, C3-C18 alkylthioalkoxyalkoxycarbonyl, C1-C10 alkenyloxycarbonyl, C3-C18 alkoxyalkoxyalkyl, C2-C12 alkoxyalkyl, C2-C12 alkylthioalkyl, C1-C10 alkylsulfonyl, and C12-C28 diarylphosphone; or a substituent R′, wherein R′ is selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, halo, amino, C1-C10 alkylamino, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 and arylalkyl; or more specifically wherein R is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, methoxymethyl, methylthiomethyl, methoxyethoxymethyl, (2-chloroethyl)oxyethyl, (2-aminoethyl) oxyethyl, phenyl, 4-methylphenyl, benzyl, cinnamyl, formyl, acetyl, propanoyl, butanoyl, pentanoyl, hexanoyl, heptanoyl, octanoyl, nonanoyl, pivaloyl, isobutanoyl, isopentanoyl, carboxyacetyl, chloroformylnonanoyl, 3-carboxypropanoyl, 4-aminobutanoyl, 4-chlorobutanoyl chloroacetyl, dichloroacetyl, trifluoroacetyl, trichloroacetyl, 3-azidopropanoyl, 4-azidobutyryl acryloyl, propioloyl, crotonoyl, benzoyl, diphenylacetyl, phenoxyacetyl, methoxyacetyl, methoxycarbonyl, 2-(methylthiomethoxy)ethoxycarbonyl, vinyloxycarbonyl, 4-methylbenzoyl, 4-chlorobenzoyl, 2-methylaminobenzoyl, 2-aminobenzoyl, 4-aminobenzoyl, 4-nitrobenzoyl, cinnamoyl, silanyl, trimethylsilanyl, triethylsilanyl, tripropylsilanyl, triisopropylsilanyl, t-butyldimethylsilanyl, 2-chlorophenyl (4-nitrophenyl)phosphono, and methylsulfonyl; or a substituent R′, wherein R′ is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, t-butyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, phenyl, benzyl, fluoro, chloro, bromo, iodo, and amino;  
 (4) the template comprises mRNA, rRNA or viral RNA;  
 (5) the template comprises cellular RNA;  
 (6) the template comprises a mixture of RNA;  
 (7) the oligo- or polynucleotide is modified by: 
 (i) contacting in a reaction medium RNA comprising an oligo or poly-ribonucleotide with a reactant capable of covalently modifying the 2′-OH position of the ribose rings of the RNA;  
 (ii) reacting the RNA with the reactant to produce modified oligo- or polynucleotide under conditions to achieve covalent modification of a proportion of the 2′-OH positions of the ribose rings; and  
 (iii) optionally separating the modified oligo- or polynucleotide from the reaction medium, wherein the reaction medium comprises an organic solvent; and further optionally wherein; 
 (A) the reaction medium comprises at least 20% organic solvent;  
 (B) the reactant comprises an acid anhydride, an acid chloride, a carboxylic acid, an N-acylimidazole, an alkoxyalkyl halide, an alkylthioalkyl halide, an alkoxyalkoxyalkyl halide, a trialkylsilane halide or a trialkylsilane imidazole; and further optionally wherein the reaction medium further comprises an acylation catalyst;  
 (C) the organic solvent comprises an organic base; or  
 (D) the organic base is the organic solvent;  
 
 
 (8) the nucleic acid polymerase comprises an RNA-dependent DNA polymerase, or more specifically wherein the RNA-dependent DNA polymerase is selected from the group consisting of: Superscript™ II (MMLV reverse transcriptase RNase H—), MMLV reverse transcriptase, HIV reverse transcriptase, AMV reverse transcriptase, RAV-2 reverse transcriptase, human T-cell leukemia virus type I (HTLV-I) reverse transcriptase, bovine leukemia virus (BLV), Rous Sarcoma virus (RSV), Tth DNA polymerase, Tfl DNA polymerase, Bst polymerase, Taq DNA polymerase, Thermoscript, C.therm polymerase, displaythermo-RT and Klenow DNA polymerase;  
 (9) the nucleic acid polymerase comprises a DNA-dependent DNA polymerase; or wherein the DNA-dependent DNA polymerase is selected from the group consisting of DNA polymerase I; DNA polymerase I-Klenow fragment; T4 DNA polymerase; T7 DNA polymerase; Taq DNA polymerase, Tli DNA polymerase, Pfu DNA polymerase; Vent™ DNA polymerase; DeepVent™ DNA polymerase; Bst DNA polymerase; Tth; Pfu Turbo™, Pfu(exo-), Pwo, Pyra™, Tfu, KlenTaq, Taq2000™, AmpliTaq; Stoffel fragment, Sequenase™, Tma, Vent® (exo-), DeepVent® (exo-), and a DNA polymerase purified from an organism selected from the group consisting of:  Thermosipho africanus, Thermotoga maritima, Desulfurococcus mobilis, Methanobacterium thermoautotrophicum, Methanothermus fervidus, Pyrococcus furious, Pyrodictium occultum, Sulfolobus acidocaldarius, S. solfataricus, Thermococcus litoralis  and  Thermoplasma acidophilum;    
 (10) wherein the nucleic acid polymerase comprises an RNA-dependent RNA polymerase; or wherein the RNA dependent RNA polymerase is selected from the group consisting of: Q beta replicase, a polymerase derived from  E. coli  phage f2, R17, MS-2 or 06, and a polymerase from a virus family selected from any one of:  
   bromoviridae, flaviviridae, picornaviridae, potyviridae, tobarnovirus, tombusviridae, leviviruses, hepatitis C-like viruses, and picomaviruses or from polio virus, yellow fever virus, tobacco mosaic virus, brome mosaic virus, influenza virus, reovirus, myxovirus, rhabdovirus and paramyxovirus;    f) replicating an oligo- or polynucleotide comprising providing the oligo- or polynucleotide as a template comprising an oligo- or polyribonucleotide, a proportion of the ribose rings of which oligo- or polyribonucleotide are covalently modified at the2′-OH position; 
 (1) producing from the template a double-stranded oligo- or polynucleotide and ligating the double-stranded oligo- or polynucleotide into a vector;  
 (2) ligating the template into a vector and producing from the template in the vector a double-stranded oligo- or polynucleotide; or  
 (3) producing from the template a double-stranded oligo- or polynucleotide in and obtaining from the double-stranded oligo- or polynucleotide the nucleic acid strand complementary to the template and ligating the nucleic acid strand into a vector; and replicating the vector in a host;  
   g) amplifying an oligo- or polynucleotide comprising:    (1) providing the template comprising an oligo- or polyribonucleotide, a proportion of the ribose rings of which oligo- or polyribonucleotide are covalently modified at the 2′-OH position; and, either; 
 (2) (A) producing from the template a double-stranded oligo- or polynucleotide; 
 (B) melting each double-stranded oligo- or polynucleotide to form single strands;  
 (C) annealing the template primer to the single strand having the nucleotide sequence of the template and annealing a second primer to the strand complementary thereto to form primed single strands;  
 (D) contacting the primed single strands with the plurality of mononucleotides in the presence of the nucleic acid polymerase to form double-stranded oligo- or polynucleotides, and optionally repeating steps (B) to (D) until sufficient amplification is achieved; and  
 (E) harvesting the amplified oligo- or polynucleotide in single or double-stranded form; or (3) (A) providing the oligo- or polynucleotide as a template comprising an oligo- or polyribonucleotide, a proportion of the ribose rings of which oligo- or polyribonucleotide are covalently modified at the 2′-OH position;  
 (B) amplifying the template in a nucleic acid sequence based amplification; and  
 (C) harvesting the amplified oligo- or polynucleotide in single or double-stranded form, wherein the step of amplifying the template includes producing from the template a double stranded oligo- or polynucleotide;  
 
   h) the production of a nucleic strand complementary to a template comprising contacting said template with a polymerase under conditions which allow the replication of said template by said polymerase;    i) diagnosing in a subject a disease indicated by the presence or absence of a target nucleotide sequence, which method comprises: (1) obtaining an oligo- or polynucleotide sample from the subject; (2) amplifying the oligo- or polynucleotide in accordance with the method of claim  1 g) to form an amplified oligo- or polynucleotide; and (3) analyzing the amplified oligo- or polynucleotide for the target nucleotide sequence;    j) a hybridization reaction comprising using of a first polynucleotide comprising mRNA, rRNA or viral RNA, a proportion of the ribose rings of which are covalently modified at the 2′-OH position; and contacting said first polynucleotide to a second polynucleotide under conditions which allows hybridization of said first polynucleotide to said second polynucleotide;    k) a hybridization reaction according to claim  3 (j), wherein: 
 (1) said hybridization reaction comprises a hybridization between a probe and a template comprising the polynucleotide, and optionally wherein the probe comprises a branched DNA probe;  
 (2) said polynucleotide comprises a mixture of oligo- or polynucleotides;  
 (3) said hybridization reaction comprises a hybridization between a template and a probe comprising the polynucleotide;  
 (4) said probe or the template is immobilized to a solid phase, and optionally further wherein; said solid phase comprises a hybridization membrane, a bead, a particle, a sheet, a gel, a matrix, a filter, an etched silicon device, a vessel, a microtiter strip, tube, fiber or capillary; and further optionally wherein the solid phase comprises a biochip; and further optionally wherein the probe is immobilized and comprises oligo(dT), whereby the template is purified from contaminants;  
 (5) said hybridization reaction comprises a blotting process;  
 (6) said probe or template is attached to another molecule or group of molecules;  
 (7) said probe or the template is labeled with a label, and optionally wherein said label comprises a fluorescent label, a radioactive label, an enzyme, a ligand or an affinant for a label;  
 (8) said polynucleotide comprises an antisense agent;  
 (9) said polynucleotide has a specific binding affinity to a ligand and the hybridization reaction comprises a hybridization between the polynucleotide and a target comprising the ligand, and optionally wherein said RNA comprises a ribozyme;  
 (10) said hybridization reaction comprises a ligase chain reaction;  
 (11) said hybridization reaction comprises a nuclease protection assay in which unhybridised polynucleotide is digested and remaining polynucleotide analyzed;  
 (12) said hybridization reaction comprises gene expression analysis;  
 (13) said method is a diagnostic assay based on the presence or absence of a specified nucleotide sequence;  
 (14) said hybridization comprises in situ hybridization;  
 (15) at least 75% of the ribose rings are covalently modified at the 2′-OH position;  
 (16) said ribose rings bear at the 2′-OH position a substituent, OR, wherein R comprises a moiety selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, C1-C10 haloalkoxyalkyl, C1-C10 aminoalkoxyalkyl, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 arylalkyl, C6-C14 arylalkenyl, C1-C10 alkanoyl, C1-C10 alkenoyl, C1-C10 haloalkanoyl, C1-C10 dihaloalkanoyl, C1-C10 trihaloalkanoyl, C2-C10 haloformylalkanoyl, C1-C10 aminoalkanoyl, C6-C14 arylalkanoyl, C6-C14 arylalkenoyl, C1-C10 alkoxyalkanoyl, C6-C14 aryloxyalkanoyl, C6-C14 alkylarylalkanoyl, C1-C10 azidoalkanoyl, C1-C10 carboxyalkanoyl, C1-C10 carboxyalkenoyl, C1-C10 carboxyalkynoyl, C6-C14 haloarylalkanoyl, C6-C14 aminoarylalkanoyl, C7-C15 alkylaminoarylalkanoyl, C1-C10 haloalkenoyl, C1-C10 haloalkynoyl, C1-C10 alkylsilanyl, C3-C10 trialkylsilanyl C1-C10 alkoxycarbonyl, C3-C18 alkylthioalkoxyalkoxycarbonyl, C1-C10 alkenyloxycarbonyl, C3-C18 alkoxyalkoxyalkyl, C2-C12 alkoxyalkyl, C2-C12 alkylthioalkyl, C1-C10 alkylsulfonyl, and C12-C28 diarylphosphone,; or a substituent R′, wherein R′ is selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, halo, amino, C1-C10 alkylamino, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 and arylalkyl; or more specifically wherein R is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, methoxymethyl, methylthiomethyl, methoxyethoxymethyl, (2-chloroethyl)oxyethyl, (2-aminoethyl) oxyethyl, phenyl, 4-methylphenyl, benzyl, cinnamyl, formyl, acetyl, propanoyl, butanoyl, pentanoyl, hexanoyl, heptanoyl, octanoyl, nonanoyl, pivaloyl, isobutanoyl, isopentanoyl, carboxyacetyl, chloroformylnonanoyl, 3-carboxypropanoyl, 4-aminobutanoyl, 4-chlorobutanoyl chloroacetyl, dichloroacetyl, trifluoroacetyl, trichloroacetyl, 3-azidopropanoyl, 4-azidobutyryl acryloyl, propioloyl, crotonoyl, benzoyl, diphenylacetyl, phenoxyacetyl, methoxyacetyl, methoxycarbonyl, 2-(methylthiomethoxy)ethoxycarbonyl, vinyloxycarbonyl, 4-methylbenzoyl, 4-chlorobenzoyl, 2-methylaminobenzoyl, 2-aminobenzoyl, 4-aminobenzoyl, 4-nitrobenzoyl, cinnamoyl, silanyl, trimethylsilanyl, triethylsilanyl, tripropylsilanyl, triisopropylsilanyl, t-butyldimethylsilanyl, 2-chlorophenyl (4-nitrophenyl)phosphono, and methylsulfonyl; or a substituent R′, wherein R′ is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, t-butyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, phenyl, benzyl, fluoro, chloro, bromo, iodo, and amino;  
 (17) said mRNA, rRNA or viral RNA is naturally-occurring; or  
 (18) said mRNA, rRNA or viral RNA comprises cellular RNA;  
   1) hybridizing a first oligo- or polynucleotide with a second modified polynucleotide comprising mRNA, rRNA or viral RNA, a proportion of the ribose rings of which are covalently modified at the 2′-OH position, comprising contacting said first oligo- or polynucleotide with said second polynucleotide under conditions that allow hybridization between said first oligo- or polynucleotide with said second polynucleotide;    m) hybridizing a first oligo- or polynucleotide with a second modified polynucleotide according to claim  3 (l), wherein the method further comprises: contacting in a reaction medium mRNA, rRNA or viral RNA with a reactant capable of covalently modifying the 2′-OH position of the ribose rings of the RNA; reacting said mRNA, rRNA or viral RNA with said reactant to produce a modified polynucleotide, wherein said modification is a covalent modification of a proportion of the 2′-OH positions of the ribose rings; and optionally separating the modified polynucleotide from the reaction medium, wherein the reaction medium comprises an organic solvent; or 
 n) producing a modified oligo- or polynucleotide according to claim  3 (a), wherein: 
 (1) at least 75% of the ribose rings are covalently modified at the 2′-OH position;  
 (2) at least 90% of the ribose rings are covalently modified at the 2′-OH position;  
 (3) said 2′-OH position of the ribose rings is covalently modified so that a single strand of the oligo- or polynucleotide is replicable by a nucleic acid polymerase to generate a second strand of a polynucleotide complementary to the single strand;  
 (4) at least some of the reactant is labeled with a label, and optionally wherein said label comprises a fluorescent label, a radioactive label, an enzyme, a ligand or an affinant for a label;  
 (5) said reactant is chosen such that the modified ribose rings bear at the 2′-OH position a substituent, OR, wherein R comprises a moiety selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, C1-C10 -haloalkoxyalkyl, C1-C10 aminoalkoxyalkyl, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 arylalkyl, C6-C14 arylalkenyl, C1-C10 alkanoyl, C1-C10 alkenoyl, C1-C10 haloalkanoyl, C1-C10 dihaloalkanoyl, C1-C10 trihaloalkanoyl, C2-C10 haloformylalkanoyl, C1-C10 aminoalkanoyl, C6-C14 arylalkanoyl, C6-C14 arylalkenoyl, C1-C10 alkoxyalkanoyl, C6-C14 aryloxyalkanoyl, C6-C14 alkylarylalkanoyl, C1-C10 azidoalkanoyl, C1-C10 carboxyalkanoyl, C1-C10 carboxyalkenoyl, C1-C10 carboxyalkynoyl, C6-C14 haloarylalkanoyl, C6-C14 aminoarylalkanoyl, C7-C15 alkylaminoarylalkanoyl, C1-C10 haloalkenoyl, C1-C10 haloalkynoyl, C1-C10 alkylsilanyl, C3-C10 trialkylsilanyl, C1-C10 alkoxycarbonyl, C3-C18 alkylthioalkoxyalkoxycarbonyl, C1-C10 alkenyloxycarbonyl, C3-C18 alkoxyalkoxyalkyl, C2-C12 alkoxyalkyl, C2-C12 alkylthioalkyl, C1-C10 alkylsulfonyl, and C12-C28 diarylphosphone; or a substituent R1, wherein R′ is selected from the group consisting of C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, halo, amino, C1-C10 alkylamino, C6-C14 aryl, C6-C14 alkylaryl, and C6-C14 arylalkyl; or more specifically wherein R is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, methoxymethyl, methylthiomethyl, methoxyethoxymethyl, (2-chloroethyl)oxyethyl, (2-aminoethyl)oxyethyl, phenyl, 4-methylphenyl, benzyl, cinnamyl, formyl, acetyl, propanoyl, butanoyl, pentanoyl, hexanoyl, heptanoyl, octanoyl, nonanoyl, pivaloyl, isobutanoyl, isopentanoyl, carboxyacetyl, chloroformylnonanoyl, 3-carboxypropanoyl, 4-aminobutanoyl, 4-chlorobutanoyl chloroacetyl, dichloroacetyl, trifluoroacetyl, trichloroacetyl, 3-azidopropanoyl, 4-azidobutyryl acryloyl, propioloyl, crotonoyl, benzoyl, diphenylacetyl, phenoxyacetyl, methoxyacetyl, methoxycarbonyl, 2-(methylthiomethoxy)ethoxycarbonyl, vinyloxycarbonyl, 4-methylbenzoyl, 4-chlorobenzoyl, 2-methylaminobenzoyl, 2-aminobenzoyl, 4-aminobenzoyl, 4-nitrobenzoyl, cinnamoyl, silanyl, trimethylsilanyl, triethylsilanyl, tripropylsilanyl, triisopropylsilanyl, t-butyldimethylsilanyl, 2-chlorophenyl (4-nitrophenyl)phosphono, and methylsulfonyl; or wherein R′ is selected from the group consisting of methyl, ethyl, vinyl, allyl, ethynyl, t-butyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, phenyl, benzyl, fluoro, chloro, bromo, iodo, and amino; and optionally wherein said reactant further comprises a compound selected from the group consisting of: acid anhydride, an acid chloride, a carboxylic acid, an N-acylimidazole, an alkoxyalkyl halide, an alkylthioalkyl halide, an alkoxyalkoxyalkyl halide, a trialkylsilane halide and a trialkylsilane imidazole;  
 (6) said reaction medium further comprises an acylation catalyst;  
 (7) said RNA is reacted with the acid anhydride and the acylation catalyst comprises a fluoride ion or aminopyridine catalyst;  
 (8) said RNA is reacted with the acid chloride and the acylation catalyst comprises an aminopyridine catalyst;  
 (9) said RNA is reacted with the N-acylimidazole and the acylation catalyst comprises an aminopyridine catalyst;  
 (10) said reaction medium further comprises water; and optionally wherein: 
 (A) said water and the organic solvent form two different phases in the reaction medium;  
 (B) said RNA is reacted with the reactant under conditions of phase transfer catalysis; (iii) said water and organic solvent are in a water:organic solvent weight ration in a range from 1:50 to 1:10;  
 
 (11) said reactant comprises a carboxylic acid in the presence of a dehydrating agent or an isocyanide catalyst;  
 (12) said reactant comprises an O-silylation agent, and optionally wherein said RNA is reacted with said O-silylation agent in the presence of an aminopyridine or lithium sulfide catalyst;  
 (13) said organic solvent comprises an organic base, and optionally wherein said organic base is the organic solvent;  
 (14) said reaction conditions are such that the covalent modification of the 2′-OH positions of the ribose rings is substantially regiospecific;  
 (15) said method further comprises, prior to said step (1) of claim  3 (a), a step of protecting the exocyclic amino groups of the bases of the RNA with a protecting group; and after said step (2) of claim  3 (a), a step of deprotecting the exocyclic amino groups by removing the protecting group; and optionally wherein said protecting group is benzoyl, N-phenoacetyl or NN-dimethylaminomethylene for adenine; benzoyl for cytosine; and isobutyl, N-phenoacetyl or N,N dimethylaminomethylene for guanine;  
 (16) said RNA comprises mRNA, rRNA or viral RNA;  
 (17) said RNA is attached to a solid phase; or  
 (18) said RNA comprises an RNA sample from a cell or blood extract, and optionally wherein said method further comprises a method for gene expression analysis comprising the steps of: (A) obtaining a polynucleotide comprising an mRNA sample from said extract, and (B) analyzing the polynucleotide.  
 
   
     
     
         4 . A kit comprising: 
 A(a) an organic solvent; and    A(b) a reaction system comprising a reactant capable of covalently modifying the 2′-OH position of the ribose rings of the oligo- or poly-ribonucleotide in the presence of the organic solvent, which reaction system is capable of achieving the covalent modification in one hour or less, and optionally wherein; 
 (1) said reactant is chosen such that the modified ribose rings bear at the 2′-OH position a substituent, OR, wherein R comprises a moiety selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, C1-C10 haloalkoxyalkyl, C1-C10 aminoalkoxyalkyl, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 arylalkyl, C6-C14 arylalkenyl, C1-C10 alkanoyl, C1-C10 alkenoyl, C1-C10 haloalkanoyl, C1-C10 dihaloalkanoyl, C1-C10 trihaloalkanoyl, C2-C10 haloformylalkanoyl, C1-C10 aminoalkanoyl, C6-C14 arylalkanoyl, C6-C14 arylalkenoyl, C1-C10 alkoxyalkanoyl, C6-C14 aryloxyalkanoyl, C6-C14 alkylarylalkanoyl, C1-C10 azidoalkanoyl, C1-C10 carboxyalkanoyl, C1-C10 carboxyalkenoyl, C1-C10 carboxyalkynoyl, C6-C14 haloarylalkanoyl, C6-C14 aminoarylalkanoyl, C7-C15 alkylaminoarylalkanoyl, C1-C10 haloalkenoyl, C1-C10 haloalkynoyl, C1-C10 alkylsilanyl, C3-C10 trialkylsilanyl C1-C10 alkoxycarbonyl, C3-C18 alkylthioalkoxyalkoxycarbonyl, C1-C10 alkenyloxycarbonyl, C3-C18 alkoxyalkoxyalkyl, C2-C12 alkoxyalkyl, C2-C12 alkylthioalkyl, C1-C10 alkylsulfonyl, and C12-C28 -diarylphosphone,; or a substituent R′, wherein R′ is selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, halo, amino, C1-C10 alkylamino, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 and arylalkyl; or more specifically wherein R is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, methoxymethyl, methylthiomethyl, methoxyethoxymethyl, (2-chloroethyl)oxyethyl, (2-aminoethyl) oxyethyl, phenyl, 4-methylphenyl, benzyl, cinnamyl, formyl, acetyl, propanoyl, butanoyl, pentanoyl, hexanoyl, heptanoyl, octanoyl, nonanoyl, pivaloyl, isobutanoyl, isopentanoyl, carboxyacetyl, chloroformylnonanoyl, 3-carboxypropanoyl, 4-aminobutanoyl, 4-chlorobutanoyl chloroacetyl, dichloroacetyl, trifluoroacetyl, s5 trichloroacetyl, 3-azidopropanoyl, 4-azidobutyryl acryloyl, propioloyl, crotonoyl, benzoyl, diphenylacetyl, phenoxyacetyl, methoxyacetyl, methoxycarbonyl, 2-(methylthiomethoxy)ethoxycarbonyl, vinyloxycarbonyl, 4-methylbenzoyl, 4-chlorobenzoyl, 2-methylaminobenzoyl, 2-aminobenzoyl, 4-aminobenzoyl, 4-nitrobenzoyl, cinnamoyl, silanyl, trimethylsilanyl, triethylsilanyl, tripropylsilanyl, triisopropylsilanyl, t-butyldimethylsilanyl, 2-chlorophenyl (4-nitrophenyl)phosphono, and methylsulfonyl; or a substituent R′, wherein R′ is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, t-butyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, phenyl, benzyl, fluoro, chloro, bromo, iodo, and amino;  
   (2) said reactant comprises an acid anhydride, an acid chloride, a carboxylic acid, an N-acylimidazole, an alkoxyalkyl halide, an alkylthioalkyl halide, an alkoxyalkoxyalkyl halide, a trialkylsilane halide or a trialkylsilane imidazole, and optionally wherein; 
 (A) said reaction system further comprises an acylation catalyst; and further optionally wherein; 
 (i) said acid anhydride and said acylation catalyst comprises a fluoride ion or aminopyridine catalyst;  
 (ii) said reactant comprises the acid chloride and said acylation catalyst comprises an aminopyridine catalyst; or  
 (iii) said reactant comprises the N-acylimidazole and said acylation catalyst comprises an aminopyridine catalyst; or  
 
 (B) said reactant comprises a carboxylic acid in the presence of a dehydrating agent or an isocyanide catalyst; or  
   (3) said reactant comprises an O-silylation agent in the presence of an aminopyridine or lithium sulfide catalyst, and optionally wherein said organic solvent comprising an organic base, and further optionally wherein said organic base is the organic solvent; or    B(a) a nucleic acid polymerase;    B(b) a reaction system for modifying the oligo- or polynucleotide to form a template, wherein reaction system optionally comprises: 
 (1) an organic solvent; and  
 (2) a reactant capable of covalently modifying the 2′-OH position of the ribose rings of the oligo- or polyribonucleotide in the presence of the organic solvent;  
   B(c) a plurality of mononucleotides comprising UTP, dTTP and/or dUTP, ATP and/or dATP, GTP and/or dGTP, and CTP and/or dCTP; and    B(d) a buffer for the nucleic acid polymerase; or    C(a) a nucleic acid polymerase;    C(b) a reaction system for modifying the oligo- or polynucleotide to form a template, wherein reaction system optionally comprises: 
 (1) an organic solvent; and  
 (2) a reactant capable of covalently modifying the 2′-OH position of the ribose rings of the oligo- or polyribonucleotide in the presence of the organic solvent;  
   C(c) a plurality of mononucleotides comprising UTP, dTTP and/or dUTP, ATP and/or dATP, GTP and/or dGTP, and CTP and/or dCTP; and    C(d) a buffer for the nucleic acid polymerase;    wherein the said reactant is chosen such that the modified ribose rings bear at the 2′-OH position a substituent, OR, wherein R′ comprises a moiety selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, C1-C10 haloalkoxyalkyl, C1-C10 aminoalkoxyalkyl, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 arylalkyl, C6-C14 arylalkenyl, C1-C10 alkanoyl, C1-C10 alkenoyl, C1-C10 haloalkanoyl, C1-C10 dihaloalkanoyl, C1-C10 trihaloalkanoyl, C2-C10 haloformylalkanoyl, C1-C10 aminoalkanoyl, C6-C14 arylalkanoyl, C6-C14 arylalkenoyl, C1-C10 alkoxyalkanoyl, C6-C14 aryloxyalkanoyl, C6-C14 alkylarylalkanoyl, C1-C10 azidoalkanoyl, C1-C10 carboxyalkanoyl, C1-C10 carboxyalkenoyl, C1-C10 carboxyalkynoyl, C6-C14 haloarylalkanoyl, C6-C14 aminoarylalkanoyl, C7-C15 alkylaminoarylalkanoyl, C1-C10 haloalkenoyl, C1-C10 haloalkynoyl, C1-C10 alkylsilanyl, C3-C10 trialkylsilanyl, C1-C10 alkoxycarbonyl, C3-C18 alkylthioalkoxyalkoxycarbonyl, C1-C10 alkenyloxycarbonyl, C3-C18 alkoxyalkoxyalkyl, C2-C12 alkoxyalkyl, C2-C12 alkylthioalkyl, C1-C10 alkylsulfonyl, and C12-C28 diarylphosphone; or a substituent R′, wherein R′ is selected from the group consisting of C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, halo, amino, C1-C10 alkylamino, C6-C14 aryl, C6-C14 alkylaryl, and C6-C14 arylalkyl; or more specifically wherein R is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, methoxymethyl, methylthiomethyl, methoxyethoxymethyl, (2-chloroethyl)oxyethyl, (2-aminoethyl)oxyethyl, phenyl, 4-methylphenyl, benzyl, cinnamyl, formyl, acetyl, propanoyl, butanoyl, pentanoyl, hexanoyl, heptanoyl, octanoyl, nonanoyl, pivaloyl, isobutanoyl, isopentanoyl, carboxyacetyl, chloroformylnonanoyl, 3-carboxypropanoyl, 4-aminobutanoyl, 4-chlorobutanoyl chloroacetyl, dichloroacetyl, trifluoroacetyl, trichloroacetyl, 3-azidopropanoyl, 4-azidobutyryl acryloyl, propioloyl, crotonoyl, benzoyl, diphenylacetyl, phenoxyacetyl, methoxyacetyl, methoxycarbonyl, 2-(methylthiomethoxy)ethoxycarbonyl, vinyloxycarbonyl, 4-methylbenzoyl, 4-chlorobenzoyl, 2-methylaminobenzoyl, 2-aminobenzoyl, 4-aminobenzoyl, 4-nitrobenzoyl, cinnamoyl, silanyl, trimethylsilanyl, triethylsilanyl, tripropylsilanyl, triisopropylsilanyl, t-butyldimethylsilanyl, 2-chlorophenyl (4-nitrophenyl)phosphono, and methylsulfonyl; or wherein R′ is selected from the group consisting of methyl, ethyl, vinyl, allyl, ethynyl, t-butyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, phenyl, benzyl, fluoro, chloro, bromo, iodo, and amino; and optionally wherein said reactant further comprises a compound selected from the group consisting of: acid anhydride, an acid chloride, a carboxylic acid, an N-acylimidazole, an alkoxyalkyl halide, an alkylthioalkyl halide, an alkoxyalkoxyalkyl halide, a trialkylsilane halide and a trialkylsilane imidazole; or    D(a) a kit as set forth in 4(A), 4(B) or 4(C), wherein: 
 (1) said kit further comprises an acylation catalyst;  
 (2) said organic solvent comprises an organic base;  
 (3) said organic base is the organic solvent;  
 (4) said nucleic acid polymerase comprises an RNA-dependent DNA polymerase or a RNA-dependent DNA polymerase selected from the group consisting of: Superscript™ I1 (MMLV reverse transcriptase RNase H-), MMLV reverse transcriptase, HIV reverse transcriptase, AMV reverse transcriptase, RAV-2 reverse transcriptase, human T-cell leukemia virus type I (HTLV-I) reverse transcriptase, bovine leukemia virus (BLV), Rous Sarcoma virus (RSV), Tth DNA polymerase, Tfl DNA polymerase, Bst polymerase, Taq DNA polymerase, Thermoscript, C.therm polymerase, displaythermo-RT and Klenow DNA polymerase;  
 (5) the nucleic acid polymerase comprises a DNA-dependent DNA polymerase or a DNA-dependent DNA polymerase selected from the group consisting of: DNA polymerase I; DNA polymerase I-Klenow fragment; T4 DNA polymerase; T7 DNA polymerase; Taq DNA polymerase, Tli DNA polymerase, Pfu DNA polymerase; Vent™ DNA polymerase; Deep Vent™ DNA polymerase; Bst DNA polymerase;  
   Tth, Pfu Turbo™, Pfu(exo-), Pwo, Pyra™, Tfu, KlenTaq, Taq2000™, AmpliTaq Stoffel fragment, Sequenase™, Tma, Vent® (exo-), Deep Vent® (exo-), and a DNA polymerase purified from  Thermosipho africanus, Thermotoga maritima, Desulfurococcus mobilis, Methanobacterium thermoautotrophicum, Methanothemus fervidus, Pyrococcus furious, Pyrodictium occultum, Sulfolobus acidocaldarius, S. solfataricus, Thermococcus litoralis  or  Thermoplasma acidophilum;  
 (6) said kit is for polymerase chain reaction;  
 (7) said nucleic acid polymerase comprises a RNA dependent DNA polymerase of (4) and a DNA dependent DNA polymerase of (5), and optionally wherein said kit is for use in reverse transcription polymerase chain reaction;  
 (8) said nucleic acid polymerase comprises a RNA dependent RNA polymerase or said nucleic acid polymerase comprises an RNA-dependent RNA polymerase selected from the group consisting of: Q beta replicase, an RNA dependent RNA polymerase derived from  E. coli  phage f2, R17, MS-2 or 06, an RNA-dependent RNA polymerase from a virus family selected from bromoviridae, flaviviridae, picornaviridae, potyviridae, tobamovirus, tombusviridae, leviviruses, hepatitis C-like viruses or picornaviruses, and an RNA-dependent RNA polymerase from the group consisting of: polio virus, yellow fever virus, tobacco mosaic virus, brome mosaic virus, influenza virus, reovirus, myxovirus, rhabdovirus and paramyxovirus or  
   E(a) an organic solvent; and    E(b) a reactant capable of covalently modifying the 2′-OH position of the ribose rings of the mRNA, rRNA or viral RNA in the presence of the organic solvent, wherein the reactant is labeled with a label; and optionally wherein; 
 (1) said label comprises a fluorescent label, a radioactive label, an enzyme, a ligand or an affinant for a label;  
 (2) said reactant is chosen such that the modified ribose rings bear at the 2′-OH position a substituent, OR, wherein R comprises a moiety selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, C1-C10 haloalkoxyalkyl, C1-C10 aminoalkoxyalkyl, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 arylalkyl, C6-C14 arylalkenyl, C1-C10 alkanoyl, C1-C10 alkenoyl, C1-C10 haloalkanoyl, C1-C10 dihaloalkanoyl, C1-C10 trihaloalkanoyl, C2-C10 haloformylalkanoyl, C1-C10 aminoalkanoyl, C6-C14 arylalkanoyl, C6-C14 arylalkenoyl, C1-C10 alkoxyalkanoyl, C6-C14 aryloxyalkanoyl, C6-C14 alkylarylalkanoyl, C1-C10 azidoalkanoyl, C1-C10 carboxyalkanoyl, C1-C10 carboxyalkenoyl, C1-C10 carboxyalkynoyl, C6-C14 haloarylalkanoyl, C6-C14 aminoarylalkanoyl, C7-C15 alkylaminoarylalkanoyl, C1-C10 haloalkenoyl, C1-C10 haloalkynoyl, C1-C10 alkylsilanyl, C3-C10 trialkylsilanyl C1-C10 alkoxycarbonyl, C3-C18 alkylthioalkoxyalkoxycarbonyl, C1-C10 alkenyloxycarbonyl, C3-C18 alkoxyalkoxyalkyl, C2-C12 alkoxyalkyl, C2-C12 alkylthioalkyl, C1-C10 alkylsulfonyl, and C12-C28 diarylphosphone,; or a substituent R′, wherein R′ is selected from the group consisting of: C1-C10 alkyl, C1-C10 alkenyl, C1-C10 alkynyl, C1-C10 haloalkyl, C1-C10 aminoalkyl, halo, amino, C1-C10 alkylamino, C6-C14 aryl, C6-C14 alkylaryl, C6-C14 and arylalkyl; or more specifically wherein R is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, methoxymethyl, methylthiomethyl, methoxyethoxymethyl, (2-chloroethyl)oxyethyl, (2-aminoethyl) oxyethyl, phenyl, 4-methylphenyl, benzyl, cinnamyl, formyl, acetyl, propanoyl, butanoyl, pentanoyl, hexanoyl, heptanoyl, octanoyl, nonanoyl, pivaloyl, isobutanoyl, isopentanoyl, carboxyacetyl, chloroformylnonanoyl, 3-carboxypropanoyl, 4-aminobutanoyl, 4-chlorobutanoyl chloroacetyl, dichloroacetyl, trifluoroacetyl, trichloroacetyl, 3-azidopropanoyl, 4-azidobutyryl acryloyl, propioloyl, crotonoyl, benzoyl, diphenylacetyl, phenoxyacetyl, methoxyacetyl, methoxycarbonyl, 2-(methylthiomethoxy)ethoxycarbonyl, vinyloxycarbonyl, 4-methylbenzoyl, 4-chlorobenzoyl, 2-methylaminobenzoyl, 2-aminobenzoyl, 4-aminobenzoyl, 4-nitrobenzoyl, cinnamoyl, silanyl, trimethylsilanyl, triethylsilanyl, tripropylsilanyl, triisopropylsilanyl, t-butyldimethylsilanyl, 2-chlorophenyl (4-nitrophenyl)phosphono, and methylsulfonyl; or a substituent R′, wherein R′ is selected from the group consisting of: methyl, ethyl, vinyl, allyl, ethynyl, t-butyl, 2-chloroethyl, 2-aminoethyl, ethyloxyethyl, phenyl, benzyl, fluoro, chloro, bromo, iodo, and amino;  
 (3) said reactant comprises an acid anhydride, an acid chloride, a carboxylic acid, an N-acylimidazole, an alkoxyalkyl halide, an alkylthioalkyl halide, an alkoxyalkoxyalkyl halide, a trialkylsilane halide or a trialkylsilane imidazole;  
 (4) said reaction medium further comprises an acylation catalyst, and optionally wherein (A) said RNA is reacted with the acid anhydride and the acylation catalyst comprises a fluoride ion or aminopyridine catalyst; (B) said RNA is reacted with the acid chloride and the acylation catalyst comprises an aminopyridine catalyst; or (C) said RNA is reacted with the N-acylimidazole and the acylation catalyst comprises an aminopyridine catalyst;  
 (5) said reactant comprises a carboxylic acid in the presence of a dehydrating agent or an isocyanide catalyst;  
 (6) said reactant comprises an O-silylation agent; and optionally wherein said O-silylation agent in the presence of an aminopyridine or lithium sulfide catalyst; or  
 (7) said organic solvent comprises an organic base or said organic base is the organic solvent.