Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
  • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
  • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
  • Y02P20/00—Technologies relating to chemical industry
  • Y02P20/50—Improvements relating to the production of bulk chemicals
  • Y02P20/55—Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
  • Y02P20/00—Technologies relating to chemical industry
  • Y02P20/50—Improvements relating to the production of bulk chemicals
  • Y02P20/582—Recycling of unreacted starting or intermediate materials

Definitions

• the present invention relates to a method for preparing oligonucleotides.
• oligonucleotides The synthesis of oligonucleotides has been the subject of investigations for a long period of time. Automated synthesis procedures have been developed and apparatus for the automated syntheses are commercially available. Most of these procedures have been developed for rather small quantities of oligonucleotides (in the range of mg). These amounts are sufficient for most investigational purposes.
• oligonucleotides synthesis by standard solid phase synthesis results in a contamination of the desired full length compound by failure sequences arising from incomplete reaction during the synthesis cycle.
• the purification of the crude oligonucleotide involves complicated isolation and chromatographic purification of the final product.
• synthesis methods for oligonucleotides consist of a four-step procedure for the elongation of the oligonucleotide
• One object of the present invention is to provide a method for the preparation of oligonucleotides suitable for large scale (kilogram to tons) synthesis.
• a further object of the present invention is to provide a method for the preparation of oligonucleotides avoiding complicated purification steps, especially chromatographic purifications, especially during synthesis cycles.
• a further object of the invention is to provide a method for the preparation of oligonucleotides allowing an effective convergent synthesis.
• this object is solved by a liquid phase synthesis method, comprising the steps of a) providing a 3′-protected compound having the formula:
• B is a heterocyclic base
• R 2 is H, a protected 2′-hydroxyl group, F, a protected amino group, an O-alkyl group, an O-substituted alkyl, a substituted alkylamino or a C4′—O 2 ′methylen linkage
• R 3 is OR′ 3 , NHR′′ 3 , NR′′ 3 R′′′ 3 , a 3′-protected nucleotide or a 3′-protected oligonucleotide,
• R′ 3 is a hydroxyl protecting group
• R′′ 3 , R′′′ 3 are independently an amine protecting group
• steps c1) and c2) optionally processing the elongated oligonucleotide with a P(III)-internucleotide bond by either or both of steps c1) and c2) in any sequence
• the method of the present invention is a solution phase synthesis wherein at least some of the reagents are solid supported.
• Solid supported covers covalently bound reagents and reagents bound to a solid support by ionic forces.
• step d) is effected by treatment with a solid supported agent or removing the 5′-protection group with a removal agent followed by addition of a solid supported scavenger or followed by extraction.
• the invention comprises a method comprising the steps of a) providing a 5′-protected compound having the formula:
• B is a heterocyclic base
• R 2 is H, a protected 2′-hydroxyl group, F, a protected amino group, an O-alkyl group, an O-substituted alkyl, a substituted alkylamino or a C4′-O 2 ′methylen linkage
• R 3 is OH, NH 2
• R 5 is a hydroxyl protecting group, a 5′-protected nucleotide or a 5′-protected oligonucleotide
• steps c1) and c2) optionally processing the elongated oligonucleotide with a P(III)-internucleotide bond by either or both of steps c1) and c2) in any sequence
• step d) is effected by treatment with a solid supported agent or removing the 3′-protection group with a removal agent followed by addition of a solid supported scaenger or followed by extraction.
• the heterocyclic base can be a natural nucleobase or a modified one including a non-base residue.
• the natural nucleobasis are adenine, guanine, thymine, cytosine and uracil. In general these bases need protection groups during the synthesis. Suitable protected nucleobases are known to persons skilled in the art for example N-4-benzoylcytosine, N-6-benzoyl adenine, N-2-isobutiryl guanine, N-4-acetyl or isobutyril cytosine, N-6-phenoxyacetyl adenine, N-2-tert-butyl phenoxyacetyl guanine.
• Suitable non-base residues include for example Hydrogen, H leading to the 1′,2′-dideoxyribose (dSpacer from Glen Research) which can be used as linker or to mimic abasic sites in an oligonucleotide (Takeshita et al., J. Biol. Chem., 1987, 262, 10171).
• Hydrogen H leading to the 1′,2′-dideoxyribose (dSpacer from Glen Research) which can be used as linker or to mimic abasic sites in an oligonucleotide (Takeshita et al., J. Biol. Chem., 1987, 262, 10171).
• nucleosides such as L, D, ⁇ , ⁇ and the like.
• a suitable protection for the 2′-hydroxyl-group include but are not limited to tert-butyl dimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM), fluorophenyl-metoxypiperidinyl (FPMP).
• TDMS tert-butyl dimethylsilyl
• TOM triisopropylsilyloxymethyl
• FPMP fluorophenyl-metoxypiperidinyl
• Suitable protecting groups for the 3′-hydroxyl-group include but are not limited to tert-butyl dimethylsilyl (TBDMS), levulinyl, benzoyle. This compound is then reacted with a nucleotide derivative with a 3′-phosphorous-synthon.
• the nucleotide derivative preferably has the following formula wherein X is a P(III)-function B is a heterocyclic base R 2 is H, a protected 2′-hydroxyl group, F, a protected amino group, an O-alkyl group, an O-substituted alkyl, a substituted alkylamino or a C4′-O2′methylen linkage R 5 is a hydroxyl protecting group, a 5′-protected nucleotide or a 5′-protected oligonucleotide.
• the nucleotide derivative preferably has the following formula wherein X is a P(III)-function B is a heterocyclic base R 2 is H, a protected 2′-hydroxyl group, F, a protected amino group, an O-alkyl group, an O-substituted alkyl, a substituted alkylamino or a C4′-O2′methylen linkage R 3 ⁇ OR′ 3 , NHR′′ 3 , NR′′ 3 R′′′ 3 , a 3′-protected nucleotide or a 3′-protected oligonucleotide, R 3 is a hydroxyl protecting group, R′ 3 , R′′′ 3 are independently an amine protecting group, R′ 3 is a hydroxyl protecting group, a 3′-protected nucleotide or a 3′-protected oligonucleotide Step b): The coupling step b):
• step b) the coupling of the nucleotide or oligonucleotides occurs.
• the chemistry of the reaction depends on the type of activated phosphorous compound.
• Several methods for coupling nucleotides are known. The most common methods are via phosphoramidite and via H-phosphonate. In each of these cases the phosphor is in an activated state which allows coupling with the free hydroxyl group of the other part.
• nucleoside or oligonucleotide-3′-O-phosphoramidite where the P(III) phosphorus is substituted with a dialkylamine (phosphite activating group) and a phosphorus protecting group (including but not limited to 2-cyanoethyl, methyl) is reacted with 5′-hydroxyl nucleoside or oligonucleotide in presence of an activator to create a phosphite triester internucleosidic linkage.
• a dialkylamine phosphite activating group
• a phosphorus protecting group including but not limited to 2-cyanoethyl, methyl
• H-phosphonate chemistry In H-phosphonate chemistry (Froehler, Methods in Molecular Biology. Protocols for oligonucleotides and analogs, Humana Press, 1993, 63-80; Strömberg and Stawinski, in unit 3.4 of Current Protocols in Nucleic Acid Chemistry, Wiley) a nucleoside or oligonucleotide-3′-O—H-phosphonate is reacted with a 5′-hydroxyl nucleoside or oligonucleotide in presence of an activator to create a H-phosphonate diester internucleosidic linkage.
• Suitable activators for the coupling step in phosphoramidite chemistry include, but are not limited to a solid support bearing a pyridinium salt, for example a solid support covalently linked to pyridine e.g. poly(vinyl)-pyridinium or the pyridinium is a counter ion of a cation exchange solid support.
• the cation exchange support can be a strong or a weak exchanger, for example a sulfonic acid or a carboxylic acid.
• the pyridinium salt can also be a substituted pyridinium salt, for example dichloropyridinium.
• It can further be a solid support bearing an optionally substituted azole (imidazole, triazole, tetrazole), or is the salt of a weak base anion exchange resin with a strong acid, or a weak cation exchange resin (carboxylic) in its protonated form (see U.S. Pat. No. 5,574,146), or a solid support bearing an optionally substituted phenol (see W. Dabkowski and al., Tet Lett, 2000, 41, 7535-7539).
• an optionally substituted azole imidazole, triazole, tetrazole
• a weak base anion exchange resin with a strong acid or a weak cation exchange resin (carboxylic) in its protonated form
• a solid support bearing an optionally substituted phenol see W. Dabkowski and al., Tet Lett, 2000, 41, 7535-7539).
• imidazole is less preferred.
• the suitable activators include, but are not limited to solid supports bearing a carboxylic acid chloride, sulfonic acid chloride, a chloroformate, a chlorosulfite or a phosphorochloridate or the respective Br-compounds. Further compounds are disclosed in WO 01/64702 A1, page 6, line 36 to page 8, line 5, incorporated by reference and C B Reese and Q Song, Nucleic Acid Res., 1999, 27, 963-971.
• Capping is understood as a reaction wherein a reagent reacts with remaining protected compounds of step a).
• the capping agent is preferably solid supported, the 3′-protected compound can be removed together with the solid supported capping agent.
• suitable capping agents include, but are not limited to activated acids for example carboxylic acid, chloride or sulfonic acid chloride, carboxylic acid bromide, azolide, substituted azolide, anhydride or chloroformate or phosphorochloridate, or a solid supported phosphoramidate, or a solid supported H-phosphonate monoester.
• the acid group is preferably an acid group covalently bound to a solid support.
• Commercially available cationic exchanger resins can be used as a starting material for synthesizing the solid supported carboxylic acids or sulfonic acids.
• the oxidizing reaction is used to oxidize the P(III)-internucleotide bond to a P(V)-internucleotide bond.
• Capping can be performed before oxidizing and vice versa.
• capping and oxidizing may also be combined in one step.
• nucleoside oligonucleotide can be facsilated by a hydrolysis step, for example with water.
• the oxidizing reagent can be any oxidizing reagent used for prior art solid phases, preferably in the form of solid supported agent, either covalently bound or bound by ionic forces.
• Suitable reagents are solid supported periodates, permanganates, osmium tetroxides, dichromates, hydroperoxides, substituted alkylamine oxides, percarboxylic acid and persulfonic acid.
• These compounds are negatively charged, therefore they can be solid supported by a suitable ion exchanger for example an ion exchanger bearing ammonium groups.
• a suitable ion exchanger for example an ion exchanger bearing ammonium groups.
• These substances could be bound to solid support consisting for example of an amino, alkyl amino, dialkyl amino or trialkyl amino anion exchanger.
• oligonucleotides synthesis for investigational purposes and especially for antisense therapeutics phosphorthioate analogs are used.
• the oxidizing is a sulfurization.
• a solid supported oxidizing reagent a solid supported sulfurization reagent is used, for example a solid supported tetrathionate, a solid supported alkyl or aryl sulfonyl disulfide, a solid supported optionally substituted dibenzoyl tetrasulfide, a solid supported bis(akyloxythiocarbonyl)tetrasulfide, a solid supported optionally substituted phenylacetyl disulfide, a solid supported. N-[(alkyl or aryl)sulfanyl] alkyl or aryl substituted succinimide and a solid supported (2-pyridinyidithio) alkyl or aryl.
• NC—CH 2 —CH 2 S—SO 3 ⁇ cyanoethylthiosulfate
• Suitable 5′-protection group include, but are not limited to trityl groups, preferably a dimethoxytrityl group (DMTr) or a monomethoxytrityl group (MMTr). These protection groups are used in conventional prior art solid phase oligonucleotides synthesis.
• Other suitable 5′-protection groups include, but are not limited to tert-butyl dimethylsilyl (TBDMS), levulinyl, benzoyle, fluorenemethoxycarbonyl (FMOC), the 9-phenylthioxanthen-9-yl (S-pixyl).
• the 3′-protection group is removed.
• Suitable 3′-protection groups include, but are not limited to 3′-O-tert butyl dimethyl silyl (TBDMS), 3′-O-acetate, 3′-O-levulinyl groups. They can be removed by a solid-supported ammonium fluoride, solid-supported ammonium hydroxide or solid-supported hydrazine.
• step d) of the first embodiment the 5′-protection group is removed. Thereafter the oligonucleotides can either be used or the oligonucleotide corresponds to the 3′-protected compound of step a) to repeat the cycle.
• Suitable reagents are also disclosed in synthetic communications 24 (17) 1994, 2323-2428.
• step d) of the second embodiment the 3′-protection group is removed. Thereafter the oligonucleotides can either be used or the oligonucleotide corresponds to the 5′-protected compound of step a) to repeat the cycle.
• the methods will be repeated at least once.
• the method of the present invention will result in a dimer. Repeating the method of the present invention will elongate the dimer to a trimer. By repeating the method of the invention several times n-mers can be synthesized.
• oligonucleotides can be synthesized of at least up to 100 nucleotides in sufficient yield, but longer oligonucleotides are also possible.
• An antisense therapy oligonucleotides are normally in the range of 8-36 nucleotides, more preferably 12-30, most commonly in the range of the 16-26 nucleotides.
• Convergent synthesis methods are methods wherein small oligonucleotides are synthesized first and the small oligonucleotides are then combined for synthesizing larger blocks. By this method the number of coupling reactions can be significantly reduced. Thereby the overall yield of the oligonucleotide is increased.
• Convergent synthesis has the further advantage, that the reaction product is essentially free of (n ⁇ 1)mers.
• the purification of oligonucleotides with a length of n from oligonucleotides with a length of n ⁇ 1 is the most difficult in purification of the oligonucleotide.
• these (n ⁇ 1)mers are nearly avoided, because larger fragments are combined.
• the method of the present invention uses dimers or trimers as the compounds in step a) and/or b).
• reagents are mostly added in a solid supported form. These solid supported reagents are preferably removed after reaction or after each reaction step. Depending on the type of reagent it is in some cases possible to remove two or more of the solid supported reagents together.
• coupling and at least final oxidizing steps are done by solid supported reagents.
• the solid supported reagent is recycled. This recycling is obviously easier if the solid supported reagents are removed separately after each reaction.
• the solid supported reagents can be removed by methods like filtration or centrifugation. Because of the ease of handling, filtration is the preferred way of removing the solid supported reagents.
• a very preferred reagent for the sulfurization is a solid supported anion exchange resin in complex with a tetrathionate having the formula S 4 O 6 , preferably a quaternary ammonium resin bearing tetrathionate as counter ion.
• the oligonucleotide in case of the use of MMT or DMT as a protection group, is purified by binding to an ion exchanger and the protection group is removed while the oligonucleotide is bound to the exchanger.
• the oligonucleotide After removal of the protection groups, the oligonucleotide is released from the ion exchanger.
• 5′-OH-T-3′-O-TBDMS 11 mg, 32.5 mmol
• 5′-O-DMTr-T-3′-cyanoethyl phosphoramidite 41 mg, 55.25 mmol, 1.7 eq
• the solution is transferred under argon in a NMR tube containing the DOWEX 50W X8 pyridinium form (100 mg, 0.30 mmol pyrH + , 9.2 eq).
• the reaction is followed by 31 P NMR. Before the NMR experiment deuterated acetonitrile (50 ml) is added. The yield is determined by 31 P NMR.
• the desired dimer T-T phosphite triester is obtained with 100% of yield compared to 5′-OH-T-3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl phosphoramidite ( 31 P NMR (CD 3 CN) ⁇ 149.14, 149.07, 14.7%), 5′-O-DMTr-T-T-3′-O-TBDMS cyanoethyl phosphite triester ( ⁇ 140.53, 70.2%), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.74, 15.1%).
• 5′-OH-T-3′-O-TBDMS 11 mg, 32.5 mmol
• 5′-O-DMTr-T-3′-cyanoethyl phosphoramidite 41 mg, 55.25 mmol, 1.7 eq
• the solution is transferred under argon in a NMR tube containing the poly(4-vinylpyridinum p-toluenesulfonate) (100 mg, 0.33 mmol tos ⁇ , 10.3 eq).
• the reaction is followed by 31 P NMR. Before the NMR experiment deuterated acetonitrile (50 ml) is added. The yield is determined by 31 P NMR.
• the desired dimer T-T phosphite triester is obtained with 82% of yield compared to 5′-OH-T-3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-T-T-3′-O-TBDMS cyanoethyl phosphite triester ( 31 P NMR (CD 3 CN) ⁇ 140.54, 48.2%), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.77, 51.8%).
• the desired dimer 5′-O-DMTr-T-T-3′-O-TBDMS cyanoethyl phosphite triester is obtained with 100% of yield compared to 5′-OH-T-3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl phosphoramidite ( 31 P NMR (CD 3 CN) ⁇ 149.17, 149.10, 5.4%), 5′-O-DMTr-T-T-3′-O-TBDMS cyanoethyl phosphite triester ( ⁇ 140.57, 140.54, 68.30%), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.75, 8.71, 26.30%).
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl thiophosphoramidate ( 31 P NMR (CD 3 CN) ⁇ 71.16, 4.0%), 5′-O-DMTr-T-T-3′-O-TBDMS cyanoethyl phosphorothioate triester (d 68.28, 68.23, 69.5%), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.75, 8.71, 26.50%).
• the AMBERLYST A26 is filtered off and the solvent are evaporated.
• the crude is dissolved in 4 ml of CH 2 Cl 2 /CH 3 OH (7/3) and cooled in an ice bath.
• To this solution is added 1 ml of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3).
• the solution is stirred 15 min at 0° C.
• the reaction is washed with 10 ml of a saturated solution of NaHCO 3 , the organic layer is separated, dried (Na 2 SO 4 ), evaporated, and purified on a silica gel column.
• the desired dimer T-T is eluted with CH 2 Cl 2 /CH 3 OH (95/5).
• trimer 5′-O-DMTr-T-T-T-3′-O-TBDMS cyanoethyl phosphite triester is obtained with 100% of yield compared to the dimer 5′-OH-T-T-3′-O-TBDMS cyanoethyl phosphorothioate triester.
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl phosphoramidite ( 31 P NMR (CD 3 CN) ⁇ 149.16, 149.10, 17.7%), 5′-O-DMTr-T-T-T-3′-O-TBDMS cyanoethyl phosphite triester ( ⁇ 140.85, 140.68, 140.37, 140.30, d 68.07, 68.02, 68.3%), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.7, 8.68, 14%).
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl thiophosphoramidate ( 31 P NMR (CD 3 CN) d 72.04, 71.17, 14.0%), 5′-O-DMTr-T-T-T-3′-O-TBDMS cyanoethyl phosphorothioate triester (d 68.17, 68.12, 68.07, 67.96, 67.80, 67.58, 73.8%), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.76, 8.71, 12.2%).
• the AMBERLYST A26 is filtered off and the solvent are evaporated.
• the crude is dissolved in 4 ml of CH 2 Cl 2 /CH 3 OH (7/3) and cooled in an ice bath.
• To this solution is added 1 ml of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3).
• the solution is stirred 45 min at 0° C.
• the reaction is washed with 10 ml of a saturated solution of NaHCO 3 , the organic layer is separated, dried (Na 2 SO 4 ), evaporated, and purified on a silica gel column.
• the desired trimer T-T-T is eluted with CH 2 Cl 2 /CH 3 OH (95/5).
• the desired dimer 5′-O-DMTr-T-dA Bz -3′-O-TBDMS cyanoethyl phosphite triester is obtained with 100% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl phosphoramidite ( 31 P NMR (CD 3 CN) ⁇ 149.10, 149.05, 12.3%), 5′-O-DMTr-T-A Bz -3′-O-TBDMS cyanoethyl phosphite triester ( ⁇ 140.52, 140.37, 50%), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.72, 8.69, 37.7%).
• Detritylation The 5′-O-DMTr-T-dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate triester is dissolved in 10 ml of CH 2 Cl 2 /CH 3 OH (7/3) and cooled in an ice bath. To this solution is added 1 ml of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3). The solution is stirred 35 min at 0° C. The reaction is washed with 20 ml of a saturated solution of NaHCO 3 , the organic layer is separated, dried (Na 2 SO 4 ), evaporated, and purified on a silica gel column.
• trimer 5′-O-DMTr-dA Bz -T-dA Bz -3′-O-TBDMS cyanoethyl phosphite triester is obtained with 62% of yield compared to the dimer 5′-OH-T-dA Bz -3′-O-TBDMS phosphorothioate triester.
• the crude is a mixture of 5′-O-DMTr-dA Bz -3′-cyanoethyl phosphoramidite ( 31 P NMR (CD 3 CN) d 149.14, 8.4%), 5′-O-DMTr-dA Bz -T-dA Bz -3′-O-TBDMS cyanoethyl phosphite triester ⁇ (140.90, 140.77, 67.85, 67.79, 43.3%), 5′-OH-T-dA Bz -3′-O-TBDMS phosphorothioate triester ( ⁇ 68.03, 67.89, 13.4%), 5′-O-DMTr-dA Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.71, 8.66, 34.9%).
• the crude is a mixture of 5′-O-DMTr-dA Bz -3′-cyanoethyl thiophosphoramidate ( 31 P NMR (CD 3 CN) d 71.88, 71.21, 10%), 5′-O-DMTr-dA Bz -T-dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate triester (25.9%) and 5′-OH-T-dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate triester (16.20%) ( ⁇ 68.08, 68.05, 67.93, 67.89, 67.85, 67.79, 67.57), 5′-O-DMTr-T-3′-cyanoethyl phosphorothioate diester ( ⁇ 57.38, 4.8%), 5′-O-DMTr-dA Bz -3′-cyanoethyl
• the desired dimer T-dC Bz phosphite triester is obtained with 100% of yield compared to 5′-OH-T-3′-O-Lev.
• the crude is a mixture of 5′-O-DMTr-dC Bz -3′-cyanoethyl phosphoramidite ( 31 P NMR (CD 3 CN) ⁇ 149.36, 149.32, 11%), 5′-O-DMTr-T-dC Bz -3′-O-TBDMS cyanoethyl phosphite triester ( ⁇ 140.52, 140.39, 70%), 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.90, 8.58, 19%).
• the desired dimer 5′-O-DMTr-d CB-T-3′-O-Lev cyanoethyl phosphite triester is obtained with 100% of yield compared to 5′-OH-T-3′-O-Lev.
• the crude is a mixture of 5′-O-DMTr-T-dC Bz -3′-O-Lev cyanoethyl phosphite triester ( 31 P NMR (CD 3 CN) ⁇ 140.59, 140.45, 64%), 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.68, 8.66, 36%).
• the crude is a mixture of 5′-O-DMTr-T-dC Bz -3-O-Lev cyanoethyl phosphorothioate triester ( 31 P NMR (CD 3 CN) ⁇ 68.05, 67.89, 83.70%), 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.63, 16.30%).
• the spectrophotometric purity determined by HPLC at 260 nm is 80%.
• the desired dimer 5′-OH-dC Bz -T-3′-O-Lev cyanoethyl phosphorothioate triester is purified by precipitation from CH 2 Cl 2 /MeOH (9/1) in diethylether.
• the spectrophotometric purity (97%) is determined by HPLC at 260 nm.
• the excess of 5′-O-DMTr-T-3′-5 cyanoethyl phosphoramidite is hydrolysed with 500 ml of water
• the desired dimer 5′-O-DMTr-T-T-3′-O-Lev cyanoethyl phosphite triester is obtained with 100% of yield compared to 5′-OH-T-3′-O-Lev.
• the AMBERLYST A26 resin is filtered off and the solvents are evaporated.
• dimer 5′-O-DMTr-dA Bz -dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate triester dimer
• 5′-OH-dA Bz -3′-O-TBDMS 100 mg, 0.21 mmol
• 5′-O-DMTr-dA Bz -3′-cyanoethyl-phosphoramidite 311 mg, 0.36 mmol, 1.7 eq
• the solution is transferred under argon in a flask containing the DOWEX 50W X8 pyridinium form (655 mg, 1.97 mmol pyrH + , 9.2 eq) and is shaken for 4 h 30 min.
• the reaction is followed by 31 P NMR.
• the yield is determined by 31 P NMR.
• the desired dA-dA phosphite triester dimer is obtained with 92% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dA Bz -3′-cyanoethyl phosphoramidite ( 31 P NMR (CD 3 CN) ⁇ 149.25, 149.13; 27.7%), 5′-O-DMTr-dA Bz -dA Bz -3′-O-TBDMS cyanoethyl phosphite triester ( ⁇ 140.75, 140.38; 53.9%), 5′-O-DMTr-dA Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.69, 8.64; 18.5%).
• the desired dimer dA-dA phosphorothioate triester is obtained with 88% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dA Bz -3′-cyanoethyl thiophosphoramidate ( 31 P NMR (CD 3 CN) ⁇ 71.85, 71.22; 29.0%), 5′-O-DMTr-dA Bz -dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate ( ⁇ 68.08, 68.01; 51.5%), 5′-O-DMTr-dA Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.66, 8.59; 19.5%).
• 5′-OH-dA Bz -3′-O-TBDMS adenosine (100 mg, 0.21 mmol) and 5′-O-DMTr-dC Bz -3′-cyanoethyl-phosphoramidite (365 mg, 0.43 mmol, 2. eq) are dissolved in anhydrous acetonitrile (15 ml).
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (655 mg, 2.17 mmol tos ⁇ , 10.2 eq) and is shaken for 5 h 50 min.
• the reaction is followed by 31 P NMR.
• the yield is determined by 31 P NMR.
• the desired dC-dA phosphite triester dimer is obtained with 100% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dC Bz -dA Bz -3′-O-TBDMS cyanoethyl phosphite triester ( 31 P NMR (CD 3 CN) ( ⁇ 140.55, 140.49; 53.9%), 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.67; 18.5%).
• the desired dC-dA phosphorothioate triester dimer is obtained with 100% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dC Bz -dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate ( 31 P NMR (CD 3 CN) (d 68.14, 68.07; 50.6%), 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate (d 8.67; 49.4%).
• 5′-OH-dA Bz -3′-O-TBDMS (102 mg, 0.22 mmol) and 5′-O-DMTr-dA Bz -3-cyanoethyl-phosphoramidite (381 mg, 0.44 mmol, 2.05 eq) are dissolved in anhydrous dichloromethane (15 ml).
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (655 mg, 2.19 mmol tos ⁇ , 10.1 eq) and is shaken for 5 h 40 min.
• the reaction is followed by 31 P NMR.
• the yield is determined by 31 P NMR.
• the desired dA-dA phosphite triester dimer is obtained with 100% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dA Bz -dA Bz -3′-O-TBDMS cyanoethyl phosphite triester ( 31 P NMR (CD 3 CN) (d 140.77, 140.46; 66.9%), 5′-O-DMTr-dA Bz -3′-cyanoethyl hydrogenophosphonate (d 8.50, 8.41; 33.1%).
• the desired dA-dA phosphorothioate triester dimer is obtained with 100% of yield compared to the 5′-OH-A Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dA Bz -dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate ( 31 P NMR (CD 3 CN) (d 68.17, 67.89; 62.3%), 5′-O-DMTr-dA Bz -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.45, 8.35; 37.7%).
• the reaction is washed with 10 ml of a saturated solution of NaHCO 3 , the organic layer is separated, dried (Na 2 SO 4 ), evaporated, and purified on a silica gel column.
• the desired dA-dA dimer is eluted with CH 2 Cl 2 /CH 3 OH (33/1). The appropriates fractions are collected and evaporated to give a colorless oil.
• 5′-OH-dA-3′-O-TBDMS 100 mg, 0.21 mmol
• 5′-O-DMTr-dG IBu -3′-cyanoethyl-phosphoramidite 352 mg, 0.42 mmol, 1.97 eq
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (655 mg, 2.19 mmol tos ⁇ , 10.3 eq) and is shaken for 5 h 30 min.
• the reaction is followed by 31 P NMR.
• the yield is determined by 31 P NMR.
• the desired dG-dA phosphite triester dimer is obtained with 100% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dG IBu -dA Bz -3′-O-TBDMS cyanoethyl phosphite triester ( 31 P NMR (CD 3 CN) ( ⁇ 140.65, 140.45; 51.2%), 5′-O-DMTr-dG IBu -3′-cyanoethyl hydrogenophosphonate ( ⁇ 9.00, 8.81; 48.8%).
• the desired dG-dA phosphorothioate triester dimer is obtained with 100% of yield compared to the 5′-OH-dA Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dG IBu -dA Bz -3′-O-TBDMS cyanoethyl phosphorothioate ( 31 P NMR (CD 3 CN) ( ⁇ 68.15, 68.02; 50.40/0), 5′-O-DMTr-dG IBu -3′-cyanoethyl hydrogenophosphonate ( ⁇ 8.91, 8.68; 49.6%).
• 5′-OH-dC Bz -3′-O-TBDMS 100 mg, 0.22 mmol
• 5′-O-DMTr-dG IBu -3′-cyanoethyl-phosphoramidite 371 mg, 0.45 mmol, 2 eq
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (690 mg, 2.3 mmol tos ⁇ , 10.3 eq) and is shaken for 5 h.
• the reaction is followed by 31 P NMR.
• the yield is determined by 31 P NMR.
• the desired dG-dC phosphite triester dimer is obtained with 100% of yield compared to the 5′-OH-dC Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dG IBu -dC Bz -3′-O-TBDMS cyanoethyl phosphite triester ( 31 P NMR (CD 3 CN) ( ⁇ 141.73, 141.26; 62.1%), 5′-O-DMTr-dG IBu -3′-cyanoethyl hydrogeno-phosphonate ( ⁇ 9.05, 8.88; 37.9%).
• the reagents loading was determined by elemental analysis, giving a value of 23.25% for sulfur (4.24% for nitrogen, 45.74% for carbon and less than 100 ppm for potassium). Loading: 1.81 mmol S 4 O 6 2 ⁇ per gram of resin.
• the commercially available strongly acidic ion-exchange resin DOWEX 50W X8H + form (Fluka) is washed successively with water, HCl 2M, water until pH 7, methanol and dichloromethane to dry the resin. Then, the resin is stirred in a solution of pyridine 2M in acetonitrile or just washed with a slight flow of the solution of pyridine 2M in acetonitrile for 15 minutes. Then, the resin is washed with acetonitrile and dichloromethane and dried under vacuum over P 2 O 5 . The reagents loading was determined by elemental analysis, giving a value of 11.56% for sulfur and 3.97% for nitrogen. Loading: 2.83 mmol pyrH + per gram of resin.
• the commercial polystyrene-bound carboxy acid RAPP Polymere (5.0 g, 1.96 mmol/g, 100-200 mesh, 1% DVB) is suspended in anhydrous CH 2 Cl 2 (80 ml) and N,N-dimethylformamide (0.3 ml).
• Thionyl chloride (1.8 ml, 3.5 eq) are added under stirring and the mixture is refluxed for 3 h.
• the resin is filtered under argon and washed with dried CH 2 Cl 2 (100 ml), ether (100 ml) and dried under vacuum for 4 h.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product was dried under vacuum. Yield 89%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 88.5%
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 77.5%.
• the spectrophotometrical purity determined by HPLC is 94%.
• the spectrophotometrical purity determined by HPLC is 95%.
• the H-phosphonate dimer 5′-O-DMTr-dA Bz -dC Bz -3′-O-Lev (120 mg, 0,106 mmol) is dissolved in 4.0 ml of CH 2 Cl 2 /MeOH (7:3) and cooled in an ice bath.
• 1.0 ml of a solution of 10% BSA (benzene sulfonic acid) in CH 2 Cl 2 /MeOH (7:3) is added drop wise under stirring and the progress of the reaction is monitored by TLC. After 15 min the mixture is quenched with a solution of NaHCO 3 .
• the organic layer is washed with water to remove any trace of base, then it is dried over Na 2 SO 4 and the solvent is evaporated.
• the product is purified by precipitation from CH 2 Cl 2 with ether and dried under vacuum. Yield 88%.
• the spectrophotometrical purity determined by HPLC is 91%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 82%.
• the H-phosphonate dimer 5′-O-DMTr-dA Bz -T-3′-O-Lev (105 mg, 0,100 mmol) is dissolved in 4.0 ml of CH 2 Cl 2 /MeOH (7:3) and cooled in an ice bath. 1.0 ml of a solution of 10% BSA in CH 2 Cl 2 /MeOH (7:3) is added drop wise under stirring and the progress of the reaction is monitored by TLC. After 15 min the mixture is quenched with a solution of NaHCO 3 . The organic layer is washed with water to remove any trace of base, then it is dried over Na 2 SO 4 and the solvent is evaporated. The product is purified by precipitation from CH 2 Cl 2 in ether and dried under vacuum. Yield 70%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 75%.
• the spectrophotometrical purity determined by HPLC is 91.5%.
• the desired T-dG phosphite triester dimer is obtained with 100% of yield compared to the 5′-OH-dG IBu -3′-O-Lev.
• the crude is a mixture of 5′-O-DMTr-T-dG IBu -3′-O-Lev cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 140.76, 139.97; 60.7%) and 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.10, 8.03; 39.3%).
• the crude is a mixture of 5′-O-DMTr-dA Bz -dG IBu -3′-O-Lev cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 140.82, 140.30), 5′-O-DMTr-dA Bz -3-cyanoethyl phosphoramidite (d 149.90) and 5′-O-DMTr-dA Bz -3′-cyanoethyl hydrogeno-phosphonate (d 8.20, 8.03).
• Detritytlation To a solution of 5′-O-DMTr-dA Bz -dG IBu -3′-O-Lev cyanoethyl phosphorothioate triester (0.46 mmol) in 20 ml CH 2 Cl 2 /CH 3 OH (7/3) is added 2 ml (1.2 mmol, 1.4 eq.) of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3). The solution is stirred 20 min at 0° C.
• the crude is a mixture of 5′-O-DMTr-dC Bz -dG IBu -3′-O-Lev cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 140.67, 140.59), 5′-O-DMTr-dC Bz -3′-cyanoethyl phosphoramidite (d 149.93) and 5′-O-DMTr-dC Bz -3-cyanoethyl hydrogeno-phosphonate (d 8.08).
• the crude is a mixture of 5′-O-DMTr-dC Bz -dG IBu -3′-O-Lev cyanoethyl phosphorothioate 31 P NMR (CDCl 3 ) (d 68.02, 67.55), 5′-O-DMTr-dC Bz -3′-cyanoethyl thiophosphoramidate (d 71.93, 71.62) and 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogeno-phosphonate (d 8.07).
• Detritytlation To a solution of 5′-O-DMTr-dC Bz -dG IBu -3′-O-Lev cyanoethyl phosphorothioate triester (0.46 mmol) in 20 ml CH 2 Cl 2 /CH 3 OH (7/3) is added 2 ml (1.2 mmol, 1.4 eq.) of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3). The solution is stirred 20 min at 0° C.
• 5′-OH-dG IBu -3′-O-Lev 200 mg, 0.46 mmol
• 5′-O-DMTr-dG IBu -3-cyanoethyl-phosphoramidite 698 mg, 0.84 mmol, 1.8 eq
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (1.38 g, 4.6 mmol tos ⁇ , 10 eq) and is shaken for 1 h 15 min.
• the resin is filtered off.
• the reaction is followed by reverse phase HPLC and 31 P NMR.
• the yield is determined by HPLC.
• HPLC at 6.34 min; Area 0%
• the crude is a mixture of 5′-O-DMTr-dG IBu -dG IBu -3′-O-Lev cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 141.91, 140.29) and 5′-C-DMTr-dG IBu -3′-cyanoethyl hydrogenophosphonate (d 8.80, 8.06).
• the crude is a mixture of 5′-O-DMTr-dA Bz -3′-cyanoethyl-phosphite-T-3′-cyanoethyl-thionophosphotriester-dG IBu -3′-O-Lev trimer 31 P NMR (CDCl 3 ) (d 140.97, 140.79, 140.40, 139.90, 67.89, 67.87, 67.83) and 5′-O-DMTr-dA Bz -3′-cyanoethyl hydrogenophosphonate (d 8.12, 8.03).
• 5′-OH-T-3′-O-Lev (340 mg, 1.0 mmol) and 5′-O-DMTr-T-3′-cyanoethyl-phosphoramidite (1266 mg, 1.7 mmol, 1.7 eq) are dissolved in anhydrous dichloromethane (10 ml).
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (3.0 g, 10 mmol tos ⁇ , 10 eq) and is shaken for 5 h 15 min. Water (50 mL) is added to hydrolyze the remaining phosphoramidite. After 1 h 15 min the resin is filtered off.
• the reaction is followed by reverse phase HPLC and 31 P NMR.
• the yield is determined by HPLC.
• the crude is a mixture of 5′-O-DMTr-T-T-3′-O-Lev cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 140.58, 140.31) and 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.10, 8.04).
• 5′-OH-T-T-3′-O-Lev cyanoethyl phosphorothioate (764 mg, 0.99 mmol) and 5′-O-DMTr-dG IBu -3′-cyanoethyl-phosphoramidite (1400 mg, 1.7 mmol, 1.7 eq) are dissolved in anhydrous dichloromethane (20 ml).
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (3.0 g, 10 mmol tos ⁇ , 10 eq) and is shaken for 2 h 50 min.
• the crude is a mixture of 5′-O-DMTr-dG IBu -3′-cyanoethyl-phosphite-T-3′-cyanoethyl-thionophosphotriester-T-3′-O-Lev trimer 31 P NMR (CDCl 3 ) (d 142.78, 142.67, 141.64, 141.50, 68.47, 68.39, 68.16, 67.93) and 5′-O-DMTr-dG IBu -3′-cyanoethyl hydrogenophosphonate (d 8.59, 8.05).
• the crude is a mixture of 5′-O-DMTr-dC Bz -3′cyanoethyl-phosphite-dG IBu -3′-cyanoethyl-thionophosphotriester-T-3′-cyanoethyl-thionophosphotriester-T-3′-O-Lev tetramer 31 P NMR (CDCl 3 ) (d 141.01, 140.93, 140.05, 139.90, 68.50, 68.09, 68.04, 67.95) and 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate (d 8.15).
• 5′-OH-dC Bz -3′-O-TBDMS 100 mg, 0.22 mmol
• 5′-O-DMTr-dC Bz -3′cyanoethyl-phosphoramidite 384 mg, 0.46 mmol, 2.1 eq
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (690 mg, 2.3 mmol tos ⁇ , 10.3 eq) and is shaken for 6 h.
• the resin is filtered off.
• the reaction is followed by 31 P NMR.
• the yield is determined by 31 P NMR.
• the desired dC-dC phosphite triester dimer is obtained with 100% of yield compared to the 5′-OH-dG IBu -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dC Bz -dC Bz -3′-O-TBDMS cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 141.06, 140.93) and 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate (d 8.67).
• the desired dC-dC phosphorothioate triester dimer is obtained with 100% of yield compared to the 5′-OH-dC Bz -3′-O-TBDMS.
• the crude is a mixture of 5′-O-DMTr-dC Bz -dC Bz -3′-O-TBDMS cyanoethyl phosphorothioate 31 P NMR (CDCl 3 ) (d 68.24, 68.19) and 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate (d 8.57).
• Detritytlation To a solution of 5′-O-DMTr-dC Bz -dC Bz -3′-O-TBDMS cyanoethyl phosphorothioate triester (0.22 mmol) in 20 ml CH 2 Cl 2 /CH 3 OH (7/3) is added 0.5 ml (0.3 mmol, 1.3 eq.) of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3). The solution is stirred 30 min at 0° C.
• 5′-OH-dA Bz -3′-O-Lev (2.235 g, 4.93 mmol) and 5′-O-DMTr-dG IBu -3′-cyanoethyl-phosphoramidite (6.13 g, 7.43 mmol, 1.5 eq) are dissolved in anhydrous dichloromethane (100 ml).
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (14.76 g, 49.3 mmol tos ⁇ , 10 eq) and is shaken for 2 h 45 min. Water (0.2 ml) is added and the mixture is shaken for 1 h 25 min.
• the resin is filtered off.
• the reaction is followed by reverse phase HPLC and 31 P NMR.
• the yield is determined by HPLC.
• the crude is a mixture of 5′-O-DMTr-dG IBu -dA Bz -3′-O-Lev cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 140.52, 140.20) and 5′-O-DMTr-dG IBu -3′-cyanoethyl hydrogenophosphonate (d 8.59, 8.09).
• the desired dG-dA phosphorothioate triester dimer is obtained with 100% of yield compared to the 5′-OH-dA Bz -3′-O-Lev.
• the crude is a mixture of 5′-O-DMTr-dG IBu -dA Bz -3′-O-Lev cyanoethyl phosphorothioate 31 P NMR (CDCl 3 ) (d 68.45, 67.73) and 5′-O-DMTr-dG IBu -3′-cyanoethyl hydrogenophosphonate (d 8.60, 8.04).
• Detritytlation To a solution of 5′-O-DMTr-dG IBu -dA Bz -3′-O-Lev cyanoethyl phosphorothioate triester (4.93 mmol) in 200 ml dichloromethane is added 50 ml methanol and 20 ml (12.6 mmol, 2.6 eq.) of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3). The solution is stirred 40 min at 0° C.
• 5′-OH-dA Bz -3′-O-Lev 200 mg, 0.44 mmol
• 5′-O-DMTr-dC Bz -3′-cyanoethyl-phosphoramidite 626 mg, 0.75 mmol, 1.7 eq
• the solution is transferred under argon in a flask containing the poly(4-vinylpyridinum p-toluenesulfonate) (1.3 g, 3 mmol tos ⁇ , 6.8 eq) and is shaken for 8 h.
• the resin is filtered off.
• the reaction is followed by reverse phase HPLC and 31 P NMR. The yield is determined by HPLC.
• the crude is a mixture of 5′-O-DMTr-dG Bz -dA Bz -3′—O-Lev cyanoethyl phosphite triester 31 P NMR (CDCl 3 ) (d 140.68, 140.58) and 5′-O-DMTr-dC Bz -3′-cyanoethyl hydrogenophosphonate (d 8.04, 8.02).
• the resin is washed with 1 l deionized water, twice with 30 ml methanol and twice with 30 ml dichloromethane and dried under reduced pressure for 3 hours to give 8.2 g of solid-supported periodate.
• the reagents loading was determined by elemental analysis, giving a value of 27.16% for iodine (3.40% for nitrogen and 40.20% for carbon. Loading: 2.14 mmol IO 4 ⁇ per gram of resin.
• the resin can be recycled applying the same protocol. Comparable resins are commercially available.
• the crude is a mixture of 5′-O-DMTr-T-T-3′-O-Lev cyanoethyl phosphite triester (d 140.62, 140.48) and of 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.81, 8.76).
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl phosphate diester (d ⁇ 2.80), 5′-O-DMTr-T-T-3′-O-Lev cyanoethyl phosphate triester (d ⁇ 1.48, ⁇ 1.63), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.69, 8.64).
• the crude is a mixture of 5′-O-DMTr-G IBu -T-T-3′-O-Lev trimer (phosphite triester linkage d 141.56, 141.50, 141.44, 141.39, 141.13, 141.05; phosphate triester linkage d ⁇ 1.35, ⁇ 1.44, ⁇ 1.52, ⁇ 1.57) and of 5′-O-DMTr-G IBu -3′-cyanoethyl hydrogenophosphonate (d 9.03, 8.84).
• the crude is a mixture of 5′-O-DMTr-G IBu -3′-cyanoethyl phosphate diester (d ⁇ 2.52), 5′-O-DMTr-G IBu -T-T-3′-O-Lev cyanoethyl phosphate triester (d ⁇ 1.23, ⁇ 1.35, ⁇ 1.43, ⁇ 1.50, ⁇ 1.55), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 9.09, 8.90).
• This low yield is due to the low solubility of the detritylated trimer in dichloromethane, acetonitrile.
• the trimer is soluble in methanol, and DMF.
• the crude is a mixture of 5′-O-DMTr-T-A Bz -3′-O-Lev cyanoethyl phosphite triester (d 140.48, 140.30) and of 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.76, 8.71).
• the crude is a mixture of 5′-O-DMTr-T-3′-cyanoethyl phosphate diester ( 31 P NMR (CD 3 CN) d ⁇ 3.01), 5′-O-DMTr-T-A Bz -3′-O-Lev cyanoethyl phosphate triester (d ⁇ 1.58, ⁇ 1.80), 5′-O-DMTr-T-3′-cyanoethyl hydrogenophosphonate (d 8.76, 8.71).
• the desired trimer 5′-O-DMTr-C Bz -A Bz -T-3′-O-Lev cyanoethyl phosphite triester is characterized by 31 P NMR.
• the crude is a mixture of 5′-O-DMTr-C Bz -A Bz -T-3′-O-Lev trimer (phosphite triester linkage d 140.76, 140.65, 140.09, 140.03; phosphate triester linkage d ⁇ 1.53, ⁇ 1.57) and of 5′-O-DMTr-C Bz -3′-cyanoethyl hydrogenophosphonate (d 8.73).
• the crude is a mixture of 5′-O-DMTr-C Bz -T-A Bz -3′-O-Lev cyanoethyl phosphate triester (d ⁇ 1.54, ⁇ 1.59, ⁇ 162, ⁇ 1.72), 5′-O-DMTr-C Bz -3′-cyanoethyl hydrogenophosphonate (d 8.74).
• the desired tetramer 5′-O-DMTr-G IBu -C Bz -A Bz -T-3′-O-Lev is characterized by 31 P NMR.
• the crude is a mixture of 5′-O-DMTr-G IBu -C Bz -A Bz -T-3′-O-Lev tetramer (phosphite triester linkage d 141.86, 141.82, 141.76, 141.61, 140.69, 140.66, 140.61; phosphate triester linkage d ⁇ 1.53, ⁇ 1.58, ⁇ 1.61, ⁇ 1.64, ⁇ 1.71, ⁇ 1.82) and of 5′-O-DMTr-G IBu -3′-cyanoethyl hydrogenophosphonate (d 9.01, 8.84).
• the crude is a mixture of 5′-O-DMTr-G IBu -3′-cyanoethyl phosphate diester ( 31 P NMR (CD 3 CN) d ⁇ 2.69), 5′-O-DMTr-G IBu -C Bz -T-A Bz -3′-O-Lev cyanoethyl phosphate triester (d ⁇ 1.38, ⁇ 1.43, ⁇ 1.53, ⁇ 1.60, ⁇ 1.64), 5′-O-DMTr-C Bz -3′-cyanoethyl hydrogenophosphonate (d 9.02, 8.38).
• the desired pentamer 5′-O-DMTr-A Bz -G IBu -C Bz -A Bz -T-3′-O-Lev is characterized by 31 P NMR.
• the crude is a mixture of 5′-O-DMTr-A Bz -G IBu -C Bz -A Bz -T-3′-O-Lev pentamer (phosphite triester linkage d 141.00, 140.78, 140.68, 140.16, 139.94; phosphate triester linkage d ⁇ 1.36, ⁇ 1.42, ⁇ 1.46, ⁇ 1.52, ⁇ 1.57, ⁇ 1.67, ⁇ 1.70, ⁇ 1.82) and of 5′-O-DMTr-A Bz -3′-cyanoethyl hydrogenophosphonate (d 8.76, 8.71).
• the crude is a mixture of 5′-O-DMTr-A Bz -3′-cyanoethyl phosphate diester ( 31 P NMR (CD 3 CN) d ⁇ 2.67), 5′-O-DMTr-A Bz -G IBu -C Bz -T-A Bz -3′-O-Lev cyanoethyl phosphate triester (d ⁇ 1.24, ⁇ 1.39, ⁇ 1.54, ⁇ 1.66, ⁇ 1.71), 5′-O-DMTr-A Bz -3′-cyanoethyl hydrogenophosphonate (d 8.82).
• Detritylation The PS—N(CH 3 ) 3 + IO 4 ⁇ is filtered off and the solvent are evaporated.
• the crude is dissolved in 50 ml of CH 2 Cl 2 , the solution is washed with 50 ml of an aqueous solution of Na 2 S 2 O 3 0.2 M. The organic layer is separated, dried (Na 2 SO 4 ) and evaporated under reduce pressure.
• the crude is dissolved in 16 ml of CH 2 Cl 2 /CH 3 OH (7/3) and cooled in an ice bath. To this solution is added 4 ml of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3). The solution is stirred 45 min at 0° C.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 70%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 72%.
• the spectrophotometrical purity determined by HPLC is 99%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 100%.
• the spectrophotometrical purity determined by HPLC is 99%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 83%.
• the spectrophotometrical purity determined by HPLC is 85%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 98%.
• the spectrophotometrical purity determined by HPLC is 99%.
• the H-phosphonate dimer 5′-O-DMTr-T-T-3′-O-Lev (115 mg, 0,123 mmol) is dissolved in 4.0 ml of CH 2 Cl 2 /MeOH (7:3) and cooled in an ice bath.
• 1.0 ml of a solution of 10% BSA (benzene sulfonic acid) in CH 2 Cl 2 /MeOH (7:3) is added drop wise under stirring and the progress of the reaction is monitored by TLC. After 15 min the solution is diluted with 20 ml of CH 2 Cl 2 and then 0.4 g of poly(4-vinyl-pyridine) are added. The mixture is shaken 5 minutes and the resin is filtered off and washed with CH 2 Cl 2 . The product is purified by precipitation from CH 2 Cl 2 with ether and dried under vacuum. Yield 94 %.
• the spectrophotometrical purity determined by HPLC is 99%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over-Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 55%.
• the H-phosphonate trimer 5′-O-DMTr-dG IBu -T-T-3′-O-Lev (84 mg, 0,064 mmol) is dissolved in 4.0 ml of CH 2 Cl 2 /MeOH (7:3) and cooled in an ice bath.
• 1.0 ml of a solution of 10% BSA (benzene sulfonic acid) in CH 2 Cl 2 /MeOH (7:3) is added drop wise under stirring and the progress of the reaction is monitored by TLC. After 15 min the solution is diluted with 20 ml of CH 2 Cl 2 and then 0.4 g of poly(4-vinyl-pyridine) are added. The mixture is shaken 5 minutes and the resin is filtered off and washed with CH 2 Cl 2 . The product is purified by precipitation from CH 2 Cl 2 with ether and dried under vacuum. Yield 71%.
• the resin is filtered, washed with CH 2 Cl 2 .
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 75%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 95%.
• the spectrophotometrical purity determined by HPLC is 96%.
• the H-phosphonate dimer 5′-O-DMTr-dC Bz -dA Bz -3′-O-Lev (180 mg, 0,158 mmol) is dissolved in 4.0 ml of CH 2 Cl 2 /MeOH (7:3) and cooled in an ice bath.
• 1.0 ml of a solution of 10% BSA (benzene sulfonic acid) in CH 2 Cl 2 /MeOH (7:3) is added drop wise under stirring and the progress of the reaction is monitored by TLC. After 15 min the solution is diluted with 20 ml of CH 2 Cl 2 and then 0.4 g of poly(4-vinyl-pyridine) are added. The mixture is shaken 5 minutes and the resin is filtered off and washed with CH 2 Cl 2 . The product is purified by precipitation from CH 2 Cl 2 with ether and dried under vacuum. Yield 83%.
• the spectrophotometrical purity determined by HPLC is 74%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. Yield 50%.
• the spectrophotometrical purity determined by HPLC is 74%.
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the isolated product is dried under vacuum. 914 mg Yield 89%.
• the H-phosphonate dimer 5′-O-DMTr-T-dG ibu -3′-O-Lev (430 mg, 0.420 mmol) is dissolved in 8.0 ml of CH 2 Cl 2 /MeOH (7:3, v/v) and cooled in an ice bath.
• 8.0 ml of CH 2 Cl 2 /MeOH (7:3, v/v) 8.0 ml of CH 2 Cl 2 /MeOH (7:3, v/v)
• BSA benzene sulfonic acid
• the pyridinium salt present in solution is removed by aqueous extraction and the aqueous phase is washed twice with CH 2 Cl 2 .
• the organic fractions are collected, dried over Na 2 SO 4 , the solvent is evaporated and the pyridine is eliminated by coevaporation with toluene.
• the product is purified by precipitation from CH 2 Cl 2 with ether and dried under vacuum. 538 mg Yield 89%.
• trimer 5′-O-DMTr-C bz -T-dG ibu -3′-O-lev H-phosphonate (118 mg, 0.084 mmol) is coevaporated twice with dry pyridine (2 ⁇ 2 ml) and dissolved in 2 ml of CH 2 Cl 2 /py (1:1). To this solution is added successively triethylamine (6 mL, 0.5 eq), trimethylsilyl chloride (100 mL, 0.84 mmol, 10 eq) and N-[(2-cyanoethyl)thio]phthalimide (78 mg, 0.336 mmol, 10 eq).
• the desired 5′-O-DMTr-3′-O-Lev cyanoethyl phosphite triester base protected dimer is characterized by 31 P NMR.
• the crude is a mixture of 5′-O-DMTr-3′-O-Lev cyanoethyl phosphite triester base protected dimer and of 5′-O-DMTr-3′-cyanoethyl H-phosphonate base protected nucleotide.
• the poly(4-vinylpyridinum p-toluenesulfonate) is filtered off, washed 3 times with 50 ml of CH 2 Cl 2 and the solution is concentrated to 100 ml.
• Detritytlation To the previous solution is added 100 ml of MeOH so that the CH 2 Cl 2 /MeOH ratio is about 7/3. The mixture is cooled at 0° C. To the resulting solution is added 90 ml (56 mmol, 5.6 eq.) of a solution of benzene sulfonic acid 10% in CH 2 Cl 2 /CH 3 OH (7/3). The solution is stirred at 0° C. The detritylation is monitored by TLC and reverse phase HPLC. The reaction time is between 30 min and 1 h. When the reaction is complete, 100 ml of H 2 O is added to the mixture, the solution is shaken for 10 min at 0° C. Then, the reaction is stopped by stirring at 0° C.
• the dimer is characterized by 31 P NMR and by MALDI-TOF. The spectrophotometric purity is determined by reverse phase HPLC at 260 nm. Dimers performed Dimers following 5′-OH- this procedure Nu-Nu-3′-O- MW HPLC- Lev (g/mol) 31 P-NMR RT (min) Yield Purity A Bz -A Bz 939.91 68.11; 10.85 91% (9.5 g) 91% 68.06* C Bz -A Bz 915.88 68.03; 11.32; 94% (8.7 g) 91% 67.80* 11.46* G iBu -T 808.77 68.48; 9.72 91% (7.4 g) 91% 68.09* G iBu -A Bz 921.89 68.02; 10.32; 98% (10.3 g) 92% 67.80* 10.68* *mixture of Sp and Rp diastereoisomeres HPLC-Gradient [col

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