Synthesis of 3′-Sugar- and Base-Modified Nucleotides and Their Application as Potent Chain Terminators in DNA Sequencing

Two 3′-modified and three base-modified ddNTPs were synthesized and tested with several DNA polymerases for incorporation activity. Starting from 3′-azido-3′-deoxythymidine (AZT; 1 ), we were able to produce 3′-deoxy-3′-isocyanato-thymidine and 3′-deoxy-3′-isothiocyanatothymidine ( 3 and 4 , resp.) in a rapid synthesis based on the solid-support approach (Scheme 1). These 3′-functionalities could be used to attach a spacer molecule via urea and thiourea groups, respectively. Since the thus-obtained tethered nucleotides 7 and 8 can be used to label with fluorescent dyes (cf. Scheme 5), they are convenient building blocks for practical applications in DNA sequencing. Furthermore, we synthesized, via 14 (Scheme 2), 17 (Scheme 3), and 19 (Scheme 4), the N⁴-modified dideoxycytidine 5′-triphosphate dye derivatives 22 , 23 , and 24 , respectively, with different lengths of linkers between the base residue and the dye (Scheme 5). Base-specific termination for the derivatives 22 and 24 was demonstrated (Fig. 2a and 2b).     

Efficient Automated Solid‐Phase Synthesis of DNA and RNA 5′‐Triphosphates

A fast, high‐yielding and reliable method for the synthesis of DNA‐ and RNA 5′‐triphosphates is reported. After synthesizing DNA or RNA oligonucleotides by automated oligonucleotide synthesis, 5‐chloro‐saligenyl‐N,N‐diisopropylphosphoramidite was coupled to the 5′‐end. Oxidation of the formed 5′‐phosphite using the same oxidizing reagent used in standard oligonucleotide synthesis led to 5′‐cycloSal‐oligonucleotides. Reaction of the support‐bonded 5′‐cycloSal‐oligonucleotide with pyrophosphate yielded the corresponding 5′‐triphosphates. The 5′‐triphosphorylated DNA and RNA oligonucleotides were obtained after cleavage from the support in high purity and excellent yields. The whole reaction sequence was adapted to be used on a standard oligonucleotide synthesizer.     

3′-Amino-Modified Nucleotides Useful as Potent Chain Terminators for current DNA sequencing methods

We describe the synthesis of modified nucleoside triphosphates of the four DNA bases containing a 3′-amino group which were prepared from the corresponding 3′-azido derivatives. Introduction of the triphosphate and subsequent reduction of the N₃ to the NH₂ group led directly to the target molecules 6a–d . Furthermore, 3′-amino-2′,3′-dideoxynucleoside 5′-triphosphates proved to be potent inhibitors of the enzymatic synthesis of DNA catalyzed by the standard sequencing enzymes T7 DNA polymerase, sequenase version 2.0, Thermus aquaticus DNA polymerase, and Thermus thermophilus DNA polymerase. Both radioactive and fluorescent sequencing methods were applied successfully to the 3′-amino-modified terminators. Investigations in view of using these chain terminators according to Sanger's sequencing method for fluorescence labeling were done.     

Enzymatic Synthesis of 7′,5′‐Bicyclo‐DNA Oligonucleotides

The selection of artificial genetic polymers with tailor‐made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo‐DNA triphosphate (i.e., 7′,5′‐bc‐TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7′,5′‐bc‐TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA‐dependent DNA synthesis and potentially also XNA‐dependent XNA synthesis. However, DNA‐dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7′,5′‐bc‐TTP.     

Single‐Stranded DNA: Replacement of Canonical by Base‐Modified Nucleosides in the Minihairpin 5′‐d(GCGAAGC)‐3′ and Constructs with the Aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′

The minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) was modified either in the loop region, in the base‐paired stem, or at the 5′‐terminus by incorporation of base‐modified nucleosides. The thermal melting was correlated to the structural changes induced by the various donor‐acceptor properties of the nucleosides. Overhanging nonpaired nucleosides at the 5′‐terminus stabilized the hairpin, while a reverse of the dG³?dA⁵ sheared base pair to dA³?dG⁵ severely affected the stability. The combination of the minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) and the thrombin‐binding aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′ ( 2 (= 46 )) resulted in the new construct 5′‐d(GGTTGGGCGAAGC GGTTGG)‐3′ ( 43 ) arising by replacement of the 5′‐d(TGT)‐3′ loop of 2 by the minihairpin. The fused oligonucleotide 43 exhibits a two‐phase thermal transition indicating the presence of the two unaltered moieties. According to slight changes of the T_m values of the construct 43 as compared to the separate units 1 and 2 , cooperative distorsions are discussed.     

Nucleosides XII.1 Synthesis of 5‐Modified Isoguanosines and Reinvestigation of 5′‐Deoxy‐N3,5′‐cycloisoguanosine

Isoguanosine ( 3 ) underwent a coupling reaction with diaryl disulfides in the presence of tri‐n‐butylphosphine when its 6‐amino group was protected by N,N‐dimethylaminomethylidene. The synthesis of 5′‐deoxy‐N³,5′‐cycloisoguanosine ( 6 ) and its 2′,3′‐O‐isopropylidene derivative ( 11 ) were accomplished in excellent yields from isoguanosines ( 3 & 10 ) in the presence of triphenylphospine and carbon tetrachloride in pyridine. Chlorination at the 5′‐position of isoguanosine ( 3 ) with thionyl chloride followed by the aqueous base‐promoted cyclization afforded the same product 6 . The structures were elucidated by spectroscopic analysis including IR, UV, 1‐D and 2‐D NMR.     

四色荧光标记二硫键可逆终端的合成及在DNA合成测序中的应用

分别以5-碘-2'-脱氧尿苷、 5-碘-2'-脱氧胞苷、 7-去氮-7-碘-2'-脱氧腺苷及7-去氮-7-碘-2'-脱氧鸟苷为原料, 以二硫键为可裂解连接单元, 通过多步反应合成了四色荧光标记不同碱基的脱氧核糖核苷酸; 研究了该类荧光标记核苷酸作为可逆终端在DNA合成测序中的应用. 所得产物结构经¹H NMR, ³¹P NMR及HRMS表征, 并对其进行了DNA高通量测序的测试. 结果表明, 该类荧光标记核苷酸作为DNA合成测序的可逆终端能够满足高通量测序的生化反应要求, 具有较好的应用前景.     

Synthesis of 3′,5′‐Cyclic Phosphate and Thiophosphate Esters of 2′‐C‐Methyl Ribonucleosides

2′‐C‐Methylnucleosides are known to exhibit antiviral activity against Hepatitis C virus. Since the inhibitory activity depends on their intracellular conversion to 5′‐triphosphates, dosing as appropriately protected 5′‐phosphates or 5′‐phosphorothioates appears attractive. For this purpose, four potential pro‐drugs of 2′‐C‐methylguanosine, i.e., 3′,5′‐cyclic phosphorothioate of 2′‐C‐methylguanosine and 2′‐C,O⁶‐dimethylguanosine, 1 and 2 , respectively, the S‐[(pivaloyloxy)methyl] ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphorothioate and the O‐methyl ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphate, 3 and 4 , respectively, have been prepared.     

Synthesis of (5′S)‐5′‐C‐Alkyl‐2′‐deoxynucleosides

We describe the synthesis of (5′S)‐5′‐C‐butylthymidine ( 5a ), of the (5′S)‐5′‐C‐butyl‐ and the (5′S)‐5′‐C‐isopentyl derivatives 16a and 16b of 2′‐deoxy‐5‐methylcytidine, as well as of the corresponding cyanoethyl phosphoramidites 9a , b and 14a , b , respectively. Starting from thymidin‐5′‐al 1 , the alkyl chain at C(5′) is introduced via Wittig chemistry to selectively yield the (Z)‐olefin derivatives 3a and 3b (Scheme 2). The secondary OH function at C(5′) is then introduced by epoxidation followed by regioselective reduction of the epoxy derivatives 4a and 4b with diisobutylaluminium hydride. In the latter step, a kinetic resolution of the diastereoisomer mixture 4a and 4b occurs, yielding the alkylated nucleoside 2a and 2b , respectively, with (5′S)‐configuration in high diastereoisomer purity (de=94%). The corresponding 2′‐deoxy‐5‐methylcytidine derivatives are obtained from the protected 5′‐alkylated thymidine derivatives 7a and 7b via known base interconversion processes in excellent yields (Scheme 3). Application of the same strategy to the purine nucleoside 2′‐deoxyadenine to obtain 5′‐C‐butyl‐2′‐deoxyadenosine 25 proved to be difficult due to the sensitivity of the purine base to hydride‐based reducing agents (Scheme 4).     

Dehydrogenative Synthesis of 2,2′‐Bipyridyls through Regioselective Pyridine Dimerization

2,2′‐Bipyridyls have been utilized as indispensable ligands in metal‐catalyzed reactions. The most streamlined approach for the synthesis of 2,2′‐bipyridyls is the dehydrogenative dimerization of unfunctionalized pyridine. Herein, we report on the palladium‐catalyzed dehydrogenative synthesis of 2,2′‐bipyridyl derivatives. The Pd catalysis effectively works with an Ag^I salt as the oxidant in the presence of pivalic acid. A variety of pyridines regioselectively react at the C2‐positions. This dimerization method is applicable for challenging substrates such as sterically hindered 3‐substituted pyridines, where the pyridines regioselectively react at the C2‐position. This reaction enables the concise synthesis of twisted 3,3′‐disubstituted‐2,2′‐bipyridyls as an underdeveloped class of ligands.     

Synthesis of various 5-substituted 2′-deoxy-3′-5′-di-O-acetyluridines

The Pd(0)-catalyzed coupling reaction of β-5-iodo-2′-deoxy-3′,5′-di-O-acetyluridine with various heteroaryltrimethylstannyl compounds gave the corresponding β-5-heteroaryl-2′-deoxy-3′,5′-di-O-acetyluridines in moderate yields. This direct coupling approach for nucleosides represented an interesting alternative to the 5-heteroaryl functionalization of pyrimidines followed by the Hilbert-Johnson glycosylation reaction which often yields mixtures of the α and β anomers.     

A Direct Synthesis of Nucleoside Analogs Homologated at the 3′‐ and 5′‐Positions

A new route is presented to prepare analogs of nucleosides homologated at the 3′‐ and 5′‐positions. This route, applicable to both the D ‐ and L ‐enantiomeric forms, is suitable for the preparation of monomeric bis‐homonucleosides needed for the synthesis of oligonucleotide analogs. It begins with the known monobenzyl ether 3 of pent‐2‐yne‐1,5‐diol, which is reduced to alkenol 4 . Sharpless asymmetric epoxidation of 4 , followed by opening of the epoxide 5 with allylmagnesium bromide, gives a mixture of diols 6 and 7 . Protection of the primary alcohol as a silyl ether followed by treatment with OsO₄, NaIO₄, and mild acid in MeOH, followed by reduction, yields (2R,3R) {{[(tert‐butyl)diphenylsilyl]oxy}methyl}tetrahydro‐2‐(2‐hydroxyethyl)‐5‐methoxyfuran (=methyl 3‐{{[(tert‐butyl)diphenylsilyl]oxy}methyl}‐2,3,5‐trideoxy‐α/β‐D ‐erythro‐hexafuranoside; 10 ) (Scheme 1). Protected nucleobases are added to this skeleton with the aid of trimethylsilyl triflate (Scheme 2). The o‐toluoyl (2‐MeC₆H₄CO) and p‐anisoyl (4‐MeOC₆H₄CO) groups were used to protect the exocyclic amino group of cytosine. The bis‐homonucleoside analogs 11 and 14a are then converted to monothiol derivatives suitable for coupling (Schemes 3 and 4) to oligonucleotide analogs with bridging S‐atoms. This synthesis replaces a much longer synthesis for analogous nucleoside analogs that begins with diacetoneglucose (=1,2 : 5,6‐di‐O‐isopropylideneglucose), with the stereogenic centers in the final products derived from the Sharpless asymmetric epoxidation. The new route is useful for large‐scale synthesis of these building blocks for the synthesis of oligonucleotide analogs.     

Synthesis and photophysical properties of 2,5,8,11‐tetrakis(5‐hexylthiophen‐2‐yl)tetrathieno[2,3‐a:3′,2′‐c:2′′,3′′‐f:3′′′,2′′′‐h]naphthalene

The title compound, C₅₈H₆₄S₈, has been prepared by Pd‐catalysed direct C—H arylation of tetrathienonaphthalene (TTN) with 5‐hexyl‐2‐iodothiophene and recrystallized by slow evaporation from dichloromethane. The crystal structure shows a completely planar geometry of the TTN core, crystallizing in the monoclinic space group P2₁/c. The structure consists of slipped π‐stacks and the interfacial distance between the mean planes of the TTN cores is 3.456 (5) Å, which is slightly larger than that of the comparable derivative of tetrathienoanthracene (TTA) with 2‐hexylthiophene groups. The packing in the two structures is greatly influenced by both the aromatic core of the structure and the alkyl side chains.     

Electron Attachment to Hydrated Oligonucleotide Dimers: Guanylyl‐3′,5′‐Cytidine and Cytidylyl‐3′,5′‐Guanosine

The dinucleoside phosphate deoxycytidylyl‐3′,5′‐deoxyguanosine (dCpdG) and deoxyguanylyl‐3′,5′‐deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5′ end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3′ end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine‐containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The π‐stacking interaction between nucleobases G and C seems unlikely to improve the electron‐capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron‐capturing ability of cytosine should be attributed to the intensified proton accepting–donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O? C σ bond and N‐glycosidic bond breakage, might be expected for the radical anions of the guanosine–cytosine mixed oligonucleotides.     

Synthesis of 5-benzyl and 5-benzyloxybenzyl-3′-azido-2′,3′-dideoxyuridine and their analogues as potential anti-AIDS agents

5-Benzyl and 5-benzyloxybenzyl-substituted 3′-azido-2′,3′-dideoxyuridine, ( 8a and 8b ), 3′-halogeno-2′,3′-dideoxyuridine, 9a, 9b, 10a, 10b, 11a and 11b , and 2′,3′-dideoxyuridine, 12a and 12b , of Scheme I were synthesized as potential anti AIDS agents. Synthesis of epimers of 8a and 8b , 5-benzyl- and 5-benzyloxybenzyl-1-(3′-azido-2′,3′-dideoxy-β-D-threo-pentafuranosyl)uracil, 15a and 15b , and 5-benzyl- and 5-benzyloxy-5′-azido-2′,5′-dideoxyuridine, 16a and 16b , shown in Scheme II, were also reported.     

Synthesis of 3′‐1,2,4‐triazolo‐ and 3′‐1,3,4‐thiadiazoliminothymidines

New 5′‐acetyl‐3′‐1,3,4‐thiadiazoliminothymidines 11, 14 were prepared, via spontaneous rearrangments, by cycloaddition of 5′‐acetyl‐3′‐deoxy‐3′‐isothiocyanatothymidine 9 with 1‐aza‐2‐azoniaallene hexachloantimonates. Similary, 3′‐cyano analogue 19 was reacted with the same cumulenes to furnish 3′‐1,2,4‐triazolo‐thymidines 22, 24 , and 26 . Deblocking of the acylated products afforded the free nucleosides. © 2003 Wiley Periodicals, Inc. Heteroatom Chem 14:298–303, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10146     

Synthesis of Some Novel Phenyl Substituted Oxothiazolidin- 1’’,3’’,4’’-thiadiazolo-[3’,4’-b]thiazoline of 3β-Substituted Cholestane

Three title compounds 4a—4c have been synthesized by the cyclodehydration of 1’-benzylidine-4’-(3β-substituted-5α-cholestane-6-yl)thiosemicarbazones 2a—2c with thioglycolic acid followed by the treatment with cold conc. H2SO4 in dioxane. The compounds 2a—2c were prepared by condensation of 3β-substituted-5α-cholestan- 6-one-thiosemicarbazones 1a—1c with benzaldehyde. These thiosemicarbazones 1a—1c were obtained by the reaction of corresponding 3β-substituted-5α-cholestan-6-ones with thiosemicarbazide in the presence of few drops of conc. HCl in methanol. The structures of the products have been established on the basis of their elemental, analytical and spectral data.