Synthesis of the thymidine building blocks for a nonhydrolyzable DNA analogue

Kawai, Stephen H.; Wang, Daguang; Just, George

doi:10.1139/v92-193

Cited by 19 publications

(9 citation statements)

References 17 publications

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“…This is exemplified by the spectrum of24 whose enlargement is shown nucleic acid duplexes with A-conformation (Scheme 3a) (19). This preference is re-inforced by the X-ray crystal structure of bicyclic nucleoside 20 (7), the solution structure of branchedchain nucleosides (7,8), and the 5'-unit of dinucleosides 5'-rT(2OH)sdT-3' and 5'-rT(2oMe)sdT-3' (8)(9)(10)12). In addition, 'H-NMR data reported on a number of 3'-deoxynucleosides are also consistent with a predominant C3'-endo pucker (20)(21)(22).…”

Section: Resultsmentioning

confidence: 90%

“…The sequences prepared (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) are shown in Table 1. Average coupling yields for dimer incorporation were -90% as assessed by the trityl assay method.…”

Section: Resultsmentioning

confidence: 99%

“…Following chain assembly, the oligonucleotides were cleaved from the support, deprotected and purified as previously described (9). The single absorption band on polyacrylamide gel found for each oligomer indicated their high purity (>95%) and the retarded mobility of the sulfide containing oligomers (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) relative to the unmodified sequence (5) (9). How do we account for: (i) the general destabilizing effect of (3'-CH2-CH2-S-CH2-5') linkages, and (ii) for the discriminatory binding properties of sulfide strands containing 2'-substituted (OH and OMe) sugars?…”

Section: Resultsmentioning

confidence: 99%

“…Our research in the antisense field has focused on oligonucleotide analogues in which some of the phosphodiester groups are replaced by the dialkyl sulfide linkage 3'-CH2-CH2-S-CH2-5' (7)(8)(9)(10)(11). This linkage is non-hydrolyzable, non-ionic, and its length approximates that of a phosphodiester linkage reasonably well.…”

Section: Introductionmentioning

confidence: 99%

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Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

et al. 1995

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INTRODUCTIONIn this report we describe the synthesis of oligonucleotides containing sulfide-linked dinucleoside units, namely rT(2'OH)dT, rT(2'0Me)5dT, dT8rU(2'OMe) and dT(2o0Me)5rU(2oMe). We also describe the interactions of such oligomers with complementary DNA and RNA targets, and provide the structural basis for their remarkable RNA binding selectivity. In all cases, the Tm values of the SIP-chimera duplexes were lower than those of the corresponding unmodified duplexes. We attribute this to steric interactions between the 5' sulfur and the atoms of the nearby base/sugar residues. The 2'-substituents (i.e., 2'OH or 2'OMe) vicinal to the alkylsulfide internucleoside linkage significantly perturb the structure and stability of the duplexes formed with DNA, and more so than with RNA. The introduction of three rT(2'OH)sdTp ( ' (5,6).Our research in the antisense field has focused on oligonucleotide analogues in which some of the phosphodiester groups are replaced by the dialkyl sulfide linkage 3'-CH2-CH2-S-CH2-5' (7-11). This linkage is non-hydrolyzable, non-ionic, and its length approximates that of a phosphodiester linkage reasonably well. More recently, we focused attention on the preparation of rT(20OH)SdT, rT(2 OMe)SdT, dTsrU(2'OMe) and rT(2'OMe)SrU(2'OMe) dimer units as well as their 3'-O-phosphoramidite derivatives for incorporation into oligonucleotides (11,12 (55°C, 16 h). The ammonia solution was collected by centrifuging the Eppendorf tube and then run through a Sephadex NAP-10 column which was pre-washed with 15 ml deionized water. The first eluting fractions (1.5 ml) were lyophilized to dryness and the resulting oligomer was redissolved in 1 ml of water. Purity of each oligomer was confmed by PAGE (26% polyacrylamide-7 M urea) run at 4°C, at a current of 10 mA, for 6-8 h (9). Melting experimentsMelting curves were measured in 10 mM NaH2PO4/Na2HPO4, 1 M NaCl buffer (pH 7.0) and analyzed the same way as described in reference 9. Circular dichroismThe CD spectrum ofeach sample was measured on a Jasco 500-C spectropolarimeter with a Jasco DP-J800/300 data processor. The cell temperature was kept at 50C. The concentration of the oligonucleotides were -2.5 jM (each strand).

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Section: Resultsmentioning

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

et al. 1995

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“…Synthesis of sulfide dimer (6) Full details of the preparation of mesylate 1 and thiol 2 have been published (31). The appropriately protected and activated sulfide dinucleoside required for incorporation into DNA was prepared according to the method outlined in Scheme 1.…”

Section: Resultsmentioning

confidence: 99%

Solid-phase synthesis and hybridization properties of DNA containing sulfide-linked dinucleosides

Kawai¹,

Wang²,

Giannaris³

et al. 1993

Nucl Acids Res

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Oligodeoxyribonucleotides incorporating non-hydrolyzable dialkyl sulfide linked thymidine dimers (TsT) were synthesized chemically by the solid-phase approach. The sulfide dimer TsT was stable to degradation by snake-venom phosphodiesterase, calf spleen phosphodiesterase, Nuclease P1 and Nuclease S1. Thermal denaturation analysis indicated that the incorporation of TsT dimers into DNA weakened, but did not prevent, binding to complementary DNA and RNA over a wide range of salt concentrations (10 mM to 2 M NaCl).

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Ein Sulfidbindungen enthaltendes Oligonucleotid‐Analogon mit selektiven Hybridisierungseigenschaften

et al. 1993

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RNA‐ von DNA‐Sequenzen zu unterscheiden gelingt effizient mit einem modifizierten Oligonucleotid, das nicht‐hydrolysierbare Sulfidbrücken enthält. Ein Dodecamer, das drei Thioether‐verknüpfte ribo‐T‐T‐Dimere 1 enthält und problemlos durch Standard‐Festphasenmethoden im Syntheseautomaten herstellbar ist, bindet kooperativ an komplementäre RNA, nicht aber an DNA. Oligonucleotide dieses neuen Typs sollten in der Antisense‐Technologie verwendbar sein.magnified image

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Synthesis of the thymidine building blocks for a nonhydrolyzable DNA analogue

Cited by 19 publications

References 17 publications

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

Solid-phase synthesis and hybridization properties of DNA containing sulfide-linked dinucleosides

Ein Sulfidbindungen enthaltendes Oligonucleotid‐Analogon mit selektiven Hybridisierungseigenschaften

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