Synthesis and properties of 4′-thioDNA: Unexpected RNA-like behavior of 4′-thioDNA

Nucleic Acids Research

Volumn 34, Issue 12, 2006, Pages 3476-3483

  Inoue, Naonori ^a   Minakawa, Noriaki ^a   Matsuda, Akira ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; NUCLEOSIDE; OLIGODEOXYRIBONUCLEOTIDE; PHOSPHODIESTERASE I; PHOSPHODIESTERASE I, SNAKE VENOM; RNA;

ARTICLE; CHEMISTRY; CIRCULAR DICHROISM; HUMAN; METABOLISM; SYNTHESIS;

CIRCULAR DICHROISM; DEOXYRIBONUCLEASE I; HUMANS; OLIGODEOXYRIBONUCLEOTIDES; PHOSPHODIESTERASE I; RNA; THIONUCLEOSIDES;

EID: 33746857804     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl491     Document Type: Article

References (35)

1. Kurreck,J. (2003) Antisense technologies; improvement through novel chemical modifications. Eur. J. Biochem., 270, 1628-1644.
2. Jayasena,S.D. (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem., 45, 1628-1650.
3. Leydier,C., Bellon,L., Barascut,J.-L., Morvan,F., Rayner,B. and Imbach,J.-L. (1995) 40-Thio-RNA: synthesis of mixed base 4′-thio- oligoribonucleotides, nuclease resistance, and base pairing properties with complementary single and double strand. Antisense Res. Dev., 5, 167-174.
4. Hancox,E.L., Connolly,B.A. and Walker,R.T. (1993) Synthesis and properties of oligodeoxynucleotides containing the analogue 2′-deoxy- 4′-thiothymidine. Nucleic Acids Res., 21, 3485-3491. (Pubitemid 23241483)
5. Kumar,S., Horton,J.R., Jones,G.D., Walker,R.T., Roberts,R.J. and Cheng,X. (1997) DNA containing 4′-thio-2′-deoxycytidine inhibits methylation by HhaI methyltransferase. Nucleic Acids Res., 25, 2773-2783. (Pubitemid 27299791)
6. Jones,G.D., Lesnik,E.A., Owens,S.R., Risen,L.M. and Walker,R.T. (1996) Investigation of some properties of oligodeoxynucleotides containing 4′ -thio-2′-deoxynucleotides: duplex hybridization and nuclease sensitivity. Nucleic Acids Res., 24, 4117-4122. (Pubitemid 26377323)
7. Jones,G.D., Altmann,K.-H., Hüsken,D. and Walker,R.T. (1997) Duplex- and triplex-forming properties of 40-thio-modified oligodeoxynucleotides. Bioorg. Med. Chem. Lett., 7, 1275-1278. (Pubitemid 27223385)
8. Naka,T., Nishizono,N., Minakawa,N. and Matsuda,A. (1999) Investigation of the stereoselective coupling of thymine with meso-thiolane-3,4-diol-1-oxide derivatives via the Pummerer reaction. Tetrehedron Lett., 40, 6297-6300. (Pubitemid 29378434)
9. Naka,T., Minakawa,N., Abe,H., Kaga,D. and Matsuda,A. (2000) The stereoselective synthesis of 40-b-thioribonucleosides via the Pummerer reaction. J. Am. Chem. Soc., 122, 7233-7243. (Pubitemid 30636710)
10. Minakawa,N., Kato,Y., Uetake,K., Kaga,D. and Matsuda,A. (2003) An improved large scale synthesis of 1,4-anhydro-4-thio-D-ribitol. Tetrahedron, 59, 1699-1702. (Pubitemid 36207547)
11. Hoshika,S., Minakawa,N. and Matsuda,A. (2004) Synthesis and physical and physiological properties of 40-thioRNA: application to post-modification of RNA aptamer toward NF-kB. Nucleic Acids Res., 32, 3815-3825. (Pubitemid 39199074)
12. Kato,Y., Minakawa,N., Komatsu,Y., Kamiya,H., Ogawa,N., Harashima,H. and Matsuda,A. (2005) New NTP analogs: the synthesis of 4′-thioUTP and 4′-thioCTP and their utility for SELEX. Nucleic Acids Res., 33, 2942-2951. (Pubitemid 41511233)
13. Hoshika,S., Minakawa,N., Kamiya,H., Harashima,H. and Matsuda,A. (2005) RNA interference induced by siRNAs modified with 4′-thioribonucleosides in cultured mammalian cells. FEBS Lett., 579, 3115-3118. (Pubitemid 40797844)
14. Dande,P., Prakash,T.P., Sioufi,N., Gaus,H., Jarres,R., Bredeja,A., Swayze,E.E., Griffey,R.H. and Bhat,B. (2006) Improving RNA interference in mammalian cells by 4′-thio-modified small interfering RNA (siRNA): effect on siRNA activity and nuclease stability when used in combination with 2′-O-alkyl modifications. J. Med. Chem., 49, 1624-1634. (Pubitemid 43376507)
15. Inoue,N., Kaga,D., Minakawa,N. and Matsuda,A. (2005) Practical synthesis of 2′-deoxy-4′-thioribonucleosides: substrates for the synthesis of 4′-thioDNA. J. Org. Chem., 70, 8597-8600. (Pubitemid 41457030)
16. Johnson,C.W.,Jr (1996) Determination of the conformation of nucleic acids by electronic CD. In Fasman,G.D. (ed.), Circular Dichroism and the Conformational Analysis of Biomolecules. Plenum Press, NY, pp. 433-468.
17. Gray,D.M., Ratliff,R.L. and Vaughan,M.R. (1992) Circular dichroism spectroscopy of DNA. Methods Enzymol., 211, 389-406.
18. Boggon,T.J., Hancox,E.L., McAuley-Hecht,K.E., Connolly,B.A., Hunter,W.N., Brown,T., Walker,R.T. and Leonard,G.A. (1996) The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4′-thio-2′-deoxythymidine nucleotides. Nucleic Acids Res., 24, 951-961.
19. Wilson,W.D., Ratmeyer,L., Zhao,M., Strekowski,L. and Boykin,B. (1993) The search for structure-specific nucleic acid-interactive drugs: effects of compound structure on RNA versus DNA interaction strength. Biochemistry, 32, 4098-4104. (Pubitemid 23127004)
20. Chen,Q., Shafer,R.H. and Kuntz,I.D. (1997) Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry, 36, 11402-11407. (Pubitemid 27408622)
21. Park,H., Arnott,S., Chandrasekaran,R. and Millane,R.P. (1987) Structure of the a-form of poly[d(A)]•poly[d(T)] and related polynucleotide duplexes. J. Mol. Biol., 197, 513-523.
22. Shaw,J.-P., Kent,K., Bird,J., Fishback,J. and Froehler,B. (1991) Modified deoxyoligonucleotides stable to exonuclease degradation in serum. Nucleic Acids Res., 19, 747-750. (Pubitemid 21913146)
23. 2 complex at 2.3 Å resolution. J. Mol. Chem., 226, 1237-1256.
24. Cummins,L.L., Owens,S.R., Risen,L.M., Lesnik,E.A., Freier,S.M., Charles,M., Guinosso,C.J. and Cook,P.D. (1995) Characterization of fully 2′-modified oligoribonucleotide hetero- and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res., 23, 2019-2024.
25. Lockard,R.E. and Kumar,A. (1981) Mapping tRNA structure in solution using double-stranded specific ribonuclease V1 from cobra venom. Nucleic Acids Res., 9, 5125-5140. (Pubitemid 12204933)
26. Auron,P.E., Weber,L.D. and Rich,A. (1982) Comparison of transfer ribonucleic acid structures using cobra venom and S1 endonucleases. Biochemistry, 21, 4700-4706. (Pubitemid 13199304)
27. Wyatt,J.R. and Walker,G.T. (1989) Deoxynucleotide-containing oligoribonucleotide duplexs: stability and susceptibility to RNase V1and RNase H. Nucleic Acids Res., 17, 7833-7842. (Pubitemid 19251950)
28. Kopka,M.L., Fratini,A.V., Drew,H.R. and Dickerson,R.E. (1983) Ordered water structure around a B-DNA dodecamer. A quantitative study. J. Mol. Biol., 163, 129-146. (Pubitemid 13142801)
29. Gryaznov,S.M., Lloyd,D.H., Chen,J., Schultz,R.G., DeDionisio,L.A., Ratmeyer,L. and Wilson,W.D. (1995) Oligonucleotide N3′ → P5′phosphoramidites. Proc. Natl Acad. Sci. USA, 92, 5798-5802.
30. Heinemann,U., Rudolph,L., Alings,C., Morr,M., Heikens,W., Frank,R. and Blöcker,H. (1991) Effect of a single 3′-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix. Nucleic Acid Res., 19, 427-433. (Pubitemid 21897022)
31. 3)-O-5′ or an MMI backbone linker. Biochemistry, 38, 12586-12596.
32. Pallan,P.S., Matt,P., Wilds,C.J., Altmann,K.-H. and Egli,M. (2006) RNA-binding affinities and crystal structure of oligonucleotides containing five-atom amide-based backbone structures. Biochemistry, 45, 8048-8057. (Pubitemid 43993225)
33. Kovács,T., Párkányi,L., Pelczer,I., Cervantes-Lee,F., Pannell,K.H. and Torrence,P.F. (1991) Solid-state and solution conformation of 3′-amino-3′-deoxythymidine, precursor to a noncompetitive inhibitor of HIV-1 reverse transcriptase. J. Med. Chem., 34, 2595-2600.
34. Koole,L.H., Plavec,J., Liu,H., Vincent,B.R., Dyson,M.R., Coe,P.L., Walker,R.T., Hardy,G.W., Rahim,S.G. and Chattopadhyaya,J. (1992) Conformation of two 4′-thio-2′-deoxynucleoside analogs studied by 500-MHz 1H NMR spectroscopy and X-ray crystallography. J. Am. Chem. Soc., 114, 9936-9943. (Pubitemid 23021942)
35. Kodama,T., Shuto,S. and Matsuda,A. (2006) Synthesis of pyrimidine 1′-fluoronucloeosides. Tetrahedron Lett., 47, 4429-4432.