Synthesis and hybridization studies of oligonucleotides containing 1-(2-deoxy-2-α-C-hydroxymethyl-β-d-ribofuranosyl)thymine (2′-α-hm-dT)

Nucleic Acids Research

Volumn 33, Issue 22, 2005, Pages 7019-7028

  Peng, Chang Geng ^a   Damha, Masad J ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

1 (2 DEOXY 2 ALPHA C HYDROXYMETHYL BETA RIBOFURANOSYL)THYMINE; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; PHOSPHORAMIDOUS ACID DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; CONTROLLED STUDY; DNA CONFORMATION; DNA MODIFICATION; DNA RNA HYBRIDIZATION; DNA STRAND; PRIORITY JOURNAL; PROTEIN DENATURATION; RNA HYBRIDIZATION; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

CIRCULAR DICHROISM; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; OLIGORIBONUCLEOTIDES; ORGANOPHOSPHORUS COMPOUNDS; RNA; RNA STABILITY; TEMPERATURE; THYMIDINE;

EID: 31144444920     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki1003     Document Type: Article

References (23)

1. Wasner,M., Arion,D., Borkow,G., Noronha,A., Uddin,A.H., Parniak,M.A. and Damha,M.J. (1998) Physicochemical and biochemical properties of 2′,5′-linked RNA and 2′,5′-RNA:3′,5′-RNA hybrid Duplexes. Biochemistry, 37, 7478-7486.
2. Peng,C.G., Hannoush,R.N. and Damha,M.J. (2005) Synthesis of a 'taller' 2′,5′-linked ribonucleic acid: 2′-α-C-hydroxymethyl 2′,5′-linked RNA. J. Biomol. Struct. Dyn., 22, 856.
3. Giannaris,P.A. and Damha,M.J. (1993) Oligoribonucleotides containing 2′,5′-phosphodiester linkages exhibit binding selectivity for 3′,5′-RNA over 3′,5′-ssDNA. Nucleic Acids Res., 21, 4742-4749.
4. Bhan,P., Bhan,A., Hong,M., Hartwell,J.G., Saunders,J.M. and Hoke,G.D. (1997) 2′,5′-Linked oligo-3′-deoxyribonucleoside phosphorothioate chimeras: Thermal stability and antisense inhibition of gene expression. Nucleic Acids Res., 25, 3310-3317.
5. Damha,M.J. and Noronha,A. (1998) Recognition of nucleic acid double helices by homopyrimidine 2′,5′-linked RNA. Nucleic Acids Res., 26, 5152-5156.
6. Torrence,P.F., Maitra,R.K., Lesiak,K., Khamnei,S., Zhou,A. and Silverman,R.H. (1993) Targeting RNA for degradation with a (2′-5′) oligoadenylate-antisense chimera. Proc. Natl Acad. Sci. USA, 90, 1300-1304.
7. Xiao,W., Li,G., Maitra,R.K., Maran,A., Silverman,R.H. and Torrence,P.F. (1997) Correlation of selective modifications to a 2′,5′-oligoadenylate-3′,5′-deoxyribonucleotide antisense chimera with affinity for the target nucleic acid and with ability to activate RNAase L. J. Med. Chem., 40, 1195-1200.
8. Kandimalla,E.R., Manning,A., Zhao,Q., Shaw,D.R., Byrn,R.A., Sasisekharan,V. and Agrawal,S. (1997) Mixed backbone antisense oligonucleotides: Design, biochemical and biological properties of oligonucleotides containing 2′-5′-ribo- and 3′-5′-deoxyribonucleotide segments. Nucleic Acids Res., 25, 370-378.
9. Damha,M.J., Giannaris,P.A. and Khan,N. (1991) 2′-5′-Linked oligonucleotides form stable complexes with complementary RNA and DNA. Nucleic Acids Symp. Ser., 290.
10. Premraj,B.J., Patel,P.K., Kandimalla,E.R., Agrawal,S., Hosur,R.V. and Yathindra,N. (2001) NMR structure of a 2′,5′ RNA favors a type duplex with compact C2′ endo nucleotide repeat. Biochem. Biophys. Res. Commun., 283, 537-543.
11. Premraj,B.J., Raja,S. and Yathindra,N. (2002) Structural basis for the unusual properties of 2′,5′ nucleic acids and their complexes with RNA and DNA. Biophys. Chem., 95, 253-272.
12. Schmit,C., Bevierre,M.-O., De Mesmaeker,A. and Altmann,K.-H. (1994) The effects of 2′- and 3′-alkyl substituents on oligonucleotide hybridization and stability. Bioorg. Med. Chem. Lett., 4, 1969-1974.
13. Freier,S.M. and Altmann,K.H. (1997) The ups and downs of nucleic acid duplex stability: Structure-stability studies on chemically-modified DNA:RNA duplexes. Nucleic Acids Res., 25, 4429-4443.
14. Martin,P. (1995) New access to 2′-O-alkylated ribonucleosides and properties of 2′-O-alkylated oligoribonucleotides. Helv. Chim. Acta, 78, 486-504.
15. Hannoush,R.N. and Damha,M.J. (2001) Remarkable stability of hairpins containing 2′,5′-linked RNA loops.J. Am. Chem. Soc., 123, 12368-12374.
16. Alberts,B. (1989) Molecular Biology of the Cell. Carland Publishing, Inc., NY, pp. 304.
17. Schmit,C. (1994) Efficient synthesis of 2′-deoxy-2′-a-C-substituted nucleosides. Synlett, 238-240.
18. Li,N.-S. and Piccirilli,J.A. (2004) Synthesis of the phosphoramidite derivatives of 2′-deoxy-2′-C-a-methylcytidine and 2′-deoxy-2′-C-a-hydroxymethylcytidine: Analogues for chemical dissection of RNA′s 2′-hydroxyl group. J. Org. Chem., 69, 4751-4759.
19. Kocienski,P.J. (2004) Protecting group. Georg Thieme, NY, pp. 215.
20. Damha,M.J. and Ogilvie,K.K. (1993) Oligoribonucleotide synthesis. The silyl-phosphoramidite method. Methods Mol. Biol., 20, 81-114.
21. Hannoush,R.N., Carriero,S., Min,K.-L. and Damha,M.J. (2004) Selective inhibition of HIV-1 reverse transcriptase (HIV-1 RT) RNase H by small RNA hairpins and dumbbells. ChemBioChem, 5, 527-533.
22. Denisov,A.Y., Hannoush,R.N., Gehring,K. and Damha,M.J. (2003) A novel RNA motif based on the structure of unusually stable 2′,5′-linked r(UUCG) loops. J. Am. Chem. Soc., 125, 11525-11531.
23. Hannoush,R.N., Min,K.-L. and Damha,M.J. (2004) Diversity-oriented solid-phase synthesis and biological evaluation of oligonucleotide hairpins as HIV-1 RT RNase H inhibitors. Nucleic Acids Res., 32, 6164-6175.