Hybridization properties and enzymatic replication of oligonucleotides containing the photocleavable 7-nitroindole base analog

Nucleic Acids Research

Volumn 33, Issue 5, 2005, Pages 1532-1543

  Crey Desbiolles, Caroline ^a   Berthet, Nathalie ^a   Kotera, Mitsuharu ^a   Dumy, Pascal ^a  

^a Centre National de la Recherche Scientifique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

7 NITROINDOLE 2' DEOXYRIBONUCLEOSIDE; DNA FRAGMENT; DNA POLYMERASE; EXONUCLEASE; INDOLE DERIVATIVE; OLIGONUCLEOTIDE; PHOSPHORAMIDOUS ACID DERIVATIVE; UNCLASSIFIED DRUG; 5 NITROINDOLE; 5 NITROINDOLE 2' DEOXYRIBOSE 5' TRIPHOSPHATE; 5-NITROINDOLE; 5-NITROINDOLE-2'-DEOXYRIBOSE-5'-TRIPHOSPHATE; 7-NITROINDOLE 2'-DEOXYRIBONUCLEOSIDE; DEOXYRIBONUCLEOSIDE; DEOXYRIBONUCLEOTIDE; DNA DIRECTED DNA POLYMERASE BETA; OLIGODEOXYRIBONUCLEOTIDE; PRIMER DNA;

ARTICLE; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA DEGRADATION; DNA HYBRIDIZATION; DNA REPLICATION; DNA TEMPLATE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME MECHANISM; GENE INSERTION; MOLECULAR RECOGNITION; PHOTOCHEMICAL EFFICIENCY; PHOTODEGRADATION; PRIORITY JOURNAL; BASE PAIRING; BIOSYNTHESIS; CHEMISTRY; LIGHT; METABOLISM; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; SYNTHESIS;

BASE PAIRING; BASE SEQUENCE; DEOXYRIBONUCLEOSIDES; DEOXYRIBONUCLEOTIDES; DNA POLYMERASE I; DNA PRIMERS; DNA REPLICATION; INDOLES; LIGHT; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; OLIGODEOXYRIBONUCLEOTIDES; TEMPLATES, GENETIC;

EID: 15044341812     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki293     Document Type: Article

References (32)

1. Sigman,D.S. (1990) Chemical nucleases. [i#Biochemistry#1i], [b#29#1b], 9097-9105.
2. 5 system results from a cytochrome P-450-type hydroxylation reaction. [i#J. Am. Chem. Soc.#1i], [b#117#1b], 2935-2936.
3. Pratviel,G., Bernadou,J. and Meunier,B. (1995) Carbon-hydrogen bonds of DNA sugar units as targets for chemical nucleases and drugs. [i#Angew. Chem. Int. Ed. Engl.#1i], [b#34#1b], 746-769.
4. Meijler,M.M., Zelenko,O. and Sigman,D.S. (1997) Chemical mechanism of DNA scission by (1,10-phenantroline) copper. Carbonyl oxygen of 5-methylenefuranone is derived from water. [i#J. Am. Chem. Soc.#1i], [b#117#1b], 1135-1136.
5. Pratviel,G., Bernadou,J. and Meunier,B. (1998) DNA and RNA cleavage by metal complexes. [i#Adv. Inorg. Chem.#1i], [b#45#1b], 251-312.
6. Armitage,B. (1998) Photocleavage of nucleic acids. [i#Chem. Rev.#1i], [b#98#1b], 1171-1200.
7. Peoc'h,D., Meyer,A., Imbach,J.-L. and Rayner,B. (1991) Efficient chemical synthesis of oligodeoxynucleotides containing a true abasic site. [i#Tetrahedron Lett.#1i], [b#32#1b], 207-210.
8. Ordoukhanian,P. and Taylor,J.-S. (1995) Design and synthesis of a versatile photocleavable DNA building block. Application to phototriggered hybridization. [i#J. Am. Chem. Soc.#1i], [b#117#1b], 9570-9571.
9. Zhang,K. and Taylor,J. S. (1999) A caged ligatable DNA strand break. [i#J. Am. Chem. Soc.#1i], [b#121#1b], 11579-11580.
10. Ordoukhanian,P. and Taylor,J.-S. (2000) Caged single and double strand breaks. [i#Bioconjug. Chem.#1i], [b#11#1b], 94-103.
11. Zhang,K. and Taylor,J.-S. (2001) Phototriggered formation and repair of DNA containing a site specific single strand break of the type produced by ionizing radiation or AP-lyase activity. [i#Biochemistry#1i], [b#40#1b] 153-159.
12. Lenox,H.J., McCoy,C.P. and Sheppard,T.L. (2001) Site-specific generation of deoxyribonolactone lesions in DNA oligonucleotides. [i#Org. Lett.#1i], [b#3#1b], 2415-2418.
13. Dussy,A., Meyer,C., Quennet,E., Bickle,T.A. and Giese,B. (2002) New light-sensitive nucleosides for caged DNA strand breaks. [i#Chembiochem#1i] [b#3#1b], 54-60.
14. Kotera,M., Bourdat,A.-G., Defrancq,E. and Lhomme,J. (1998) A highly efficient synthesis of oligodeoxyribonucleotides containing the 2′-deoxyribonolactone lesion. [i#J. Am. Chem. Soc.#1i], [b#120#1b], 11810-11811.
15. Averbuch-Pichot,M.T., Bourdat,A.G., Defrancq,E., Durif,A., Kotera,M. and Lhomme,J. (1998) Crystal structure of 7-nitro-1(2′-deoxy-β-D-ribofuranosyl)-indole. [i#Zeitschrift fur Kristallographie#1i], [b#213#1b], 181-182.
16. Kotera,M., Roupioz,Y., Defrancq,E., Bourdat,A.-G., Garcia,J., Coulombeau,C. and Lhomme,J. (2000) The 7-nitroindole nucleoside as a photochemical precursor of 2′-deoxyribonolactone: Access to DNA fragments containing this oxydative abasic lesion. [i#Chem. Eur. J.#1i], [b#6#1b], 4163-4169.
17. Loakes,D. and Brown,D.M. (1994) 5-Nitroindole as an universal base analogue. [i#Nucleic Acids Res.#1i], [b#22#1b], 4039-4043.
18. Loakes,D., Brown,D.M., Linde,S. and Hill,F. (1995) 3-Nitropyrrole and 5-nitrindole as universal bases in primers for DNA sequencing and PCR. [i#Nucleic Acids Res.#1i], [b#23#1b], 2361-2366.
19. Loakes,D., Hill,F., Linde,S. and Brown,D.M. (1995) Nitroindoles as universal bases. [i#Nucleosides Nucleotides#1i], [b#14#1b], 1001-1003.
20. 8-(2′-deoxyribofuranoside) of 8-aza-7-deazaadenine: A universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents. [i#Nucleic Acids Res.#1i] [b#28#1b], 3224-3232.
21. He,J. and Seela,F. (2002) Base pairing of 8-aza-7-deazapurine-2,6-diamine linked via the N(8)-position to the DNA backbone: Universal base-pairing properties and formation of highly stable duplexes when alternating with dT. [i#Helv. Chim. Acta#1i], [b#85#1b] 1340-1355.
22. McMinn,D.L., Ogawa,A.K., Wu,Y., Liu,J., Schultz,P.G. and Romesberg,F.E. (1999) Efforts toward the expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base. [i#J. Am. Chem. Soc.#1i], [b#121#1b], 11585-11586.
23. Berger,M., Ogawa,A.K., McMinn,D.L, Schultz,P.G. and Romesberg,F.E. (2000) Stable and selective hybridization of oligonucleotides with unnatural hydrophobic bases. [i#Angew. Chem. Int. Ed. Engl.#1i], [b#39#1b] 2940-2942.
24. Berger,M., Wu,Y., Ogawa,A.K., McMinn,D.L., Schultz,P.G. and Romesberg,F.E. (2000) Universal bases for hybridization, replication and chain termination. [i#Nucleic Acids Res.#1i], [b#28#1b], 2911-2914.
25. Wu,Y., Ogawa,A.K., Berger,M., McMinn,D.L., Schultz,P.G and Romesberg,F.E. (2000) Efforts toward the expansion of the genetic alphabet: Optimization of interbase hydrophobic interactions. [i#J. Am. Chem. Soc.#1i], [b#122#1b], 7621-7632.
26. Ogawa,A.K., Wu,Y., McMinn,D.L., Liu,J., Schultz,P.G. and Romesberg,F.E. (2000) Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs. [i#J. Am. Chem. Soc.#1i], [b#122#1b], 3274-3287.
27. Henry,A.A., Yu,C. and Romesberg,F.E. (2003) Determinants of unnatural nucleobase stability and polymerase recognition. [i#J. Am. Chem. Soc.#1i] [b#125#1b], 9638-9646.
28. Pirrung,M.C., Zhao,X. and Harris,S.V. (2001) A universal, photocleavable DNA base: Nitropiperonyl 2′-deoxyriboside. [i#J. Org. Chem.#1i], [b#66#1b] 2067-2071.
29. Ludwig,J. and Eckstein,F.J. (1989) Rapid and efficient synthesis of nucleoside 5′-0-(1-thiotriphosphates), 5′-triphosphates and 2′,3′-cyclophosphorothioates using 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one. [i#J. Org. Chem.#1i], [b#54#1b] 631-635.
30. Goodman,M.F., Creighton,S., Bloom,L.B. and Petruska,J. (1993) Biochemical basis of DNA replication fidelity. [i#Crit. Rev. Biochem. Mol. Biol.#1i], [b#28#1b], 83-126.
31. Smith,C.L., Simmonds,A.C., Felix,I.R., Hamilton,A.L., Kumar,S., Nampalli,S., Loakes,D., Hill,F. and Brown,D.M. (1998) DNA polymerase incorporation of universal base triphosphates. [i#Nucleosides Nucleotides#1i], [b#17#1b], 541-554.
32. Loakes,D. (2001) The applications of universal DNA base analogues. [i#Nucleic Acids Res.#1i], [b#29#1b], 2437-2447.