Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide

Nucleic Acids Research

Volumn 35, Issue 9, 2007, Pages 2904-2912

  Gallego, José ^a   Loakes, David ^b  

^a CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

5 NITROINDOLE; 5 NITROINDOLE 3 CARBOXAMIDE; DOUBLE STRANDED DNA; INDOLE DERIVATIVE; UNCLASSIFIED DRUG; 5-NITROINDOLE; 5-NITROINDOLE-3-CARBOXAMIDE; ADENINE; DNA; OLIGODEOXYRIBONUCLEOTIDE; THYMINE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA CONFORMATION; DNA HELIX; DNA STRUCTURE; INTERCALATION COMPLEX; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; CHEMICAL STRUCTURE; CHEMISTRY; NUCLEAR MAGNETIC RESONANCE; SOLUTION AND SOLUBILITY; TEMPERATURE;

ADENINE; BASE PAIRING; DNA; INDOLES; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; OLIGODEOXYRIBONUCLEOTIDES; SOLUTIONS; TEMPERATURE; THYMINE;

EID: 34250617956     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm074     Document Type: Article

References (21)

1. Nichols,R., Andrews,P.C., Zhang,P. and Bergstrom,D.E. (1994) Synthesis, structure and biochemical applications of a nucleic-acid spacer: 1-(2′-deoxy-β-D-ribofuranosyl)-3-nitropyrrole. Nature, 369 492-493.
2. Loakes,D. and Brown,D.M. (1994) 5-Nitroindole as an universal base analogue. Nucleic Acids Res., 22, 4039-4043.
3. Loakes,D., Brown,D.M., Linde,S. and Hill,F. (1995) 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR. Nucleic Acids Res., 23, 2361-2366.
4. Ball,S., Reeve,M.A., Robinson,P.S., Hill,F., Brown,D.M. and Loakes,D. (1998) The use of tailed octamer primers for cycle sequencing. Nucleic Acids Res., 26, 5225-5227.
5. Zheng,D. and Raskin,L. (2000) Quantification of Methanosaeta species in anaerobic bioreactors using genus- and species-specific hybridisation probes. Microb. Ecol., 39, 246-262.
6. Burgner,D., D'Amato,M., Kwiatowski,D.P. and Loakes,D. (2004) Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatch. Nucleosides Nucleotides Nucleic Acids, 23, 755-765.
7. Ganova-Raeva,L., Smith,A.W., Fields,H. and Khudyakov,Y. (2004) New calicivirus isolated from walrus. Virus Res., 102, 207-213.
8. Klewer,D.A., Hoskins,A., Zhang,P., Davisson,V.J., Bergstrom,D.E. and LiWang,A.C. (2000) NMR structure of a DNA duplex containing nucleoside analogue 1-(2′-deoxy-b-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control. Nucleic Acids Res., 28, 4514-4522.
9. 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. Nucleosides Nucleotides, 17, 541-554.
10. Too,K., Brown,D.M., Holliger,P. and Loakes,D. (2006) Effect of a hydrogen bonding carboxamide group on universal bases. Coll. Czech. Chem. Commun., 71, 899-911.
11. Ghadessy,F.J., Ramsay,N., Boudsocq,F., Loakes,D., Brown,A., Iwai,S., Vaisman,A., Woodgate,R. and Holliger,P. (2004) Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat. Biotechnol., 22, 755-759.
12. Delaglio,F., Grzesiek,S., Vuister,G.W., Zhu,G., Pfeifer,J. and Bax,A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR, 6, 277-293.
13. Goddard,T.D. and Kneller,D.G. (2001) Sparky 3. University of California, San Francisco, CA, USA.
14. Kim,S.G., Lin,L.J. and Reid,B.R. (1992) Determination of nucleic acid backbone conformation by 1H NMR. Biochemistry, 31, 3564-3574.
15. Case,D.A., Darden,T.A., Cheatham,T.E.III, Simmerling,C.L., Wang,J., Duke,R.E., Luo,R., Merz,K.M., Wang,B. et al. (2004) AMBER 8. University of California, San Francisco, CA, USA.
16. Schmidt,M.W., Baldridge,K.K., Boatz,J.A., Elbert,S.T., Gordon,M.S., Jensen,J.H., Koseki,S., Matsunaga,N., Nguyen,K.A. et al. (1993) General atomic and molecular electronic structure system. J. Comput. Chem., 14, 1347-1363.
17. Pigache,A., Cieplak,P. and Dupradeau,F.-Y. (2004) Automatic and highly reproducible RESP and ESP charge derivation: Application to the development of programs RED and X RED. In 227th ACS National Meeting, Anaheim, CA.
18. Allen,F.H. (2002) The cambridge structural database: A quarter of a million crystal structures and rising. Acta Crystallogr., B58 380-388.
19. Robinson,J.M.A., Philp,D., Harris,K.D.M. and Kariuki,B.M. (2000) Weak interactions in crystal engineering - understanding the recognition properties of the nitro group. New J. Chem., 24, 799-806.
20. Wheaton,C.A., Dobrowolski,S.L., Millen,A.L. and Wetmore,S.D. (2006) Nitrosubstituted aromatic molecules as universal nucleobases: computational analysis of stacking interactions. Chem. Phys. Lett. 428, 157-166.
21. Bhattacharya,P.K., Cha,J. and Barton,J.K. (2002) H-1 NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches. Nucleic Acids Res., 30, 4740-4750.