Stability and structure of DNA oligonucleotides containing non-specific base analogues

Journal of Molecular Biology

Volumn 270, Issue 3, 1997, Pages 426-435

  Loakes, David ^a   Hill, Fergal ^a   Brown, Daniel M ^a   Salisbury, Stephen A ^b  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

^b CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE   (United Kingdom)

Author keywords

5 Nitroindole; Circular dichroism; Polymerase chain reaction; Stacking interactions; X ray structure

Indexed keywords

5 NITROINDOLE; DOUBLE STRANDED DNA; INDOLE DERIVATIVE; OLIGODEOXYNUCLEOTIDE; OLIGOMER; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA STRUCTURE; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; THERMODYNAMICS; X RAY ANALYSIS;

EID: 0031577265     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1129     Document Type: Article

References (31)

1. Allen F. H., Davies J. E., Galloy J. J., Johnson O., Kennard O., Macrae C. F., Mitchell E., Mitchell G. F., Smith J. M., Watson D. G. Development of versions 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sci. 31:1991;187-204.
2. Arnott S., Hukins D. W. L. Optimised parameters forAB. Biochem. Biophys. Res. Commun. 47:1972;1504-1510.
3. Bergstrom D. E., Zhang P., Toma P. H., Andrews P. C., Nichols R. Synthesis, structure and deoxyribonucleic acid sequencing with a universal base: 1-(2′deoxy-β-D. J. Am. Chem. Soc. 117:1995;1201-1209.
4. Bergstrom D. E., Zhang P. M., Johnson W. T. Design and synthesis of heterocyclic carboxamides as natural nucleic-acid base mimics. Nucleosides Nucleotides. 15:1996;59-68.
5. Bischofberger N., Matteucci M. D. Synthesis of novel polycyclic nucleoside analogues, incorporation into oligodeoxynucleotides, and interaction with complementary sequences. J. Am. Chem. Soc. 111:1989;3041-3046.
6. Clark J. M. Novel non-templated nucleotide addition-reactions catalysed by prokaryotic and eukaryotic DNA-polymerases. Nucl. Acids Res. 16:1988;9677-9686.
7. Gibson, T. J. 1983, Studies on the Epstein-Barr virus genome. PhD thesis, University of Cambridge.
8. Gralla J., Crothers D. M. Free energy of imperfect nucleic acid helices. III. Small internal loops resulting from mismatches. J. Mol. Biol. 78:1973;301-319.
9. Guckian K. M., Schweitzer B. A., Ren R. X-F., Sheils C. J., Paris P. L., Tahmassebi D. C., Kool E. T. Experimental measurement of aromatic stacking affinities in the context of duplex DNA. J. Am. Chem. Soc. 118:1996;8182-8183.
10. Hunter C. A., Sanders J. K. M. The nature of PI-PI interactions. J. Am. Chem. Soc. 112:1990;5525-5534.
11. Ichihara Y., Kurosawa Y. Construction of new T-vectors for direct cloning of PCR products. Gene. 130:1993;153-154.
12. Joshua-Tor L., Frolow F., Appella E., Hope H., Rabinovich D., Sussman J. L. Three-dimensional structures of bulge-containing DNA fragments. J. Mol. Biol. 225:1992;397-431.
13. Kalnik M. W., Norman D. G., Zagorski M. G., Swann P. F., Patel D. J. Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution. Biochemistry. 28:1989;294-303.
14. Kalnik M. W., Norman D. G., Li B. F., Swann P. F., Patel D. J. Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. J. Biol. Chem. 265:1990;636-647.
15. 2. Biochemistry. 31:1992;12087-12095.
16. Loakes D., Brown D. M. 5-Nitroindole as an universal base analogue. Nucl. Acids Res. 22:1994;4039-4043.
17. Loakes D., Brown D. M., Linde S., Hill F. 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR. Nucl. Acids Res. 23:1995;2361-2366.
18. Martin F. H., Castro M. M., Aboul-ela F., Tinoco I. Base-pairing involving deoxyinosine-implications for probe design. Nucl. Acids Res. 13:1985;8927-8938.
19. Newcomb L. F., Gellman S. H. Aromatic stacking interactions in aqueous solution: evidence that neither classical hydrophobic effects nor dispersion forces are important. J. Am. Chem. Soc. 116:1994;4993-4994.
20. Nichols R., Andrews P. C., Zhang P., Bergstrom D. E. Synthesis, structure and biochemical applications of a universal nucleic-acid spacer - 1-(2′-deoxy-β-D. Nature. 369:1994;492-493.
21. Parinov S., Barsky V., Yershov G., Kirillov E., Timofeev E., Belgovskiy A., Mirzabekov A. DNA-sequencing by hybridization to microchip octanucleotide and decanucleotide extended by stacked pentanucleotides. Nucl. Acids. Res. 24:1996;2998-3004.
22. Patel D. J., Kozlowski S. A., Marky L. A., Rice J. A., Broka C., Itakura K., Breslauer K. J. Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution. Biochemistry. 21:1982;445-451.
23. Pochet S., Dugue L. Oligodeoxynucleotides embodying the ambiguous base-Z, 5-amino-imidazole-4-carboxamide. Nucleosides Nucleotides. 14:1995;1195-1210.
24. Saenger W. Principles in Nucleic Acid Structure. 1984;Springer Verlag, New York.
25. Sala M., Pezo V., Pochet S., Wainhobson S. Ambiguous base-pairing of the purine analogue 1-(2-deoxy-β-D. Nucl. Acids Res. 24:1996;3302-3306.
26. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
27. Schweitzer B. A., Kool E. T. Aromatic nonpolar nucleosides as hydrophobic isosteres of pyrimidine and purine nucleosides. J. Org. Chem. 59:1994;7238-7242.
28. Seela F., Bourgeois W., Rosemeyer H., Wenzel T. Synthesis of 4-substituted 1H benzimidazole 2′-deoxyribonucleosides and utility of the 4-nitro compound as universal base. Helv. Chim. Acta. 79:1996;488-498.
29. Sheldrick G. M. Phase annealing in SHELX-90 - direct methods for larger structures. Acta Crystallog. sect. A. 46:1990;467-473.
30. Sheldrick, G. M. 1993, SHELXL-93 program for the refinement of crystal structures, University of Göttingen, Germany.
31. 1. Biochemistry. 27:1988;436-445.