A mutate-and-map strategy for inferring base pairs in structured nucleic acids: Proof of concept on a DNA/RNA helix

Biochemistry

Volumn 49, Issue 35, 2010, Pages 7414-7416

  Kladwang, Wipapat ^a   Das, Rhiju ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES;

BASE PAIRS; CHEMICAL MAPPING; CHEMICAL STRATEGY; DIMETHYL SULFATES; HIGH-THROUGHPUT; PROOF OF CONCEPT; SEQUENCE VARIATIONS; THREE DIMENSIONS;

NUCLEIC ACIDS;

DNA; RNA; RIBONUCLEOPROTEIN;

ARTICLE; BASE PAIRING; DNA DETERMINATION; DNA HELIX; DNA SEQUENCE; GENE DELETION; GENE MUTATION; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; CHEMISTRY; CONFORMATION; METABOLISM; MUTAGENESIS; NUCLEOTIDE SEQUENCE;

BASE PAIRING; BASE SEQUENCE; DNA; MUTAGENESIS; NUCLEIC ACID CONFORMATION; RIBONUCLEOPROTEINS; RNA;

EID: 77956144376     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101123g     Document Type: Article

References (25)

1. Collins, K. (2006) Nat. Rev. Mol. Cell Biol. 7, 484-494
2. Staley, J. P. and Guthrie, C. (1998) Cell 92, 315-326
3. Panning, B., Dausman, J., and Jaenisch, R. (1997) Cell 90, 907-916
4. Moazed, D. (2009) Nature 457, 413-420
5. Cruz, J. A. and Westhof, E. (2009) Cell 136, 604-609
6. Noller, H. F. (2005) Science 309, 1508-1514
7. Peattie, D. A. and Gilbert, W. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 4679-4682
8. Latham, J. A. and Cech, T. R. (1989) Science 245, 276-282
9. Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M. A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., Kern, A. D., Dehay, C., Igel, H., Ares, M., Jr., Vanderhaeghen, P., and Haussler, D. (2006) Nature 443, 167-172
10. Das, R., Karanicolas, J., and Baker, D. (2010) Nat. Methods 7, 291-294
11. Krol, A. and Carbon, P. (1989) Methods Enzymol. 180, 212-227
12. Tijerina, P., Mohr, S., and Russell, R. (2007) Nat. Protoc. 2, 2608-2623
13. Garcia, I. and Weeks, K. M. (2004) Biochemistry 43, 15179-15186
14. Tullius, T. D. (1991) Free Radical Res. Commun. 12-13 (Part 2) 521-529
15. Adilakshmi, T., Lease, R. A., and Woodson, S. A. (2006) Nucleic Acids Res. 34, e64
16. Schroeder, R., Grossberger, R., Pichler, A., and Waldsich, C. (2002) Curr. Opin. Struct. Biol. 12, 296-300
17. Mitra, S., Shcherbakova, I. V., Altman, R. B., Brenowitz, M., and Laederach, A. (2008) Nucleic Acids Res. 36, e63
18. Wilkinson, K. A., Gorelick, R. J., Vasa, S. M., Guex, N., Rein, A., Mathews, D. H., Giddings, M. C., and Weeks, K. M. (2008) PLoS Biol. 6, e96
19. Watts, J. M., Dang, K. K., Gorelick, R. J., Leonard, C. W., Bess, J. W., Jr., Swanstrom, R., Burch, C. L., and Weeks, K. M. (2009) Nature 460, 711-716
20. Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292
21. Deigan, K. E., Li, T. W., Mathews, D. H., and Weeks, K. M. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 97-102
22. Pyle, A. M., Murphy, F. L., and Cech, T. R. (1992) Nature 358, 123-128
23. Duncan, C. D. and Weeks, K. M. (2008) Biochemistry 47, 8504-8513
24. Baum, D. A. and Silverman, S. K. (2008) Cell. Mol. Life Sci. 65, 2156-2174
25. Wilkinson, K. A., Merino, E. J., and Weeks, K. M. (2006) Nat. Protoc. 1, 1610-1616