NMR spectroscopy and molecular dynamics simulation of r(CCGCUGCGG)2 reveal a dynamic UU internal loop found in myotonic dystrophy type 1

Biochemistry

Volumn 50, Issue 5, 2011, Pages 599-601

  Parkesh, Raman ^a   Fountain, Matthew ^b   Disney, Matthew D ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b STATE UNIVERSITY OF NEW YORK AT FREDONIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOND STRUCTURES; DYNAMICS SIMULATION; ENERGY CONFORMATION; INTERNAL LOOPS; MOLECULAR DYNAMICS SIMULATIONS; MYOTONIC DYSTROPHY; NMR SPECTROSCOPY; NMR STRUCTURES; SMALL MOLECULES;

HYDROGEN BONDS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; RNA;

HYDROGEN;

CYTOSINE; GUANINE; OLIGONUCLEOTIDE;

ARTICLE; CONFORMATIONAL TRANSITION; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; MYOTONIC DYSTROPHY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; RNA STRUCTURE; SIMULATION;

3' UNTRANSLATED REGIONS; BASE SEQUENCE; HUMANS; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR DYNAMICS SIMULATION; MYOTONIC DYSTROPHY; NUCLEIC ACID CONFORMATION; PROTEIN-SERINE-THREONINE KINASES; RNA; THERMODYNAMICS; TRINUCLEOTIDE REPEATS;

EID: 79952075736     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101896j     Document Type: Article

References (22)

1. Thomas, J. R., and Hergenrother, P. (2008) Chem. Rev. 108, 1171-1224.
2. Liquori, C. L., Ricker, K., Moseley, M. L., Jacobsen, J. F., Kress, W., Naylor, S. L., Day, J. W., and Ranum, L. P. (2001) Science 293, 864-867.
3. Mankodi, A., Logigian, E., Callahan, L., McClain, C., White, R., Henderson, D., Krym, M., and Thornton, C. A. (2000) Science 289, 1769-1772.
4. Savkur, R. S., Philips, A. V., and Cooper, T. A. (2001) Nat. Genet. 29, 40-47.
5. Lueck, J. D., Mankodi, A., Swanson, M. S., Thornton, C. A., and Dirksen, R. T. (2007) J. Gen. Physiol. 129, 79-94.
6. Wheeler, T. M., Sobczak, K., Lueck, J. D., Osborne, R. J., Lin, X., Dirksen, R. T., and Thornton, C. A. (2009) Science 325, 336-339.
7. Warf, M. B., Nakamori, M., Matthys, C. M., Thornton, C. A., and Berglund, J. A. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 18551-18556.
8. Arambula, J. F., Ramisetty, S. R., Baranger, A. M., and Zimmerman, S. C. (2009) Proc. Natl. Acad. Sci. U.S.A 106, 16068-16073.
9. Gareiss, P. C., Sobczak, K., McNaughton, B. R., Palde, P. B., Thornton, C. A., and Miller, B. L. (2008) J. Am. Chem. Soc. 130, 16254-16261.
10. Lee, M. M., Pushechnikov, A., and Disney, M. D. (2009) ACS Chem. Biol. 4, 345-355.
11. Pushechnikov, A., Lee, M. M., Childs-Disney, J. L., Sobczak, K., French, J. M., Thornton, C. A., and Disney, M. D. (2009) J. Am. Chem. Soc. 131, 9767-9779.
12. Disney, M. D., Lee, M. M., Pushechnikov, A., and Childs-Disney, J. L. (2010) ChemBioChem 11, 375-382.
13. Lee, M. M., Childs-Disney, J. L., Pushechnikov, A., French, J. M., Sobczak, K., Thornton, C. A., and Disney, M. D. (2009) J. Am. Chem. Soc. 131, 17464-17472.
14. Nonin, S., Leroy, J. L., and Gueron, M. (1995) Biochemistry 34, 10652-10659.
15. Schroeder, K. T., Skalicky, J. J., and Greenbaum, N. L. (2005) RNA 11, 1012-1016.
16. Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., and Woods, R. J. (2005) J. Comput. Chem. 26, 1668-1688.
17. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Debolt, S., Ferguson, D., Seibel, G., and Kollman, P. (1995) Comput. Phys. Commun. 92, 1-41.
18. Limer, S. (1997) Prog. Nucleic Acid Res. Mol. Biol. 57, 1-39.
19. Fogolari, F., Brigo, A., and Molinari, H. (2002) J. Mol. Recognit. 15, 377-392.
20. Mooers, B. H., Logue, J. S., and Berglund, J. A. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 16626-16631.
21. Kiliszek, A., Kierzek, R., Krzyzosiak, W. J., and Rypniewski, W. (2009) Nucleic Acids Res. 37, 4149-4156.
22. Davis, A. R., Kirkpatrick, C. C., and Znosko, B. M. (2010) Nucleic Acids Res. 28, 1-14.