DNA hairpin, pseudoknot, and cruciform stability in a solvent-free environment

Journal of Physical Chemistry B

Volumn 113, Issue 6, 2009, Pages 1722-1727

  Baker, Erin Shammel ^a   Dupuis, Nicholas F ^a   Bowers, Michael T ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MATERIALS; DNA; DNA SEQUENCES; GENES; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETERS; MASS SPECTROMETRY; MOLECULAR DYNAMICS; NUCLEIC ACIDS;

BIOLOGICAL FUNCTIONS; CHARGE STATE; COLLISION CROSS SECTIONS; CROSS SECTIONS; DNA HAIRPINS; ION MOBILITIES; ION MOBILITY SPECTROMETRIES; MASS SPECTRUM; MOLECULAR DYNAMICS CALCULATIONS; NANO-ESI; PSEUDO-KNOTS; PSEUDOKNOT; SECONDARY STRUCTURES; SOLVENT-FREE; WATSON-CRICK PAIRS;

DYNAMICS;

EID: 61949398417     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp807529m     Document Type: Article

References (32)

1. Watson, J. D.; Crick, F. H. Nature 1953, 171, 1303.
2. Singleton, C. K. J. Biol. Chem. 1983, 258, 7661.
3. Sullivan, K. M.; Lilley, D. M. J. Mol. Biol. 1987, 193, 397.
4. Glucksmann, M. A.; Markiewicz, P.; Malone, C.; Rothman-Deenes, L. B. Cell 1992, 70, 491.
5. Larsen, A.; Weintraub, H. Cell 1982, 29, 609.
6. Huertas, D.; Azorin, F. Biochemistry 1996, 35, 13125.
7. Heller, M. J. Annu. Rev. Biomed. Eng. 2002, 4, 129.
8. Gaylord, B. S.; Heeger, A. J.; Bazan, G. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10954.
9. Tyagi, S.; Kramer, F. R. Nat. Biotechnol. 1996, 14, 303.
10. Fan, C.; Plaxco, K. W.; Heeger, A. J. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 9134.
11. von Helden, G.; Hsu, M.-T.; Kemper, P. R.; Bowers, M. T. J. Chem. Phys. 1991, 95, 3835.
12. Wyttenbach, T.; von Helden, G.; Bowers, M. T. Int. J. Mass Spectrom. Ion Proc. 1997, 165/166, 377.
13. Wyttenbach, T.; Bowers, M. T. Top. Curr. Chem. 2003, 225, 207.
14. Wyttenbach, T.; Kemper, P. R.; Bowers, M. T. Int. J. Mass Spectrom. 2001, 212, 13.
15. Mason, E. A.; McDaniel, E. W. Transport Properties of Ions in Gases; Wiley, New York, NY, 1988.
16. HyperChem 7.0; Hypercube Inc.: Gainesville, FL, 2002.
17. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Wang, J.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M; Tsui, V.; Gohlke, H.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 7; University of California: San Francisco, 2002.
18. Mesleh, M. F.; Hunter, J. M.; Shvartsburg, A. A.; Schwartz, G. C.; Jarrold, M. F. J. Phys. Chem. 1996, 100, 16082.
19. Shvartsburg, A. A.; Jarrold, M. F. Chem. Phys. Lett. 1996, 261, 86.
20. Lee, S.; Gotts, N. G.; von Helden, G.; Bowers, M. T. Science 1995, 267, 999.
21. Wyttenbach, T.; von Helden, G.; Bowers, M. T. J. Am. Chem. Soc. 1996, 118, 8355.
22. Wyttenbach, T.; Bushnell, J. E.; Bowers, M. T. J. Am. Chem. Soc. 1998, 120, 5098.
23. Hoaglund, C. S.; Liu, Y.; Ellington, A. D.; Pagel, M; Clemmer, D. E. J. Am. Chem. Soc. 1997, 119, 9051.
24. Gidden, J.; Ferzoco, A.; Baker, E. S.; Bowers, M. T. J. Am. Chem. Soc. 2004, 126, 15132.
25. Baker, E. S.; Bowers, M. T. J. Am. Soc. Mass Spectrom. 2007, 18, 1188.
26. Gidden, J.; Baker, E. S.; Ferzoco, A.; Bowers, M. T. Int. J. Mass Spectrom. 2005, 240, 183.
27. Veenstra, T. D. Biochem. Biophys. Res. Commun. 1999, 257, 1.
28. Riazance, J. H.; Baase, W. A.; Johnson, W. C, Jr.; Hall, K.; Cruz, P.; Tinoco, I., Jr Nucleic Acids Res. 1985, 13, 4983.
29. Segersnolten, G. M. J.; Sijtsema, N. M.; Otto, C. Biochemistry 1997, 36, 13241.
30. Poehl, F. M.; Jovin, T. M. J. Mol. Biol. 1972, 67, 375.
31. Trantirek, L.; Stefl, R.; Vorlickova, M.; Koca, J.; Sklenar, V.; Kypr, J. J. Mol. Biol. 2000, 297, 907.
32. Franklin, R. E.; Gosling, R. G. Acta Crystallogr. 1953, 6, 673.