Fifty years of DNA "breathing": Reflections on old and new approaches

Biopolymers

Volumn 99, Issue 12, 2013, Pages 923-954

  Von Hippel, Peter H ^a   Johnson, Neil P ^a   Marcus, Andrew H ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

DNA base analogue spectroscopy; DNA replication; formaldehyde probing; hydrogen exchange; protein nucleic acid interactions; single molecule DNA protein interactions studies; two dimensional fluorescence spectroscopy

Indexed keywords

DNA REPLICATIONS; DNA-PROTEIN INTERACTION; HYDROGEN EXCHANGE; MELTING PHASE TRANSITION; PHYSIOLOGICAL TEMPERATURE; PROTEIN-NUCLEIC ACID INTERACTION; REGULATORY COMPLEXES; REGULATORY PROTEIN;

DNA; FLUORESCENCE SPECTROSCOPY; FORMALDEHYDE; GENE EXPRESSION; HYDROGEN; MELTING; PHYSIOLOGY; PROTEINS;

DNA SEQUENCES;

ACRIDINE ORANGE; ADENINE; AROMATIC AMINO ACID; BINDING PROTEIN; DEUTERIUM; DNA; DNA BASE; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; ETHIDIUM BROMIDE; FLUORESCENT DYE; FORMALDEHYDE; HELICASE; HYDROGEN; NTP PROTEIN; NUCLEIC ACID; REGULATOR PROTEIN; RNA POLYMERASE; THYMINE; TRITIUM; UNCLASSIFIED DRUG;

AT RICH SEQUENCE; BREATHING; BREATHING RATE; CALF (BOVINE); CHEMICAL REACTION; CHRONOLOGY; COMPLEX FORMATION; COVALENT BOND; DEUTERIUM HYDROGEN EXCHANGE; DNA CONFORMATION; DNA DENATURATION; DNA PROTEIN COMPLEX; DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; ELECTRON MICROSCOPY; ENERGY; EQUILIBRIUM CONSTANT; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENCE SPECTROSCOPY; FREE ENERGY SURFACE; GENE EXPRESSION; GENE TARGETING; HYDROGEN BOND; INTERCALATION COMPLEX; ION EXCHANGE; LINEAR DICHROISM; MACROMOLECULE; MASS SPECTROMETRY; MELTING POINT; MOLECULAR DYNAMICS; MOLECULAR PROBE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN HYDROLYSIS; PROTEIN STABILITY; PROTON TRANSPORT; REVIEW; SINGLE MOLECULE FLUORESCENCE DETECTED LINEAR DICHROISM; STEADY STATE; TEMPERATURE DEPENDENCE; THYMUS; TITRIMETRY; TWO DIMENSIONAL FLUORESCENCE SPECTROSCOPY; CHEMISTRY; CONFORMATION; SPECTROSCOPY;

DNA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; SPECTRUM ANALYSIS;

EID: 84884926908     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.22347     Document Type: Review

References (67)

1. Watson, J. D.,;, Crick, F. H., Nature 1953, 171, 737-738.
2. Lehman, I. R.,;, Bessman, M. J.,;, Simms, E. S.,;, Kornberg, A., J Biol Chem 1958, 233, 163-170.
3. Weiss, S., Gladstone, L. J., Am. Chem. Soc. 1959, 81, 4118-4119.
4. Benson, E. E.,;, Linderstrom-Lang, K., Biochim Biophys Acta 1959, 32, 579-581.
5. Linderstrom-Lang, K., Biochim Biophysi Acta 1955, 18, 308.
6. Hvidt, A.,;, Linderstrom-Lang, K., Biochim Biophys Acta 1954, 14, 574-575.
7. Kalman, S. M.,;, Linderstrom-Lang, K.,;, Ottesen, M.,;, Richards, F. M., Biochim Biophys Acta 1955, 16, 297-299.
8. Englander, S. W., Biochemistry 1963, 2, 798-807.
9. Printz, M. P.,;, von Hippel, P. H., Biochemistry 1968, 7, 3194-3206.
10. Printz, M. P.,;, von Hippel, P. H., Proc Natl Acad Sci USA 1965, 53, 363-370.
11. McConnell, B.,;, von Hippel, P. H., J Mol Biol 1970, 50, 317-332.
12. McConnell, B.,;, von Hippel, P. H., J Mol Biol 1970, 50, 297-316.
13. Teitelbaum, H.,;, Englander, S. W., J Mol Biol 1975, 92, 79-92.
14. Teitelbaum, H.,;, Englander, S. W., J Mol Biol 1975, 92, 55-78.
15. Gueron, M.,;, Kochoyan, M.,;, Leroy, J. L., Nature 1987, 328, 89-92.
16. Gueron, M.,;, Leroy, J. L., Methods Enzymol 1995, 261, 383-413.
17. Hu, W.,;, Walters, B. T.,;, Kan, Z. Y.,;, Mayne, L.,;, Rosen, L. E.,;, Marqusee, S.,;, Englander, S. W., Proc Natl Acad Sci USA 2013, 110, 7684-7689.
18. Bothe, J. R.,;, Nikolova, E. N.,;, Eichhorn, C. D.,;, Chugh, J.,;, Hansen, A. L.,;, Al-Hashimi, H. M., Nat Methods 2011, 8, 919-931.
19. Delagoutte, E.,;, von Hippel, P. H., Quat Rev Biophys 2002, 35, 431-478.
20. Inman, R. B., J Mol Biol 1966, 18, 464-476.
21. Morris, C. F.,;, Sinha, N. K.,;, Alberts, B. M., Proc Natl Acad Sci USA 1975, 72, 4800-4804.
22. Nossal, N. G., J Biol Chem 1979, 254, 6026-6031.
23. Nossal, N. G.,;, Peterlin, B. M., J Biol Chem 1979, 254, 6032-6037.
24. McGhee, J. D.,;, von Hippel, P. H., Biochemistry 1975, 14, 1297-1303.
25. McGhee, J. D.,;, von Hippel, P. H., Biochemistry 1975, 14, 1281-1296.
26. McGhee, J. D.,;, von Hippel, P. H., Biochemistry 1977, 16, 3267-3276.
27. McGhee, J. D.,;, von Hippel, P. H., Biochemistry 1977, 16, 3276-3293.
28. Bohnuud, T.,;, Beglov, D.,;, Ngan, C. H.,;, Zerbe, B.,;, Hall, D. R.,;, Brenke, R.,;, Vajda, S.,;, Frank-Kamenetskii, M. D.,;, Kozakov, D., Nucleic Acids Res 2012, 40, 7644-7652.
29. Kitayner, M.,;, Rozenberg, H.,;, Rohs, R.,;, Suad, O.,;, Rabinovich, D.,;, Honig, B.,;, Shakked, Z., Nat Struct Mol Biol 2010, 17, 423-429.
30. Nikolova, E. N.,;, Kim, E.,;, Wise, A. A.,;, O'Brien, P. J.,;, Andricioaei, I.,;, Al-Hashimi, H. M., Nature 2011, 470, 498-502.
31. Lepecq, J. B.,;, Yot, P.,;, Paoletti, C., C R Hebd Seances Acad Sci 1964, 259, 1786-1789.
32. Lerman, L. S., J Mol Biol 1961, 3, 18-30.
33. Waring, M., J. Annu Rev Biochem 1981, 50, 159-192.
34. Wilhelm, M.,;, Mukherjee, A.,;, Bouvier, B.,;, Zakrzewska, K.,;, Hynes, J. T.,;, Lavery, R., J Am Chem Soc 2012, 134, 8588-8596.
35. Sung, R. J.,;, Zhang, M.,;, Qi, Y.,;, Verdine, G. L., J Biol Chem 2013, 288, 10012-10023.
36. von Hippel, P. H.,;, Delagoutte, E., Cell 2001, 104, 177-190.
37. Alberts, B. M.,;, Frey, L., Nature 1970, 227, 1313-1318.
38. Jose, D.,;, Weitzel, S. E.,;, von Hippel, P. H., Proc Natl Acad Sci USA 2012, 109, 14428-14433.
39. Johnson, N. P.,;, Baase, W. A.,;, von Hippel, P. H., Proc Natl Acad Sci USA 2004, 101, 3426-3431.
40. Johnson, N. P.,;, Baase, W. A.,;, von Hippel, P. H., J Biol Chem 2005, 280, 32177-32183.
41. Johnson, N. P.,;, Baase, W. A.,;, von Hippel, P. H., Proc Natl Acad Sci USA 2005, 102, 7169-7173.
42. Datta, K.,;, Johnson, N. P.,;, von Hippel, P. H., J Mol Biol 2006, 360, 800-813.
43. Datta, K.,;, von Hippel, P. H., J Biol Chem 2008, 283, 3537-3549.
44. Baase, W. A.,;, Jose, D.,;, Ponedel, B. C.,;, von Hippel, P. H.,;, Johnson, N. P., Nucleic Acids Res 2009, 37, 1682-1689.
45. Jose, D.,;, Datta, K.,;, Johnson, N. P.,;, von Hippel, P. H., Proc Natl Acad Sci USA 2009, 106, 4231-4236.
46. Datta, K.,;, Johnson, N. P.,;, von Hippel, P. H., Proc Natl Acad Sci USA 2010, 107, 17980-17985.
47. Datta, K., Johnson, N. P., Villani, G., Marcus, A. H., von Hippel, P. H., Nucleic Acids Res 2012, 40, 1191-1202.
48. Jose, D.,;, Weitzel, S. E.,;, Jing, D.,;, von Hippel, P. H., Proc Natl Acad Sci USA 2012, 109, 13596-13601.
49. Lee, W.,;, Jose, D.,;, Phelps, C.,;, Marcus, A. H.,;, von Hippel, P. H., Biochemistry 2013, 52, 3157-3170.
50. Callen, H. B., Thermodynamics and an Introduction to Thermostatistics; John Wiley & Sons: New York, 1985.
51. Hamdan, S. M.,;, van Oijen, A. M., J Biol Chem 2010, 285, 18979-18983.
52. Neuman, K. C., J Biol Chem 2010, 285, 18967-18971.
53. McKinney, S. A.,;, Freeman, A. D. J.,;, Lilley, D. M. J.,;, Ha, T., Proc Natl Acad Sci USA 2005, 102, 5715-5720.
54. Ha, T.,;, Rasnik, I.,;, Cheng, W.,;, Babcock, H. P.,;, Gauss, G. H.,;, Lohman, T. M.,;, Chu, S., Nature 2002, 419, 638-641.
55. Altan-Bonnet, G.,;, Libchaber, A.,;, Krichevsky, O., Phys Rev Lett 2003, 90, 138101-138104.
56. Peyrard, M.,;, Cuesta-Lopez, S.,;, James, G., J Biol Phys 2009, 35, 73-89.
57. Cheatham, T. E., III,;, Kollman, P. A., Annu Rev Phys Chem 2000, 51, 435-471.
58. Jonas, D. M., Science 2003, 300, 1515-1517.
59. Widom, J. R., Johnson N. J., von Hippel P. H., Marcus A. H., New J Phys 2013, 15, 025029-025016.
60. Lott, G. A.,;, Perdomo-Ortiz, A.,;, Utterbach, J. K.,;, Widom, J. R.,;, Aspuru-Guzik, A.,;, Marcus, A. H., Proc Natl Acad Sci USA 2011, 108, 16521-16526.
61. Perdomo-Ortiz, A.,;, Widom, J. R.,;, Lott, G. A.,;, Aspuru-Guzik, A.,;, Marcus, A. H., J Phys Chem B 2012, 116, 10757-10770.
62. Widom, J. R.,;, Lee, W.,;, Perdomo-Ortiz, A.,;, Rappoport, D.,;, Molinski, T. F.,;, Aspuru-Guzik, A.,;, Marcus, A. H., J Phys Chem A, 2013, 117, 6171-6184.
63. Tekavec, P. F.,;, Lott, G. A.,;, Marcus, A. H., J Chem Phys 2007, 127, 214307-214321.
64. Phelps, C.,;, Lee, W.,;, Jose, D.,;, von Hippel, P. H.,;, Marcus, A. H., Proc Natl Acad Sci USA, (2013) in press.
65. Richardson, R. W.,;, Nossal, N., J Biol Chem 1989, 264, 4725-4731.
66. Dong, F.,;, Gogol, E. P.,;, von Hippel, P. H., J Biol Chem 1995, 270, 7462.
67. Dong, F.,;, von Hippel, P. H., J Biol Chem 1996, 271, 19625-19631.