Hydration of watson crick base pairs and dehydration of hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions

Journal of the American Chemical Society

Volumn 131, Issue 10, 2009, Pages 3522-3531

  Miyoshi, Daisuke ^a,b   Nakamura, Kaori ^a,c   Tateishi Karimata, Hisae ^a,b,c   Ohmichi, Tatsuo ^a,b   Sugimoto, Naoki ^a,b,c  

^a KONAN UNIVERSITY   (Japan)

^b Frontier Institute for Biomolecular Engineering Research (FIBER)   (Japan)

^c Ishinomaki Senshu University   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AVERAGE MOLECULAR WEIGHT; BASE PAIRS; CONCENTRATION OF; CRITICAL FACTORS; DNA DUPLEXES; DNA STRANDS; FREE ENERGY CHANGE; IN-VITRO; IN-VIVO; MOLECULAR CROWDING; PAIR FORMATION; PEG 200; STRUCTURAL POLYMORPHISMS; THERMO DYNAMIC ANALYSIS; WATER MOLECULE; WATSON-CRICK BASE PAIRS;

DNA; GENES; POLYETHYLENE GLYCOLS; POLYETHYLENE OXIDES; THERMOANALYSIS;

NUCLEIC ACIDS;

DOUBLE STRANDED DNA; MACROGOL 200; PRIMER DNA; WATER;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CONCENTRATION (PARAMETERS); DEHYDRATION; DNA BINDING; DNA POLYMORPHISM; ENERGY; HOOGSTEEN BASE PAIR; HYDRATION; THERMODYNAMICS; WATSON CRICK BASE PAIR; CHEMISTRY; CIRCULAR DICHROISM; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS;

BASE PAIRING; BASE SEQUENCE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CIRCULAR DICHROISM; DNA PRIMERS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; THERMODYNAMICS; WATER;

EID: 67749110113     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja805972a     Document Type: Article

References (46)

1. Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737-738.
2. Turner, D. H. Conformational Changes; Bloomfield, V. A., Crothers, D. M., Tinoco, I., Jr., Eds.; University Science Books: Mill Valley, CA, 2000; pp 259-334.
3. Miyoshi, D.; Sugimoto, N. Recent DeV. Nucleic Acids Res. 2006, 2, 49-70.
4. Zimmerman, S. B.; Minton, A. P. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 27-65.
5. Minton, A. P. J. Biol. Chem. 2001, 276, 10577-10580.
6. Ellis, R. J.; Minton, A. P. Nature 2003, 425, 27-28.
7. Sasaki, Y.; Miyoshi, D.; Sugimoto, N. Nucleic Acids Res. 2007, 35, 4086-4093.
8. Kurland, C. G.; Collins, L. J.; Penny, D. Science 2006, 312, 1011- 1014.
9. Trepat, X.; Deng, L.; An, S. S.; Navajas, D.; Tschumperlin, D. J.; Gerthoffer, W. T.; Butler, J. P.; Fredberg, J. J. Nature 2007, 447, 592- 595.
10. Goobes, R.; Kahana, N.; Cohen, O.; Minsky, A. Biochemistry 2003, 42, 2431-2440.
11. Miyoshi, D.; Matsumura, S.; Nakano, S.; Sugimoto, N. J. Am. Chem. Soc. 2004, 126, 165-169.
12. Li, J.; Correia, J. J.; Wang, L.; Trent, J. O.; Chaires, J. B. Nucleic Acids Res. 2005, 33, 4649-4659.
13. Miyoshi, D.; Karimata, H.; Sugimoto, N. Angew. Chem., Int. Ed. 2005, 24, 3740-3744.
14. Kan, Z. Y.; Lin, Y.; Wang, F.; Zhuang, X. Y.; Zhao, Y.; Pang, D. W.; Hao, Y. H.; Tan, Z. Nucleic Acids Res. 2007, 35, 3646-3653.
15. Miyoshi, D.; Karimata, H.; Sugimoto, N. J. Am. Chem. Soc. 2006, 128, 7957-7963.
16. Nakano, S.; Karimata, H.; Ohmichi, T.; Kawakami, J.; Sugimoto, N. J. Am. Chem. Soc. 2004, 126, 14330-14331.
17. Spink, C. H.; Chaires, J. B. J. Am. Chem. Soc. 1995, 117, 12887- 12888.
18. Goobes, R.; Minsky, A. J. Am. Chem. Soc. 2001, 123, 12692-12693.
19. Richards, E. G. Use of tables in calculation of absorption, optical rotatory dispersion and circular dichroism of polyribonucleotides. Fasman, G. D., Ed.; Handbook of Biochemistry and Molecular Biology, 3rd ed.; CRC Press: Cleveland, OH, 1975; Vol. 1, pp 596-603.
20. Ishikata, H.; Knapp, E. J. Am. Chem. Soc. 2004, 126, 8059-8064.
21. Sugimoto, N.; Wu, P.; Hara, H.; Kawamoto, Y. Biochemistry 2001, 40, 9396-9405.
22. Ohmichi, T.; Kawamoto, Y.; Wu, P.; Miyoshi, D.; Karimata, H.; Sugimoto, N. Biochemistry 2005, 44, 7125-7130.
23. Liu, K.; Todd Miles, H.; Frazier, J.; Sasisekharan, V. Biochemistry 1993, 32, 11802-11809.
24. Mergny, J. L.; Li, J.; Lacroix, L.; Amrane, S.; Chaires, J. B. Nucleic Acids Res. 2006, 33, e138.
25. Colombo, M. F.; Rau, D. C.; Parsegian, V. A. Science 1992, 256, 655-659.
26. Parsegian, V. A.; Rand, R. P.; Rau, D. C. Methods Enzymol. 1995, 259, 43-94.
27. Parsegian, V. A.; Rand, R. P.; Rau, D. C. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 3987-3992.
28. Robinson, C. R.; Sligar, S. G. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 2186-2191.
29. Webb, J. N.; Webb, S. D.; Cleland, J. L.; Carpenter, J. F.; Randolph, T. W. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 7259-7264.
30. Shimizu, S. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 1195-1199.
31. Timasheff, S. N. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 9721-9726.
32. Courtenay, E. S.; Capp, M. W.; Anderson, C. F.; Record, M. T., Jr. Biochemistry 2000, 39, 4455-4471.
33. Radhakrishnan, I.; Patel, D. J. Biochemistry 1994, 33, 11405-11416.
34. Ouali, M.; Gousset, H.; Geinguenaud, F.; Liquier, J.; Gabarro-Arpa, J.; Le Bret, M.; Taillandier, E. Nucleic Acids Res. 1997, 25, 4816- 4824.
35. Smith, P. E. Biophys. J. 2006, 91, 849-856.
36. Sidorova, N.; Muradymov, S.; Rau, D. C. J. Biol. Chem. 2006, 281, 35656-35666.
37. Stanley, C.; Rau, D. C. Biophys. J. 2006, 91, 912-920.
38. Timasheff, S. N. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 67- 97.
39. Pal, S. K.; Peon, J.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1763-1768.
40. Suck, D.; Oefner, C. Nature 1986, 321, 620-625.
41. Breyer, W. A.; Matthews, B. W. Nat. Struct. Biol. 2000, 7, 1125- 1128.
42. Hu, Y.; Yang, X.; Yin, H. D.; Mahadevan, J.; Kuczera, K.; Schowen, L. R.; Borchardt, T. R. Biochemistry 2001, 40, 15143-15152.
43. Woods, K. K.; Lan, T.; McLaughlin, W. L.; Williams, D. L. Nucleic Acids Res. 2003, 31, 1536-1540.
44. Parvathy, V. R.; Bhaumik, S. R.; Chary, K. V. R.; Govil, G.; Liu, K.; Howard, F. B.; Miles, H. T. Nucleic Acids Res. 2002, 30, 1500-1511.
45. Liepinsh, E.; Leupin, W.; Otting, G. Nucleic Acids Res. 1994, 22, 2249-2254.
46. Ai, X.; Zhou, Z.; Bai, Y.; Choy, W.-Y. J. Am. Chem. Soc. 2006, 128, 3916-3917.