Sequence-specific thermal fluctuations identify start sites for DNA transcription

Europhysics Letters

Volumn 68, Issue 1, 2004, Pages 127-133

  Kalosakas, G ^a,c   Rasmussen, K O ^a   Bishop, A R ^a   Choi, C H ^b   Usheva, A ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c MAX PLANCK INSTITUT FÜR PHYSIK KOMPLEXER SYSTEME   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 5744255023     PISSN: 02955075     EISSN: None     Source Type: Journal    
DOI: 10.1209/epl/i2004-10167-8     Document Type: Article

References (27)

1. FRAUENFELDER H., SLIGAR S. G. and WOLYNES P. G., Science, 254 (1991) 1598.
2. VOLKMAN B. F., LIPSON D., WEMMER D. E. and KERN D., Science, 291 (2001) 2429.
3. EISENMESSER E. Z., BOSCO D. A., AKKE M. and KERN D., Science, 295 (2002) 1520.
4. PEYRARD M. and BISHOP A. R., Phys. Rev. Lett., 62 (1989) 2755.
5. DAUXOIS T., PEYRARD M. and BISHOP A. R., Phys. Rev. E, 47 (1993) R44.
6. MORRIS J. R. and GOODING R. J., Phys. Rev. Lett., 65 (1990) 1769; Phys. Rev. B, 43 (1991) 6057.
7. MORRIS J. R. and GOODING R. J., Phys. Rev. Lett., 65 (1990) 1769; Phys. Rev. B, 43 (1991) 6057.
8. KERR W. C., HAWTHORNE A. M., GOODING R. J., BISHOP A. R. and KRUMHANSL J. A., Phys. Rev. B, 45 (1992) 7036.
9. The importance of entropic terms for enhancing cooperativity and providing distinct transitions, similarly to the case of the model we used, has also been stressed recently in a different context, viz. β-hairpin folding models. See Guo C., LEVINE H. and KESSLER D. A., Phys. Rev. Lett., 84 (2000) 3490.
10. DAUXOIS T. and PEYRARD M., Phys. Rev. E, 51 (1995) 4027.
11. ZENG Y., MONTRICHOK A. and ZOCCHI G., Phys. Rev. Lett., 91 (2003) 148101.
12. We note that these large-amplitude bubbles (breathers) are not traveling, in contrast to mobile low-amplitude nonlinear excitations proposed to account for hydrogen exchange experiments in, e.g., ENGLANDER S. W., KALLENBACH N. R., HEEGER A. J., KRUMHANSL J. A. and LITWIN S., Proc. Natl. Acad. Sci. USA, 77 (1980) 7222.
13. CAMPA A. and GIANSANTI A., Phys. Rev. E, 58 (1998) 3585.
14. CULE D. and HWA T., Phys. Rev. Lett., 79 (1997) 2375.
15. KOMINEAS S., KALOSAKAS G. and BISHOP A. R., Phys. Rev. E, 65 (2002) 061905.
16. MANIADIS P., KALOSAKAS G., RASMUSSEN K. O. and BISHOP A. R., Phys. Rev. B, 68 (2003) 174304.
17. PEYRARD M. and FARAGO J., Physica A, 288 (2000) 199.
18. KALOSAKAS G., RASMUSSEN K. Ø. and BISHOP A. R., J. Chem. Phys., 118 (2003) 3731; Synth. Met., 141 (2004) 93.
19. KALOSAKAS G., RASMUSSEN K. Ø. and BISHOP A. R., J. Chem. Phys., 118 (2003) 3731; Synth. Met., 141 (2004) 93.
20. The adeno-associated viral P5 has a single-stranded DNA. However, once the virus infects a host, the protective coating is shed and this DNA is replicated, resulting in transcriptionally active double-stranded DNA. The promoter is in its active form once it has become double-stranded. See, for example, STRYER L., Biochemistry, 3rd edition (W. H. Freeman) 1988;
21. FIELDs B. N., KNIPE D. M. and HOWLEY P. M. (Editors), Fields Virology, Vol. 3 (Lippincott-Raven) 1990.
22. CHOI C. H., KALOSAKAS G., RASMUSSEN K. Ø., HIROMURA M., BISHOP A. R. and USHEVA A., Nucleic Acids Res., 32 (2004) 1584.
23. USHEVA A. and SHENK T., Cell, 76 (1994) 1115.
24. CONCINO M. F., LEE R. F., MERRYWEATHER J. P. and WEINMANN R., Nucleic Acids Res., 12 (1984) 7423.
25. SANCHEZ A. and BISHOP A. R., SIAM Rev., 40 (1998) 579.
26. YERAMIAN E., Gene, 255 (2000) 139;
27. YERAMIAN E. and JONES L., Nucleic Acids Res., 31 (2003) 3843.