DNA dynamically directs its own transcription initiation

Nucleic Acids Research

Volumn 32, Issue 4, 2004, Pages 1584-1590

  Choi, Chu H ^b   Kalosakas, George ^a   Rasmussen, Kim Ø ^a   Hiromura, Makoto ^b,c   Bishop, Alan R ^a   Usheva, Anny ^b  

^a CENTER FOR NONLINEAR STUDIES   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA FRAGMENT; DOUBLE STRANDED DNA; NUCLEASE S1; DNA; SINGLE STRANDED DNA; TRANSCRIPTION FACTOR IIB;

ACCURACY; ADENO ASSOCIATED VIRUS; ADENOVIRUS; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA DENATURATION; DNA DETERMINATION; DNA SEQUENCE; ENZYME DEGRADATION; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR DYNAMICS; NONHUMAN; NONLINEAR SYSTEM; NUCLEOTIDE SEQUENCE; PHYSICAL PARAMETERS; PRIORITY JOURNAL; PROMOTER REGION; THERMAL EXPOSURE; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; VIRUS MUTANT; CHEMISTRY; COMPUTER SIMULATION; GENETICS; MOLECULAR GENETICS;

ADENOVIRIDAE;

ADENOVIRIDAE; BASE SEQUENCE; COMPUTER SIMULATION; DEPENDOVIRUS; DNA; DNA, SINGLE-STRANDED; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; PROMOTER REGIONS (GENETICS); TRANSCRIPTION FACTOR TFIIB; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EID: 2342498193     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh335     Document Type: Article

References (43)

1. Benham,C.J. (1992) Energetics of the strand separation transition in superhelical DNA. J. Mol. Biol., 225, 835-847.
2. Benham,C.J. (1993) Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci. Proc. Natl Acad. Sci. USA, 90, 2999-3003.
3. Benham,C.J. (1996) Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol., 255, 425-434.
4. Breslauer,K.J., Frank,R., Blocker,H. and Marky,L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
5. Packer,M.J., Dauncey,M.P. and Hunter,C.A. (2000) Sequence-dependent DNA structure: tetranucleotide conformational maps. J. Mol. Biol., 295, 85-103.
6. Lankas,F., Sponer,J., Hobza,P. and Langowski,J. (2000) Sequence-dependent elastic properties of DNA. J. Mol. Biol., 299, 695-709.
7. Pedersen,A.G., Baldi,P., Chauvin,Y. and Brunak,S. (1999) The biology of eukaryotic promoter prediction - a review. Comput. Chem., 23, 191-207.
8. Dornberger,U., Leijon,M. and Fritzsche,H. (1999) High base pair opening rates in tracts of GC base pairs. J. Biol. Chem., 274, 6957-6962.
9. Kearns,D.R. (1984) NMR studies of conformational states and dynamics of DNA. CRC Crit. Rev. Biochem., 15, 237-290.
10. Levitt,M. (1983) Computer simulation of DNA double-helix dynamics. Cold Spring Harb. Symp. Quant. Biol., 47 (Pt 1), 251-262.
11. Korzheva,N., Mustaev,A., Kozlov,M., Malhotra,A., Nikiforov,V., Goldfarb,A. and Darst,S.A. (2000) A structural model of transcription elongation. Science, 289, 619-625.
12. Zhang,G., Campbell,E.A., Minakhin,L., Richter,C., Severinov,K. and Darst,S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell, 98, 811-824.
13. Murakami,K.S., Masuda,S., Campbell,E.A., Muzzin,O. and Darst,S.A. (2002) Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science, 296, 1285-1290.
14. Kalosakas,G., Rasmussen,K.O. and Bishop,A.R. (2003) Charge trapping in DNA due to intrinsic vibrational hot spots. J. Chem. Phys., 118, 3731-3735.
15. Hwa,T., Marinari,E., Sneppen,K. and Tang,L.H. (2003) Localization of denaturation bubbles in random DNA sequences. Proc. Natl Acad. Sci. USA, 100, 4411-4416.
16. Dauxois,T., Peyrard,M. and Bishop,A.R. (1993) Entropy-driven DNA denaturation. Phys. Rev. E. Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics, 47, R44-R47.
17. Lilley,D.M. (1988) DNA opens up-supercoiling and heavy breathing. Trends Genet., 4, 111-114.
18. Banerjee,A. and Sobell,H.M. (1983) Presence of nonlinear excitations in DNA structure and their relationship to DNA premelting and to drug intercalation. J. Biomol. Struct. Dyn., 1, 253-262.
19. Prohofsky,E.W. (1988) Solitons hiding in DNA and their possible significance in RNA transcription. Phys. Rev. A, 38, 1538-1541.
20. Peyrard,M. and Bishop,A.R. (1989) Statistical mechanics of a nonlinear model for DNA denaturation. Phys. Rev. Lett., 62, 2755-2758.
21. Dauxois,T., Peyrard,M. and Bishop,A.R. (1993) Dynamics and thermodynamics of a nonlinear model for DNA denaturation. Phys. Rev. E. Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics, 47, 684-695.
22. Usheva,A. and Shenk,T. (1994) TATA-binding protein-independent initiation: YY1, TFIIB and RNA polymerase II direct basal transcription on supercoiled template DNA. Cell, 76, 1115-1121.
23. Malik,S., Hisatake,K., Sumimoto,H., Horikoshi,M. and Roeder,R.G. (1991) Sequence of general transcription factor TFIIB and relationships to other initiation factors. Proc. Natl Acad. Sci. USA, 88, 9553-9557.
24. Benham,C.J. (1990) Theoretical analysis of heteropolymeric transitions in superhelical DNA molecules of specified sequence. J. Chem. Phys., 92, 6294-6305.
25. Campa,A. and Giansanti,A. (1998) Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains. Phys. Rev. E. Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics, 58, 3585-3588.
26. Wiegand,R.C., Godson,G.N. and Radding,C.M. (1975) Specificity of the S1 nuclease from Aspergillus oryzae. J. Biol. Chem., 250, 8848-8855.
27. Berk,A.J. (1986) Adenovirus promoters and E1A transactivation. Annu. Rev. Genet., 20, 45-79.
28. Shenk,T. (1996) In Fields,B., Knipe,D. and Howley,P. (eds) Fields' Virology, 3rd edn. Lippincott-Raven Publishers, Philadelphia, PA, Vol. 2, pp. 2111-2148.
29. Pastor,N., Pardo,L. and Weinstein,H. (1997) Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein. Biophys. J., 73, 640-652.
30. Flatters,D. and Lavery,R. (1998) Sequence-dependent dynamics of TATA-Box binding sites. Biophys. J., 75, 372-381.
31. Patel,D.J., Ikuta,S., Kozlowski,S. and Itakura,K. (1983) Sequence dependence of hydrogen exchange kinetics in DNA duplexes at the individual base pair level in solution. Proc. Natl Acad. Sci. USA, 80, 2184-2188.
32. Pastor,N., Weinstein,H., Jamison,E. and Brenowitz,M. (2000) A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding. J. Mol. Biol., 304, 55-68.
33. Kim,Y., Geiger,J.H., Hahn,S. and Sigler,P.B. (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520.
34. Wu,J., Parkhurst,K.M., Powell,R.M., Brenowitz,M. and Parkhurst,L.J. (2001) DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent. J. Biol. Chem., 276, 14614-14622.
35. Tratschin,J.D., Miller,I.L. and Carter,B.J. (1984) Genetic analysis of adeno-associated virus: properties of deletion mutants constructed in vitro and evidence for an adeno-associated virus replication function. J. Virol., 51, 611-619.
36. Labow,M.A., Hermonat,P.L. and Berns,K.I. (1986) Positive and negative autoregulation of the adeno-associated virus type 2 genome. J. Virol., 60, 251-258.
37. Houbaviy,H.B., Usheva,A., Shenk,T. and Burley,S.K. (1996) Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proc. Natl Acad. Sci. USA, 93, 13577-13582.
38. Usheva,A. and Shenk,T. (1996) YY1 transcriptional initiator: protein interactions and association with a DNA site containing impaired strands. Proc. Natl Acad. Sci. USA, 93, 13571-13576.
39. Hyde-DeRuyscher,R.P., Jennings,E. and Shenk,T. (1995) DNA binding sites for the transcriptional activator/repressor YY1. Nucleic Acids Res., 23, 4457-4465.
40. Coleman,R.A. and Pugh,B.F. (1995) Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. J. Biol. Chem., 270, 13850-13859.
41. Giudice,E. and Lavery,R. (2003) Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations. J. Am. Chem. Soc., 125, 4998-4999.
42. Hoopes,B.C., LeBlanc,J.F. and Hawley,D.K. (1998) Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II. J. Mol. Biol., 277, 1015-1031.
43. Frauenfelder,H., McMahon,B.H., Austin,R.H., Chu,K. and Groves,J.T. (2001) The role of structure, energy landscape, dynamics and allostery in the enzymatic function of myoglobin. Proc. Natl Acad. Sci. USA, 98, 2370-2374.