Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 κB site: Evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex

Journal of Molecular Biology

Volumn 279, Issue 1, 1998, Pages 127-142

  Tisné, Carine ^a   Hantz, Edith ^a   Hartmann, Brigitte ^a   Delepierre, Muriel ^a  

^a CNRS   (France)

Author keywords

31P NMR; DNA structure; Molecular modelling; NF B; NMR

Indexed keywords

CURVED DNA; DOUBLE STRANDED DNA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; SUGAR;

ARTICLE; DNA STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; X RAY ANALYSIS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0032577320     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1757     Document Type: Article

References (63)

1. Aggarwal A.K. A gripping end to NF-κB. Struct. Biol. 2:(3):1995;184-186
2. Baeuerle P.A. The inducible transcription activator NF-κB regulation by distinct protein subunits. Biochim. Biophys. Acta. 1072:1991;63-80
3. Baleja J.D., Germann M.W., van de Sande J.H., Sykes B.D. Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement. J. Mol. Biol. 215:1990;411-428
4. Baltimore D., Beg A.A. A butterfly flutters by. Nature. 373:1995;287-288
5. Bax A., Davis D.G. MLEV-17-based two-dimensional homonuclear magnetisation transfer spectroscopy. J. Magn. Reson. 65:1985;355-360
6. Bertrand H.-O., Ha-Duond T., Fermandjian S., Hartmann B. Flexibility of B-DNA backbone effects of local and neighbouring sequences on pyrimidine-purine steps. Nucl. Acids Res. 26:1998;1261-1267
7. Chou S.-H., Cheng J.-W., Fedoroff O.Y., Chuprina V.P., Reid B.R. Adjacent G:A mismatch base-pairs contain BII phosphodiesters in solution. J. Am. Chem. Soc. 114:1992;3114-3115
8. Chou S.-H., Cheng J.-W., Reid B.R. Solution structure of (d(ATGAGCGAATA))2:Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups. J. Mol. Biol. 228:1992;138-155
9. Chytil M., Verdine G.L. The Rel family of eukaryotic transcription factors. Curr. Opin. Struct. Biol. 6:1996;91-100
10. Clark L., Matthews J.R., Hay R.T. Interaction of enhancer-binding protein EBP1 (NF-κB) with the human immunodeficiency virus type 1 enhancer. J. Virol. 64:1990;1335-1344
11. Clore G.M., Gronenborn A.M. Probing the three-dimensional structures of DNA and RNA oligonucleotides in solution by nuclear Overhauser enhancement measurements. FEBS Letters. 179:1985;187-198
12. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M.J., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197
13. 1H NMR of the HIV-1 enhancer the transcription factor NF-κB and Sp1 binding domains. Magn. Reson. Chem. 34:1996;s67-s80
14. Desvaux H., Berthault P., Birlikis N., Goldman M., Piotto M. Improved version of off-resonance ROESY. J. Magn. Reson. ser. A. 113:1995;47-52
15. El Antri S., Mauffret O., Monnot M., Lescot E., Convert O., Fermandjian S. Structural deviations at CpG provide a plausible explanation for the high frequency of mutation at this site. J. Mol. Biol. 230:1993;373-378
16. Flatters D., Zakrzewska K., Lavery R. Internal coordinate modelling of DNA force field comparisons. J. Comput. Chem. 18:1997;1043-1055
17. Geen H., Freeman R. Band-selective radiofrequency pulses. J. Magn. Reson. 93:1991;93-141
18. Ghosh G., Van Duyne G., Ghosh S., Sigler P.S. Structure of NF-κB p50 homodimer bound to a κB site. Nature. 373:1995;303-310
19. Gonzalez C., Rullmann J.A.C., Bonvin A.M.J.J., Boelens R., Kaptein R. Towards an NMR R factor. J. Magn. Reson. 91:1991;659-664
20. 31P NMR of DNA. Lilley D.M.J., Dahlberg J.E. Methods in Enzymology DNA Structures, part A, Synthesis and Physical Analysis of DNA. vol. 211:1992;254-286 Academic Press Ltd, London
21. 1H spin system identification in macromolecules. J. Am. Chem. Soc. 110:1988;7870-7872
22. Grzeskowiak K., Yanagi K., Privé G.G., Dickerson R.E. The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. J. Biol. Chem. 266:1991;8861-8883
23. Hartmann B., Lavery R. Modelling DNA conformational mechanics. Biophy. Chem. 50:1994;33-45
24. Hartmann B., Piazzola D., Lavery R. BI-BII transitions in B-DNA. Nucl. Acids Res. 21:1993;561-568
25. James T.L. Relaxation matrix analysis of two-dimensional nuclear Overhauser effect spectra. Curr. Opin. Struct. Biol. 1:1991;1042-1053
26. Jones K.A., Kadonaga J.T., Luciw P.A., Tjian R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science. 232:1986;755-759
27. Kim S.-G., Reid B.R. Automated NMR structure refinement via NOE peak volumes. Application to a dodecamer DNA duplex. J. Magn. Reson. 100:1992;382-390
28. 1H NMR. Biochemistry. 31:1992;3564-3574
29. Kupce E., Freeman R. Band-selective correlation spectroscopy. J. Magn. Reson. ser. A. 112:1995;134-137
30. Kupce E., Boyd J., Campbell I.D. Short selective pulses for biochemical applications. J. Magn. Reson. ser. B. 106:1995;300-303
31. Kuriyan J., Thanos D. Structure of the NF-κB transcription factor a holistic interaction with DNA. Structure. 3:1995;135-141
32. Lavery R. Junctions and bends in nucleic acids a new theoretical modelling approach. Olson W.K., Sarma R.H., Sarma M.H., Sundaralingam M. Structure and Expression. vol. 3:1988;191-211 Adenine Press, New York
33. Lavery R., Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6:(1):1988;63-91
34. Lavery R., Parker I., Kendrick J. A general approach to the optimization of the conformation of ring molecules with an application to valynomicin. J. Biomol. Struct. Dynam. 4:1986;443-461
35. Lavery R., Sklenar H., Zakrzewska K., Pullman B. The flexibility of the nucleic acids (II) the calculation of internal energy and applications to mononucleotide repeat DNA. J. Biomol. Struct. Dynam. 3:1986;989-1014
36. Lefebvre A., Mauffret O., Hartmann B., Lescot E., Fermandjian S. The structural behaviour of the CpG step in two related oligonucleotides reflects its malleability in solution. Biochemistry. 34:(37):1995;12019-12029
37. Lefebvre A., Mauffret O., Lescot E., Hartmann B., Fermandjian S. Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG. Biochemistry. 35:1996;12560-12569
38. Lefebvre A., Fermandjian S., Hartmann B. Sensibility of NMR internucleotide distances to B-DNA conformation underlying mechanics. Nucl. Acids Res. 25:1997;3855-3862
39. Liu J., Sodeoka M., Lane W.S., Verdine G.L. Evidence for a non-helical DNA-binding motif in Rel homology region. Proc. Natl Acad. Sci. USA. 91:1994;908-912
40. Marion D., Bax A. P. COSY, a sensitive alternative for double-quantum filtered COSY. J. Magn. Reson. 80:1988;528-533
41. Mauffret O., Hartmann B., Convert O., Lavery R., Fermandjian S. The fine structure of two DNA dodecamers containing the sequence CRE and its inverse NMR and molecular simulation studies. J. Mol. Biol. 227:1992;852-875
42. Müller C.W., Rey F.A., Sodeoka M., Verdine G.L., Harrison S.C. Structure of the NF-κB p50 homodimer bound to DNA. Nature. 373:1995;311-317
43. Müller C.W., Rey F.A., Harrison S.C. Comparison of two different DNA-binding modes of the NF-κB p50 homodimer. Nature Struct. Biol. 3:1996;224-227
44. Nabel G., Baltimore D. An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature. 326:1987;711-713
45. 31P NMR spectra and restrained molecular dynamics structure of a mismatched GA decamer oligodeoxyribonucleotide duplex. Biochemistry. 29:1990;8845-8858
46. 15N spectroscopy. J. Magn. Reson. 87:1990;488-501
47. Poncin M., Hartmann B., Lavery R. Conformational sub-states in B-DNA. J. Mol. Biol. 226:1992;775-794
48. 31P NMR spectra. Biochemistry. 29:1990;5245-5258
49. Schreck R., Zorbas H., Winnacker E.L., Baeuerle P.A. The NF-κB transcription factor induces DNA bending which is modulated by its 65-kD subunit. Nucl. Acids Res. 18:1990;6497-6502
50. Singh M.P., Fregeau N.L., Pon R.T., Lown J.W. High resolution 2D-NMR studies including complete assignments and conformational characteristics of the NF-κB binding enhancer element of HIV-LTR. J. Biomol. Struct. Dynam. 13:1995;269-284
51. 31P coupling constants in double-stranded DNA fragments. J. Am. Chem. Soc. 25:1987;7525-7526
52. Smallcombe S.H., Patt S.L., Keifer P.A. WET solvent suppression and its application to LC NMR and high-resolution NMR spectroscopy. J. Magn. Reson. ser. A. 117:1995;295-303
53. Sodano P., Delepierre M. Binomial frequency response to non-binomial pulse sequences for efficient water suppression. J. Biomol. NMR. 3:1993;471-477
54. Sodano P., Hartmann B., Rose T., Wain-Hobson S., Delepierre M. Solution structure of a homopyrimidine-Homopurine dodecamer encoded by the HIV-1 envelope gene NMR and molecular simulation studies. Biochemistry. 34:1995;6900-6910
55. States D.J., Haberkorn R.A., Ruben D.J. A two-dimensional nuclear Overhauser experiment with pure absorption phase in four quadrants. J. Magn. Reson. 48:1982;286-292
56. 3J P-H coupling constants. Magn. Reson. Chem. 34:1996;s115-s124
57. 31P NMR conformational studies of non-palindromic DNA duplexes related to HIV-1 enhancer. J. Chim. Phys. 2:1998;412-417
58. Van de Ven F.J.M., Hilbers C.W. Resonance assignments of non-exchangeable protons in B type DNA oligomers, an overview. Nucl. Acids Res. 16:1988;5713-5720
59. Virelizier J.L. Cellular activation and human immunodeficiency virus infection. Curr. Opin. Immunol. 2:1990;409-413
60. Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S.J., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784
61. Wijmenga S.S., Mooren M.M.W., Hilbers C.W. NMR of nucleic acids; from spectrum to structure. Roberts G.C.K. NMR in Macromolecules A Practical Approach. 1993;217-288 Oxford University Press
62. Wilker W., Leibfritz D., Kerssebaum R., Bermel W. Gradient selection in inverse heteronuclear correlation spectroscopy. Magn. Reson. Chem. 31:1993;287-292
63. Wüthrich K. Resonance assignments and structure determination in nucleic acids. NMR of Proteins and Nucleic Acids. 1986;203-233 Wiley J. & Sons, New York