Modelling base pair opening: the role of helical twist

被引：38

作者：

Bernet, J

Zakrzewska, K

Lavery, R

机构：

[1] Lab. de Biochimie Théorique, CNRS UPR 9080, Inst. de Biologie Physico-Chimique, Paris 75005, 13, rue Pierre et Marie Curie

来源：

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM | 1997年 / 398卷

关键词：

molecular modelling; DNA deformation; hydrogen exchange; solvent effects;

D O I：

10.1016/S0166-1280(96)04974-3

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Molecular modelling with the JUMNA program has been used to study the conformational and energetic aspects of base pair opening within a B-DNA double helix. Using new geometrical restraints, it has been possible to map base opening into the minor and major grooves of the double helix, without fixing an axis of rotation or the plane in which the base moves. The results show notably that minor groove opening is favoured by locally unwound DNA. Although the modelling is carried out with a simple distance-dependent dielectric function, the DelPhi program is also used to check that more realistic Poisson-Boltzmann electrostatics yields similar results. (C) 1997 Elsevier Science B.V.

引用

页码：473 / 482

页数：10

共 35 条

[1] ALIGNMENT AND SENSITIVE DETECTION OF DNA BY A MOVING INTERFACE
BENSIMON, A
SIMON, A
CHIFFAUDEL, A
CROQUETTE, V
HESLOT, F
BENSIMON, D
[J]. SCIENCE, 1994, 265 (5181) : 2096 - 2098
[2] STRETCHING DNA WITH A RECEDING MENISCUS - EXPERIMENTS AND MODELS
BENSIMON, D
SIMON, AJ
CROQUETTE, V
BENSIMON, A
[J]. PHYSICAL REVIEW LETTERS, 1995, 74 (23) : 4754 - 4757
[3] EVIDENCE FOR THE STOCHASTIC NATURE OF BASE PAIR OPENING IN DNA - A BROWNIAN DYNAMICS SIMULATION
BRIKI, F
RAMSTEIN, J
LAVERY, R
GENEST, D
[J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1991, 113 (07) : 2490 - 2493
[4] Transcription - Picking up the TAB
Burley, SK
[J]. NATURE, 1996, 381 (6578) : 112 - 113
[5] DNA: An extensible molecule
Cluzel, P
Lebrun, A
Heller, C
Lavery, R
Viovy, JL
Chatenay, D
Caron, F
[J]. SCIENCE, 1996, 271 (5250) : 792 - 794
[6] THE ELECTROSTATIC CONTRIBUTION TO DNA BASE-STACKING INTERACTIONS
FRIEDMAN, RA
HONIG, B
[J]. BIOPOLYMERS, 1992, 32 (02) : 145 - 159
[7] 3-CENTER HYDROGEN-BONDS IN DNA - MOLECULAR-DYNAMICS OF POLY(DA).POLY(DT)
FRITSCH, V
WESTHOF, E
[J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1991, 113 (22) : 8271 - 8277
[8] CALCULATION OF THE TOTAL ELECTROSTATIC ENERGY OF A MACROMOLECULAR SYSTEM - SOLVATION ENERGIES, BINDING-ENERGIES, AND CONFORMATIONAL-ANALYSIS
GILSON, MK
HONIG, B
[J]. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1988, 4 (01): : 7 - 18
[9] CALCULATING THE ELECTROSTATIC POTENTIAL OF MOLECULES IN SOLUTION - METHOD AND ERROR ASSESSMENT
GILSON, MK
SHARP, KA
HONIG, BH
[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 1988, 9 (04) : 327 - 335
[10] GUERON M, 1992, NUCLEIC ACIDS MOL BI, V6, P1

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