B -> A -> B transitions in a molecular dynamics trajectory of low salt DNA solution

A N Real; R J Greenall

B -> A -> B transitions in a molecular dynamics trajectory of low salt DNA solution

Physics

Research output: Contribution to journal › Article › peer-review

Abstract

A molecular dynamics simulation of the DNA dodecamer d(CGCATATATGCG) has been performed with AMBER 5.0 under low salt conditions. Both B --> A and A --> B transitions are observed. This may have biological significance for the formation of complexes between DNA and TATA-box binding proteins.

Original language	English
Pages (from-to)	654-658
Number of pages	5
Journal	Journal of molecular modeling
Volume	6
Issue number	12
Publication status	Published - 2000

Keywords

molecular dynamics
simulation
1DN9
A-DNA
B-DNA
conformational transitions
PARTICLE MESH EWALD
NUCLEIC-ACIDS
FORCE-FIELD
A-TRANSITION
DOUBLE HELIX
TATA-BOX
SIMULATIONS
BINDING
PROTEINS
CONFORMATION

Cite this

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title = "B -> A -> B transitions in a molecular dynamics trajectory of low salt DNA solution",

abstract = "A molecular dynamics simulation of the DNA dodecamer d(CGCATATATGCG) has been performed with AMBER 5.0 under low salt conditions. Both B --> A and A --> B transitions are observed. This may have biological significance for the formation of complexes between DNA and TATA-box binding proteins.",

keywords = "molecular dynamics, simulation, 1DN9, A-DNA, B-DNA, conformational transitions, PARTICLE MESH EWALD, NUCLEIC-ACIDS, FORCE-FIELD, A-TRANSITION, DOUBLE HELIX, TATA-BOX, SIMULATIONS, BINDING, PROTEINS, CONFORMATION",

author = "Real, {A N} and Greenall, {R J}",

year = "2000",

language = "English",

volume = "6",

pages = "654--658",

journal = "Journal of molecular modeling",

issn = "0948-5023",

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T1 - B -> A -> B transitions in a molecular dynamics trajectory of low salt DNA solution

AU - Real, A N

AU - Greenall, R J

PY - 2000

Y1 - 2000

N2 - A molecular dynamics simulation of the DNA dodecamer d(CGCATATATGCG) has been performed with AMBER 5.0 under low salt conditions. Both B --> A and A --> B transitions are observed. This may have biological significance for the formation of complexes between DNA and TATA-box binding proteins.

AB - A molecular dynamics simulation of the DNA dodecamer d(CGCATATATGCG) has been performed with AMBER 5.0 under low salt conditions. Both B --> A and A --> B transitions are observed. This may have biological significance for the formation of complexes between DNA and TATA-box binding proteins.

KW - molecular dynamics

KW - simulation

KW - 1DN9

KW - A-DNA

KW - B-DNA

KW - conformational transitions

KW - PARTICLE MESH EWALD

KW - NUCLEIC-ACIDS

KW - FORCE-FIELD

KW - A-TRANSITION

KW - DOUBLE HELIX

KW - TATA-BOX

KW - SIMULATIONS

KW - BINDING

KW - PROTEINS

KW - CONFORMATION

M3 - Article

SN - 0948-5023

VL - 6

SP - 654

EP - 658

JO - Journal of molecular modeling

JF - Journal of molecular modeling

IS - 12

ER -