Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition

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Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition. / Real, A N; Greenall, R J.

In: Journal of biomolecular structure & dynamics, Vol. 21, No. 4, 02.2004, p. 469-487.

Research output: Contribution to journalArticlepeer-review

Harvard

Real, AN & Greenall, RJ 2004, 'Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition', Journal of biomolecular structure & dynamics, vol. 21, no. 4, pp. 469-487.

APA

Real, A. N., & Greenall, R. J. (2004). Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition. Journal of biomolecular structure & dynamics, 21(4), 469-487.

Vancouver

Real AN, Greenall RJ. Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition. Journal of biomolecular structure & dynamics. 2004 Feb;21(4):469-487.

Author

Real, A N ; Greenall, R J. / Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition. In: Journal of biomolecular structure & dynamics. 2004 ; Vol. 21, No. 4. pp. 469-487.

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@article{e96b7a2e2d104455a873760a0a9db55b,
title = "Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition",
abstract = "The effect of spermine on the A-DNA to B-DNA transition in d(CGCGAATTCGCG)(2) has been investigated by five A-start molecular dynamics simulations, using the Cornell et al. potential. In the absence of spermine an A-->B transition is initiated immediately and the DNA becomes equidistant from the A- and B-forms at 200ps. In three DNA-spermine simulations, when a spermine is located across the major groove of A-DNA in one of three different initial locations, the time taken to reach equidistance from the A- and B-forms is delayed until 800, 950 or 1000ps. In each case the A-form appears to be temporarily stabilized by spermine's electrostatic interactions with phosphates on both sides of the major groove. The onset of the A-->B transition can be correlated with the spermine losing contact with phosphates on one side of the groove and with A-like --> B-like sugar pucker transitions in the vicinity of the spermine bridge. However in the fifth trajectory, in which the spermine initially threads from the major groove via the backbone into the minor groove, the B-->A transition occurs rapidly once again and the DNA is equidistant between the A- and B-forms within 300ps. This indicates that the mere presence of spermine is insufficient to delay the transition and that major groove binding stabilizes A-DNA.",
keywords = "NUCLEIC-ACID INTERACTIONS, PARTICLE MESH EWALD, B-DNA, A-DNA, CRYSTAL-STRUCTURE, MINOR-GROOVE, TATA-BOX, SEQUENCE SPECIFICITY, OCTAMER D(GTGTACAC), DOUBLE HELIX",
author = "Real, {A N} and Greenall, {R J}",
year = "2004",
month = feb,
language = "English",
volume = "21",
pages = "469--487",
journal = "Journal of biomolecular structure & dynamics",
issn = "0739-1102",
publisher = "Adenine Press",
number = "4",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Influence of spermine on DNA conformation in a molecular dynamics trajectory of d(CGCGAATTCGCG)(2): Major groove binding by one spermine molecule delays the A -> B transition

AU - Real, A N

AU - Greenall, R J

PY - 2004/2

Y1 - 2004/2

N2 - The effect of spermine on the A-DNA to B-DNA transition in d(CGCGAATTCGCG)(2) has been investigated by five A-start molecular dynamics simulations, using the Cornell et al. potential. In the absence of spermine an A-->B transition is initiated immediately and the DNA becomes equidistant from the A- and B-forms at 200ps. In three DNA-spermine simulations, when a spermine is located across the major groove of A-DNA in one of three different initial locations, the time taken to reach equidistance from the A- and B-forms is delayed until 800, 950 or 1000ps. In each case the A-form appears to be temporarily stabilized by spermine's electrostatic interactions with phosphates on both sides of the major groove. The onset of the A-->B transition can be correlated with the spermine losing contact with phosphates on one side of the groove and with A-like --> B-like sugar pucker transitions in the vicinity of the spermine bridge. However in the fifth trajectory, in which the spermine initially threads from the major groove via the backbone into the minor groove, the B-->A transition occurs rapidly once again and the DNA is equidistant between the A- and B-forms within 300ps. This indicates that the mere presence of spermine is insufficient to delay the transition and that major groove binding stabilizes A-DNA.

AB - The effect of spermine on the A-DNA to B-DNA transition in d(CGCGAATTCGCG)(2) has been investigated by five A-start molecular dynamics simulations, using the Cornell et al. potential. In the absence of spermine an A-->B transition is initiated immediately and the DNA becomes equidistant from the A- and B-forms at 200ps. In three DNA-spermine simulations, when a spermine is located across the major groove of A-DNA in one of three different initial locations, the time taken to reach equidistance from the A- and B-forms is delayed until 800, 950 or 1000ps. In each case the A-form appears to be temporarily stabilized by spermine's electrostatic interactions with phosphates on both sides of the major groove. The onset of the A-->B transition can be correlated with the spermine losing contact with phosphates on one side of the groove and with A-like --> B-like sugar pucker transitions in the vicinity of the spermine bridge. However in the fifth trajectory, in which the spermine initially threads from the major groove via the backbone into the minor groove, the B-->A transition occurs rapidly once again and the DNA is equidistant between the A- and B-forms within 300ps. This indicates that the mere presence of spermine is insufficient to delay the transition and that major groove binding stabilizes A-DNA.

KW - NUCLEIC-ACID INTERACTIONS

KW - PARTICLE MESH EWALD

KW - B-DNA

KW - A-DNA

KW - CRYSTAL-STRUCTURE

KW - MINOR-GROOVE

KW - TATA-BOX

KW - SEQUENCE SPECIFICITY

KW - OCTAMER D(GTGTACAC)

KW - DOUBLE HELIX

M3 - Article

VL - 21

SP - 469

EP - 487

JO - Journal of biomolecular structure & dynamics

JF - Journal of biomolecular structure & dynamics

SN - 0739-1102

IS - 4

ER -