Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing

K Bryson; R J Greenall

Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing

Physics

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

Abstract

Molecular dynamics simulations with simulated annealing are performed on polyamine-DNA systems in order to determine the binding sites of putrescine, cadaverine, spermidine and spermine on A- and B-DNA. The simulations either contain no additional counterions or sufficient Na+ ions, together with the charge on the polyamine, to provide 73% neutralisation of the charges on the DNA phosphate. The stabilisation energies of the complexes indicate that all four polyamines should stabilise A-DNA in preference to B-DNA, which is in agreement with experiment in the case of spermine and spermidine, but not in the case of putrescine or cadaverine. The major groove is the preferred binding site on A-DNA of all the polyamines. Putrescine and cadaverine tend to bind to the sugar-phosphate backbone of B-DNA, whereas spermidine and spermine occupy more varied sites, including binding along the backbone and bridging both the major and minor grooves.

Original language	English
Pages (from-to)	393-412
Number of pages	20
Journal	Journal of biomolecular structure & dynamics
Volume	18
Issue number	3
Publication status	Published - Dec 2000

Keywords

MOLECULAR-DYNAMICS
Z TRANSITION
NUCLEIC-ACIDS
FORCE-FIELD
A-DNA
MECHANICS
SEQUENCE
PROTEINS
LIGAND

Cite this

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title = "Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing",

abstract = "Molecular dynamics simulations with simulated annealing are performed on polyamine-DNA systems in order to determine the binding sites of putrescine, cadaverine, spermidine and spermine on A- and B-DNA. The simulations either contain no additional counterions or sufficient Na+ ions, together with the charge on the polyamine, to provide 73% neutralisation of the charges on the DNA phosphate. The stabilisation energies of the complexes indicate that all four polyamines should stabilise A-DNA in preference to B-DNA, which is in agreement with experiment in the case of spermine and spermidine, but not in the case of putrescine or cadaverine. The major groove is the preferred binding site on A-DNA of all the polyamines. Putrescine and cadaverine tend to bind to the sugar-phosphate backbone of B-DNA, whereas spermidine and spermine occupy more varied sites, including binding along the backbone and bridging both the major and minor grooves.",

keywords = "MOLECULAR-DYNAMICS, Z TRANSITION, NUCLEIC-ACIDS, FORCE-FIELD, A-DNA, MECHANICS, SEQUENCE, PROTEINS, LIGAND",

author = "K Bryson and Greenall, {R J}",

year = "2000",

month = dec,

language = "English",

volume = "18",

pages = "393--412",

journal = "Journal of biomolecular structure & dynamics",

issn = "0739-1102",

publisher = "Adenine Press",

number = "3",

}

TY - JOUR

T1 - Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing

AU - Bryson, K

AU - Greenall, R J

PY - 2000/12

Y1 - 2000/12

N2 - Molecular dynamics simulations with simulated annealing are performed on polyamine-DNA systems in order to determine the binding sites of putrescine, cadaverine, spermidine and spermine on A- and B-DNA. The simulations either contain no additional counterions or sufficient Na+ ions, together with the charge on the polyamine, to provide 73% neutralisation of the charges on the DNA phosphate. The stabilisation energies of the complexes indicate that all four polyamines should stabilise A-DNA in preference to B-DNA, which is in agreement with experiment in the case of spermine and spermidine, but not in the case of putrescine or cadaverine. The major groove is the preferred binding site on A-DNA of all the polyamines. Putrescine and cadaverine tend to bind to the sugar-phosphate backbone of B-DNA, whereas spermidine and spermine occupy more varied sites, including binding along the backbone and bridging both the major and minor grooves.

AB - Molecular dynamics simulations with simulated annealing are performed on polyamine-DNA systems in order to determine the binding sites of putrescine, cadaverine, spermidine and spermine on A- and B-DNA. The simulations either contain no additional counterions or sufficient Na+ ions, together with the charge on the polyamine, to provide 73% neutralisation of the charges on the DNA phosphate. The stabilisation energies of the complexes indicate that all four polyamines should stabilise A-DNA in preference to B-DNA, which is in agreement with experiment in the case of spermine and spermidine, but not in the case of putrescine or cadaverine. The major groove is the preferred binding site on A-DNA of all the polyamines. Putrescine and cadaverine tend to bind to the sugar-phosphate backbone of B-DNA, whereas spermidine and spermine occupy more varied sites, including binding along the backbone and bridging both the major and minor grooves.

KW - MOLECULAR-DYNAMICS

KW - Z TRANSITION

KW - NUCLEIC-ACIDS

KW - FORCE-FIELD

KW - A-DNA

KW - MECHANICS

KW - SEQUENCE

KW - PROTEINS

KW - LIGAND

M3 - Article

SN - 0739-1102

VL - 18

SP - 393

EP - 412

JO - Journal of biomolecular structure & dynamics

JF - Journal of biomolecular structure & dynamics

IS - 3

ER -