A study of the hydrogen-bonded network around the left-handed and right-handed DNA in an ionic solution

Nam Sook Kang; Kyung Tai No; Shik Jhon Mu

doi:10.1080/0892702031000065764

A study of the hydrogen-bonded network around the left-handed and right-handed DNA in an ionic solution

Nam Sook Kang, Kyung Tai No, Shik Jhon Mu

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

2 Citations (Scopus)

Abstract

Molecular dynamics simulations were carried out for a right-handed and left-handed DNA heteropolymeric fragment, in which four different types of nucleotides constituted the sequence. The average structures obtained from the simulation converged to within ∼ 1.4 Å rms fluctuation for the left-handed and for the right-handed DNA. The distribution of hydration sites and the hydrogen-bonded circular network of water molecules around guanine and cytosine bases were distinctively different in two DNA conformations. The hydrogen-bonded circular network, ring structure, of water molecules within 4.0 A around two DNA molecules was better formed in the right-handed DNA than in the left-handed DNA, showing a higher ratio of hexameric ring to pentameric ring (R₆/R₅).

Original language	English
Pages (from-to)	83-89
Number of pages	7
Journal	Molecular Simulation
Volume	29
Issue number	2
DOIs	https://doi.org/10.1080/0892702031000065764
Publication status	Published - 2003 Jan 1

Bibliographical note

Funding Information:
This work was supported in part by the Korea Research Center for Theoretical Physics and Chemistry. N.S. Kang would like to thank the Department of Chemistry of Soong Sil University for the financial support of the BK program.

All Science Journal Classification (ASJC) codes

Chemistry(all)
Information Systems
Modelling and Simulation
Chemical Engineering(all)
Materials Science(all)
Condensed Matter Physics

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10.1080/0892702031000065764

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title = "A study of the hydrogen-bonded network around the left-handed and right-handed DNA in an ionic solution",

abstract = "Molecular dynamics simulations were carried out for a right-handed and left-handed DNA heteropolymeric fragment, in which four different types of nucleotides constituted the sequence. The average structures obtained from the simulation converged to within ∼ 1.4 {\AA} rms fluctuation for the left-handed and for the right-handed DNA. The distribution of hydration sites and the hydrogen-bonded circular network of water molecules around guanine and cytosine bases were distinctively different in two DNA conformations. The hydrogen-bonded circular network, ring structure, of water molecules within 4.0 A around two DNA molecules was better formed in the right-handed DNA than in the left-handed DNA, showing a higher ratio of hexameric ring to pentameric ring (R6/R5).",

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AU - Kang, Nam Sook

AU - No, Kyung Tai

AU - Mu, Shik Jhon

N1 - Funding Information: This work was supported in part by the Korea Research Center for Theoretical Physics and Chemistry. N.S. Kang would like to thank the Department of Chemistry of Soong Sil University for the financial support of the BK program.

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N2 - Molecular dynamics simulations were carried out for a right-handed and left-handed DNA heteropolymeric fragment, in which four different types of nucleotides constituted the sequence. The average structures obtained from the simulation converged to within ∼ 1.4 Å rms fluctuation for the left-handed and for the right-handed DNA. The distribution of hydration sites and the hydrogen-bonded circular network of water molecules around guanine and cytosine bases were distinctively different in two DNA conformations. The hydrogen-bonded circular network, ring structure, of water molecules within 4.0 A around two DNA molecules was better formed in the right-handed DNA than in the left-handed DNA, showing a higher ratio of hexameric ring to pentameric ring (R6/R5).

AB - Molecular dynamics simulations were carried out for a right-handed and left-handed DNA heteropolymeric fragment, in which four different types of nucleotides constituted the sequence. The average structures obtained from the simulation converged to within ∼ 1.4 Å rms fluctuation for the left-handed and for the right-handed DNA. The distribution of hydration sites and the hydrogen-bonded circular network of water molecules around guanine and cytosine bases were distinctively different in two DNA conformations. The hydrogen-bonded circular network, ring structure, of water molecules within 4.0 A around two DNA molecules was better formed in the right-handed DNA than in the left-handed DNA, showing a higher ratio of hexameric ring to pentameric ring (R6/R5).

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A study of the hydrogen-bonded network around the left-handed and right-handed DNA in an ionic solution

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

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