The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA

Norio Yoshida, Yasuomi Kiyota, Fumio Hirata

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

A new approach for investigating solvent effects on the electronic structure of solvated macromolecules is proposed. The method is constructed by combining the quantum and molecular mechanics (QM/MM) methods with the reference interaction site model (RISM) theory. The system treated with the method is divided into three regions, quantum and molecular mechanical regions of solute, and the solvent region. The two solute regions are treated by the ordinary QM/MM method, while the solvent region is handled with the RISM theory. The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.

Original languageEnglish
Pages (from-to)83-92
Number of pages10
JournalJournal of Molecular Liquids
Volume159
Issue number1
DOIs
Publication statusPublished - Feb 15 2011
Externally publishedYes

Fingerprint

Proflavine
Intercalation
intercalation
Electronic structure
DNA
deoxyribonucleic acid
electronic structure
Molecular mechanics
Quantum theory
Solvation
solvation
solutes
interactions
Coulomb interactions
penalties
Macromolecules
Dehydration
macromolecules
dehydration
Free energy

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Condensed Matter Physics
  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Materials Chemistry

Cite this

The electronic-structure theory of a large-molecular system in solution : Application to the intercalation of proflavine with solvated DNA. / Yoshida, Norio; Kiyota, Yasuomi; Hirata, Fumio.

In: Journal of Molecular Liquids, Vol. 159, No. 1, 15.02.2011, p. 83-92.

Research output: Contribution to journalArticle

@article{444249715e09474bb7bb4d71bbdeffd1,
title = "The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA",
abstract = "A new approach for investigating solvent effects on the electronic structure of solvated macromolecules is proposed. The method is constructed by combining the quantum and molecular mechanics (QM/MM) methods with the reference interaction site model (RISM) theory. The system treated with the method is divided into three regions, quantum and molecular mechanical regions of solute, and the solvent region. The two solute regions are treated by the ordinary QM/MM method, while the solvent region is handled with the RISM theory. The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.",
author = "Norio Yoshida and Yasuomi Kiyota and Fumio Hirata",
year = "2011",
month = "2",
day = "15",
doi = "10.1016/j.molliq.2010.04.019",
language = "English",
volume = "159",
pages = "83--92",
journal = "Journal of Molecular Liquids",
issn = "0167-7322",
publisher = "Elsevier",
number = "1",

}

TY - JOUR

T1 - The electronic-structure theory of a large-molecular system in solution

T2 - Application to the intercalation of proflavine with solvated DNA

AU - Yoshida, Norio

AU - Kiyota, Yasuomi

AU - Hirata, Fumio

PY - 2011/2/15

Y1 - 2011/2/15

N2 - A new approach for investigating solvent effects on the electronic structure of solvated macromolecules is proposed. The method is constructed by combining the quantum and molecular mechanics (QM/MM) methods with the reference interaction site model (RISM) theory. The system treated with the method is divided into three regions, quantum and molecular mechanical regions of solute, and the solvent region. The two solute regions are treated by the ordinary QM/MM method, while the solvent region is handled with the RISM theory. The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.

AB - A new approach for investigating solvent effects on the electronic structure of solvated macromolecules is proposed. The method is constructed by combining the quantum and molecular mechanics (QM/MM) methods with the reference interaction site model (RISM) theory. The system treated with the method is divided into three regions, quantum and molecular mechanical regions of solute, and the solvent region. The two solute regions are treated by the ordinary QM/MM method, while the solvent region is handled with the RISM theory. The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.

UR - http://www.scopus.com/inward/record.url?scp=79952009095&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79952009095&partnerID=8YFLogxK

U2 - 10.1016/j.molliq.2010.04.019

DO - 10.1016/j.molliq.2010.04.019

M3 - Article

AN - SCOPUS:79952009095

VL - 159

SP - 83

EP - 92

JO - Journal of Molecular Liquids

JF - Journal of Molecular Liquids

SN - 0167-7322

IS - 1

ER -