Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes

A molecular dynamics simulation study

Suresh Gorle, U. Deva Priyakumar

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Abstract Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2′-position attribute special properties to nucleic acids when compared to other modifications. 2′-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2′-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2′-O-methyl modified counterparts to investigate the effect of 2′-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.

Original languageEnglish (US)
Article number6581
Pages (from-to)150-159
Number of pages10
JournalJournal of Molecular Graphics and Modelling
Volume61
DOIs
StatePublished - Aug 10 2015
Externally publishedYes

Fingerprint

Nucleic acids
RNA
Nucleic Acids
Molecular dynamics
Thermodynamic stability
DNA
deoxyribonucleic acid
inclusions
molecular dynamics
nucleic acids
thermodynamics
Computer simulation
Free energy
simulation
Sugars
Conformations
free energy
Deoxyribose
sugars
Hydrophobicity

Keywords

  • Antisense therapy
  • Chemically modified nucleic acids
  • Hydrophobicity
  • MD simulations
  • MM-GBSA method
  • Steric interaction
  • Thermodynamic stability

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

Cite this

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title = "Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study",
abstract = "Abstract Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2′-position attribute special properties to nucleic acids when compared to other modifications. 2′-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2′-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2′-O-methyl modified counterparts to investigate the effect of 2′-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.",
keywords = "Antisense therapy, Chemically modified nucleic acids, Hydrophobicity, MD simulations, MM-GBSA method, Steric interaction, Thermodynamic stability",
author = "Suresh Gorle and Priyakumar, {U. Deva}",
year = "2015",
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doi = "10.1016/j.jmgm.2015.07.009",
language = "English (US)",
volume = "61",
pages = "150--159",
journal = "Journal of Molecular Graphics and Modelling",
issn = "1093-3263",
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TY - JOUR

T1 - Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes

T2 - A molecular dynamics simulation study

AU - Gorle, Suresh

AU - Priyakumar, U. Deva

PY - 2015/8/10

Y1 - 2015/8/10

N2 - Abstract Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2′-position attribute special properties to nucleic acids when compared to other modifications. 2′-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2′-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2′-O-methyl modified counterparts to investigate the effect of 2′-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.

AB - Abstract Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2′-position attribute special properties to nucleic acids when compared to other modifications. 2′-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2′-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2′-O-methyl modified counterparts to investigate the effect of 2′-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.

KW - Antisense therapy

KW - Chemically modified nucleic acids

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KW - MD simulations

KW - MM-GBSA method

KW - Steric interaction

KW - Thermodynamic stability

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