Theoretical study of sequence selectivity and preferred binding mode of psoralen with DNA

Patricia Saenz-Méndez; Rita C. Guedes; Daniel J.V.A. dos Santos; Leif A. Eriksson

Theoretical study of sequence selectivity and preferred binding mode of psoralen with DNA

Patricia Saenz-Méndez, Rita C. Guedes, Daniel J.V.A. dos Santos, Leif A. Eriksson

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

Abstract

Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand.We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5 -TpA in (AT)n sequences.

Original language	English
Title of host publication	Physical Chemistry
Subtitle of host publication	Chemical Kinetics and Reaction Mechanisms
Publisher	Apple Academic Press
Pages	273-283
Number of pages	11
ISBN (Electronic)	9781466559813
ISBN (Print)	9781926692616
Publication status	Published - 1 Jan 2011

Bibliographical note

Publisher Copyright:
© 2011 by Apple Academic Press, Inc.

Cite this

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AU - dos Santos, Daniel J.V.A.

AU - Eriksson, Leif A.

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N2 - Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand.We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5 -TpA in (AT)n sequences.

AB - Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand.We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5 -TpA in (AT)n sequences.

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M3 - Chapter

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PB - Apple Academic Press

ER -

Theoretical study of sequence selectivity and preferred binding mode of psoralen with DNA

Abstract

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