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

doi:10.1155/2007/60623

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

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5 Citations (Scopus)

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
Article number	60623
Journal	Research Letters in Physical Chemistry
Volume	2007
DOIs	https://doi.org/10.1155/2007/60623
Publication status	Published - 2007
Externally published	Yes

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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.",

author = "Patricia Saenz-M{\'e}ndez and Guedes, {Rita C.} and {dos Santos}, {Daniel J.V.A.} and Eriksson, {Leif A.}",

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AU - Saenz-Méndez, Patricia

AU - Guedes, Rita C.

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

AU - Eriksson, Leif A.

PY - 2007

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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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JO - Research Letters in Physical Chemistry

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

Abstract

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