Theoretical Study of Sequence Selectivity and Preferred Binding Mode of Psoralen with DNA | Zendy

Patricia SaenzMéndez | Zendy; Rita C. Guedes | Zendy; Daniel J. V. A. dos Santos | Zendy; Leif A. Eriksson | Zendy

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Theoretical Study of Sequence Selectivity and Preferred Binding Mode of Psoralen with DNA

Author(s) -

Patricia SaenzMéndez,

Rita C. Guedes,

Daniel J. V. A. dos Santos,

Leif A. Eriksson

Publication year - 2007

Publication title -

research letters in physical chemistry

Language(s) - English

Resource type - Journals

eISSN - 1687-6881

pISSN - 1687-6873

DOI - 10.1155/2007/60623

Subject(s) - intercalation (chemistry) , selectivity , ligand (biochemistry) , sequence (biology) , chemistry , crystallography , materials science , inorganic chemistry , biochemistry , catalysis , receptor

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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