Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition | Zendy

Christian Bailly | Zendy

AI Assistant Blog Pricing

Home ZAIA Blog

Open Access

Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition

Author(s) -

Christian Bailly

Publication year - 2003

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkg237

Subject(s) - footprinting , dna footprinting , dna , ligand (biochemistry) , benzimidazole , hydrogen bond , base pair , surface plasmon resonance , molecule , recognition sequence , biology , stereochemistry , biophysics , dna binding protein , biochemistry , materials science , base sequence , receptor , chemistry , gene , restriction enzyme , nanotechnology , organic chemistry , transcription factor , nanoparticle

The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in explicit solvent. The footprinting and SPR methods find that the former compound has enhanced affinity and selectivity for AT sequences in DNA. The molecular modeling studies have suggested that, due to the presence of the oxygen atom in each side chain of the former compound, a water molecule is immobilized and effectively bridges between side chain and DNA base edges via hydrogen bonding interactions. This additional contribution to ligand-DNA interactions would be expected to result in enhanced DNA affinity, as is observed.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research