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Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants
- Source :
- Nucleic Acids Research
- Publication Year :
- 2012
- Publisher :
- Oxford University Press (OUP), 2012.
-
Abstract
- N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.
- Subjects :
- Models, Molecular
Imidazoles
Torsion, Mechanical
DNA
Surface Plasmon Resonance
Biology
Dihedral angle
Nylons
Crystallography
chemistry.chemical_compound
Reaction rate constant
chemistry
Biochemistry
Amide
Polyamide
Genetics
Nucleic Acid Conformation
Imidazole
Pyrroles
Surface plasmon resonance
Molecular Biology
Pyrrole
Subjects
Details
- ISSN :
- 13624962 and 03051048
- Volume :
- 40
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....4e0d5c18458e2980a80d355daae24ce1