title: Molecular Origin of DNA Kinking by Transcription Factors.
abstract: Binding of transcription factor (TF) proteins with DNA may cause severe kinks in the latter. Here, we investigate the molecular origin of the DNA kinks observed in the TF-DNA complexes using small molecule intercalation pathway, crystallographic analysis, and free energy calculations involving four different transcription factor (TF) protein-DNA complexes. We find that although protein binding may bend the DNA, bending alone is not sufficient to kink the DNA. We show that partial, not complete, intercalation is required to form the kink at a particular place in the DNA. It turns out that while amino acid alone can induce the desired kink through partial intercalation, protein provides thermodynamic stabilization of the kinked state in TF-DNA complexes.
authors.affiliation: Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India.
authors.forename: Reman Kumar
authors.initials: RK
authors.lastname: Singh
authors.affiliation: Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India.
authors.forename: Wilbee D
authors.initials: WD
authors.lastname: Sasikala
authors.affiliation: Department of Chemistry, Indian Institute of Science Education and Research , Pune, Maharashtra 411021, India.
authors.forename: Arnab
authors.initials: A
authors.lastname: Mukherjee
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D004247:DNA / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D014157:Transcription Factors; D004247:DNA