Protein-induced bending and DNA cyclization.
We have applied T4 ligase-mediated DNA cyclization kinetics to protein-induced bending in DNA. The presence and direction of a static bend can be inferred from J factors for cyclization of 150- to 160-base-pair minicircles, which include a catabolite activator protein binding site phased against a sequence-directed bend. We demonstrate a quasi-thermodynamic linkage between cyclization and protein binding; we find that properly phased DNAs bind catabolite activator protein approximately 200-fold more tightly as circles than as linear molecules. The results unambiguously distinguish DNA bends from isotropically flexible sites and can explain cooperative binding by proteins that need not contact each other.
Kahn
J D
JD
Department of Chemistry, Yale University, New Haven, CT 06511.
Crothers
D M
DM
D001483:Base Sequence; D002373:Cyclic AMP Receptor Protein / Q000378:metabolism; D004247:DNA / Q000737:chemistry*; D004270:DNA, Circular / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D003852:Deoxyribonucleoproteins / Q000737:chemistry*; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D013816:Thermodynamics
D002373:Cyclic AMP Receptor Protein; D004270:DNA, Circular; D004268:DNA-Binding Proteins; D003852:Deoxyribonucleoproteins; D046911:Macromolecular Substances; D009838:Oligodeoxyribonucleotides; D004247:DNA