Protein-induced bending and DNA cyclization.

Kahn JD; Crothers DM

Department of Chemistry, Yale University, New Haven, CT 06511.

Proc Natl Acad Sci U S A 89: 6343-7 (1992)

Abstract
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.

Mesh Headings

Base Sequence

Catabolite Gene Activator Proteins

Deoxyribonucleoproteins*

DNA*

DNA-Binding Proteins*

DNA, Circular

Macromolecular Systems

Molecular Sequence Data

Nucleic Acid Conformation*

Oligodeoxyribonucleotides

Support, U.S. Gov't, P.H.S.

Thermodynamics

Unique Identifier: 92335294

Chemical Identifiers (Names)

9007-49-2 (DNA)