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 s...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 1992-07, Vol.89 (14), p.6343-6347
Main Authors: Kahn, Jason D., Crothers, Donald M.
Format: Article
Language:English
Subjects:
Base Sequence
Bending
Binding sites
Biochemistry
Biological and medical sciences
Circles
Circular DNA
Cyclic AMP Receptor Protein - metabolism
Deoxyribonucleic acid
Deoxyribonucleoproteins - chemistry
DNA
DNA - chemistry
DNA, Circular - chemistry
DNA-Binding Proteins - chemistry
Fundamental and applied biological sciences. Psychology
Gels
Interactions. Associations
Intermolecular phenomena
Kinetics
Ligation
Macromolecular Substances
Molecular biophysics
Molecular Sequence Data
Molecules
Nucleic Acid Conformation
Oligodeoxyribonucleotides - chemistry
Polymerase chain reaction
Proteins
Thermodynamics
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Summary: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 quasithermodynamic linkage between cyclization and protein binding; we find that properly phased DNAs bind catabolite activator protein ≈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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.89.14.6343