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Helical repeat and linking number of surface-wrapped DNA
J H White1, N R Cozzarelli, W R Bauer
1Department of Mathematics, University of California, Los Angeles 90024.
Science (New York, N.Y.)
|July 15, 1988
Summary
DNA geometry changes when wrapped on protein surfaces. A new formula links DNA's helical repeat and surface geometry to its overall structure, aiding biological studies.
Area of Science:
- Structural biology
- Biophysics
- Molecular genetics
Background:
- Duplex DNA exhibits specific geometric properties.
- Wrapping DNA around protein surfaces alters these properties.
- Understanding these alterations is crucial for DNA-protein interactions.
Purpose of the Study:
- To define and analyze the geometric properties of surface-wrapped DNA.
- To introduce a new geometric constant, the surface linking number (SLk).
- To relate theoretical DNA properties (twist, writhe) to experimental quantities.
Main Methods:
- Geometric analysis of surface-wrapped closed circular DNA.
- Mathematical formulation relating linking number to winding number and SLk.
- Application of the model to plectonemic supercoiling, catenated DNA, and minichromosomes.
Main Results:
- The linking number is decomposed into winding number (phi) and surface linking number (SLk).
- Helical repeat (h) and winding number changes are predictable from surface geometry and superhelix density (sigma).
- The framework successfully models DNA behavior in various biological contexts.
Conclusions:
- Surface geometry significantly impacts DNA's topological and geometric properties.
- The SLk provides a quantitative measure of these surface-induced effects.
- This framework offers a powerful tool for studying DNA in complex biological systems.