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Literature DB >> 8475384

Knotting of a DNA chain during ring closure.

Abstract

The formation of knotted species on random ring closure of two DNAs that are 5.6 kilobase pairs (kbp) and 8.6 kbp in length was measured, and these data were used to calculate the effective DNA helix diameter as a function of sodium ion and magnesium ion concentration. In the presence of more than 50 mM magnesium ion, interactions between DNA segments appear to be attractive rather than repulsive. The free energy of formation of relaxed trefoil and figure-eight DNA knots and of supercoiled trefoil DNA knots was also evaluated.

Entities: Chemical

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Year: 1993 PMID： 8475384 DOI： 10.1126/science.8475384

Source DB: PubMed Journal: Science ISSN： 0036-8075 Impact factor: 47.728

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Cited

66 in total

Knotting of a DNA chain during ring closure.

1. Brownian dynamics simulation of DNA condensation.

2. Intermolecular interactions and water structure in a condensed phase B-DNA crystal.

3. Novel display of knotted DNA molecules by two-dimensional gel electrophoresis.

4. Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.

5. Identification and characterization of the helix-destabilizing activity of rotavirus nonstructural protein NSP2.

6. Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting.

7. Topoisomerase IV, alone, unknots DNA in E. coli.

8. Computational analysis of DNA gyrase action.

9. Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots.

10. Winding of the DNA helix by divalent metal ions.