Topology of Viral DNA

The following sections are included:

• Introduction:The Organization of Double-Stranded DNA in Bacteriophage Capsids

  • Spooling Models

  • Toroidal Models

  • Spiral-Fold Model

  • Liquid Crystalline Model

  • Other Models

• Knot Theory and Its Applications to Molecular Biology

  • Mathematical Knots

  • Knots and DNA

  • Computer Models of DNA Knotting

  • Algorithms for Generating Ensembles of Random Knots

• DNA Knots in Bacteriophage P4

  • Bacteriophage P4

  • Experimental Methods: P4 Production and DNA Extraction

  • Experimental Results

• Models of Random Packing

  • Computational Methods

  • Results

    • Knotting probability, average crossing number and writhe in confined random polygons

  • Distributions of Knots for Low Crossing Numbers: Non-Random Packing of DNA in Bacteriophage P4

  • Knotting Probability and Complexity in Biased Models

• Conclusions and Future Challenges

• Acknowledgements

• References