Using DNA Knots To Assay Packing of DNA in Phage Capsids

摘要

Bacteriophages are viruses that infect bacteria. They pack their double-stranded DNA genomes to near-crystalline density in viral capsids and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies some essential properties of the packaging geometry of the DNA inside the phage capsid are still unknown. Although viral DNA is linear double-stranded with sticky ends, the linear viral DNA quickly becomes cyclic when removed from the capsid, and for some viral DNA the observed knot probability is an astounding 95%. By comparing the observed viral knot spectrum with the simulated knot spectrum, we conclude that the packing geometry of the DNA inside the capsid is non-random and writhe-directed.