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Organizers |
DNA knots reveal a chiral organization of DNA in phage capsids
by
Javier Arsuaga
Comprehensive Cancer Center, UCSF
Coauthors: Mariel Vazquez, Paul McGuirk, De Witt Sumners, Joaquim Roca
It is believed that all icosahedral bacteriophages package their double-stranded DNA genomes to near-crystalline density in similar fashion. Nevertheless despite numerous studies, the organization of DNA inside viruses such as lambda, T4, T7, P2, P4, and Phi29 is still unknown. We propose a new approach to this problem. We recently showed that most DNA molecules extracted from bacteriophage P4 are highly knotted due to the cyclization of the linear DNA molecule confined inside the viral capsid. Here we show that these knots provide information about the global arrangement of the DNA inside the phage. We analysed the viral distributions of DNA knots by high-resolution gel electrophoresis and performed Monte Carlo computer simulations of random knotting confined to spherical volumes. A rigorous proof of non-random packaging of the phage DNA is given by comparing the knot distributions obtained by both techniques. Furthermore, our results indicate that the packaging geometry of the DNA inside the viral capsid is writhe directed.
Date received: October 15, 2004
Copyright © 2004 by the author(s). The author(s) of this work and the organizers of the conference have granted their consent to include this abstract in Topology Atlas. Document # capf-09.