Edinburgh Research Explorer

DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting

Research output: Contribution to journalArticle

  • Davide Marenduzzo
  • Enzo Orlandini
  • Andrzej Stasiak
  • De Witt Sumners
  • Luca Tubiana
  • Cristian Micheletti

Related Edinburgh Organisations

Original languageEnglish
Pages (from-to)22269-22274
Number of pages6
JournalProceedings of the National Academy of Sciences
Volume106
Issue number52
DOIs
StatePublished - 29 Dec 2009

Abstract

Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids is both highly knotted and neatly structured. What is the physical basis of this organization? Here we show evidence fromstochastic simulation techniques that suggests that a key element is the tendency of contacting DNA strands to order, as in cholesteric liquid crystals. This interaction favors their preferential juxtaposition at a small twist angle, thus promoting an approximately nematic (and apolar) local order. The ordering effect dramatically impacts the geometry and topology of DNA inside phages. Accounting for this local potential allows us to reproduce the main experimental data on DNA organization in phages, including the cryo-EM observations and detailed features of the spectrum of DNA knots formed inside viral capsids. The DNA knots we observe are strongly delocalized and, intriguingly, this is shown not to interfere with genome ejection out of the phage.

    Research areas

  • DNA packaging, Monte Carlo simulations, PHAGE CAPSIDS, VIRAL CAPSIDS, CIRCULAR DNA, EJECTION, DYNAMICS, KNOTS, RECOMBINATION, ORGANIZATION, POLYMER, PACKING

ID: 1452454