A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains

PLoS Comput Biol. 2016 Sep 15;12(9):e1005029. doi: 10.1371/journal.pcbi.1005029. eCollection 2016 Sep.

Abstract

We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on experimental knotting probabilities of short DNA strands, it reproduces the correct persistence length of DNA. This indicates that knots are not only a fine gauge for structural properties, but a promising tool for the design of polymer models.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • DNA / ultrastructure*
  • Molecular Dynamics Simulation*
  • Monte Carlo Method
  • Nanopores
  • Nucleic Acid Conformation

Substances

  • DNA

Grants and funding

This work received financial support from the Graduate School of Excellency Materials Science in Mainz. The funders had no role in study design, data analysis, decision to publish, or preparation of the manuscript.