Open AccessProbability of DNA knotting and the effective diameter of the DNA double helix.
Author(s) -
Valentin V. Rybenkov,
Nicholas R. Cozzarelli,
Alexander Vologodskii
Publication year - 1993
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.90.11.5307
Subject(s) - dna , knot (papermaking) , helix (gastropod) , molecule , polymer , excluded volume , chemistry , double strand , crystallography , materials science , biology , dna repair , biochemistry , ecology , organic chemistry , snail , composite material
During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution of knot types produced by random cyclization of phage P4 DNA via its long cohesive ends. The simplest knots (trefoils) predominated, but more complex knots were also detected. The fraction of knots greatly diminished with decreasing solution Na+ concentration. By comparing these experimental results with computer simulations of knotting probability, we calculated the effective diameter of the DNA double helix. This important excluded-volume parameter is a measure of the electrostatic repulsion between segments of DNA molecules. The calculated effective DNA diameter is a sensitive function of electrolyte concentration and is several times larger than the geometric diameter in solutions of low monovalent cation concentration.