End-to-end attraction of duplex DNA
Open Access
- 11 January 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (9), 3812-3821
- https://doi.org/10.1093/nar/gkr1220
Abstract
Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276–1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5′-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.Keywords
This publication has 56 references indexed in Scilit:
- Chromatin Ionic Atmosphere Analyzed by a Mesoscale Electrostatic ApproachBiophysical Journal, 2010
- Free Energy Calculations Reveal Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its InhibitionBiophysical Journal, 2010
- Understanding biology by stretching proteins: recent progressCurrent Opinion in Structural Biology, 2010
- Closing the lid on DNA end-to-end stacking interactionsApplied Physics Letters, 2008
- Molecular dynamics simulations of nucleic acid–protein complexesCurrent Opinion in Structural Biology, 2008
- Ionic effects on viral DNA packaging and portal motor function in bacteriophage φ29Proceedings of the National Academy of Sciences of the United States of America, 2007
- Scalable molecular dynamics with NAMDJournal of Computational Chemistry, 2005
- Mechanism and regulation of human non-homologous DNA end-joiningNature Reviews Molecular Cell Biology, 2003
- Finite representation of an infinite bulk system: Solvent boundary potential for computer simulationsThe Journal of Chemical Physics, 1994
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983