Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles.
We propose a method for analyzing the magnitude and direction of curvature within nucleic acids, based on the curvilinear helical axis calculated by Curves+. The method is applied to analyzing curvature within minicircles constructed with varying degrees of over- or under-twisting. Using the molecular dynamics trajectories of three different minicircles, we are able to quantify how curvature varies locally both in space and in time. We also analyze how curvature influences the local environment of the minicircles, notably via increased heterogeneity in the ionic distributions surrounding the double helix. The approach we propose has been integrated into Curves+ and the utilities Canal (time trajectory analysis) and Canion (environmental analysis) and can be used to study a wide variety of static and dynamic structural data on nucleic acids.
MMSB, University of Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69367 Lyon, France.
Marco
M
Pasi
MMSB, University of Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69367 Lyon, France.
Krystyna
K
Zakrzewska
Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland.
John H
JH
Maddocks
MMSB, University of Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69367 Lyon, France.
Richard
R
Lavery
D004270:DNA, Circular / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011188:Potassium / Q000737:chemistry; D012984:Software
D004270:DNA, Circular; D007477:Ions; D011188:Potassium