[en] DNA oligomers are promising building blocks for the development of bottom-up nano-devices and molecular logic machines. To control and exploit their unique capabilities of self-assembling and molecular recognition a deep understanding of their dynamical properties is essential. We theoretically investigate the dynamics of a DNA dodecamer and its complexes with two common ligands, Hoechst33258 and the ethidium cation, by means of classical Molecular Dynamics (MD) simulations and Principal Component Analysis (PCA). We study the structural relation between the flexibility of the double helix and the binding process. The dynamics of a terminal base pair unbinding is also analysed as an example of process that involves multiple energy minima in the underlying free energy landscape.
Disciplines :
Chemistry
Author, co-author :
Fresch, Barbara ; Université de Liège - ULiège > Département de chimie (sciences) > Laboratoire de chimie physique théorique
Remacle, Françoise ; Université de Liège - ULiège > Département de chimie (sciences) > Laboratoire de chimie physique théorique
Language :
English
Title :
An atomistic view of DNA dynamics and its interaction with small binders: insights from Molecular Dynamics and Principal Component Analysis
Publication date :
2015
Main work title :
Advances in Atom and Single Molecule Machines
Editor :
Joachim, Christian
Publisher :
Springer, Berlin, Germany
Collection name :
Advances in Atom and Single Molecule Machines vol. 7, p17-33