Structure and Conformational Behavior of the DNA Oligonucleotide Attached to the Charged Surface: A Molecular Dynamics Study


O. Kroutil2, F. Lankaš1, M. Šíp2, M. Předota and M. Kabeláč*1,3,


1 Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic

2 Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, 37 011 České Budějovice, Czech Republic

3 Faculty of Natural Sciences, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic

* email:


Although surface plays an important role in microarray hybridization, many software tools available for the probe design are still based on standard hybridization conditions, i.e. nucleic acids in solution, not being attached to a surface. First steps to estimate some aspects concerning the influence of the surface have already been made, based both on experiments  and on theoretical considerations, but the underlying phenomena remain poorly understood.

In our theoretical study we focused on the role of the electric field on structure and conformational behavior of DNA anchored to the surface. The surface is represented by a graphene monolayer with partial charges on carbon atoms varying from -0.1 to +0.1e in the simulations. It corresponds to the typical values of charge densities in similar experiments. Both single strand and double strand oligonucleotides were studied to mimic conditions before and after hybridization. The single stranded decanucleotide 5’-CCACTAGTGG-3’ was attached to the graphene layer via a C6 aliphatic linker.

Two types of interactions of DNA with surface are crucial for the stabilization of the DNA – surface system. Whereas for surface with zero or  low positive  charge density the dispersion forces between the closest base/base pair and the surface dominate, higher charge densities on the surface lead to strong electrostatic interaction between the phosphate groups of DNA and the surface and ions.


We gratefully acknowledge support from the Grant Agency of the Czech Republic 204/09/J010