BIOPHYSICAL THEORY AND MODELING |
Molecular dynamics simulations of insertion of chemically modified DNA nanostructures into water-chloroform interface
Jianping Lin 1, Nadrian C Seeman 2 and Nagarajan Vaidehi 1*
1 Beckman Research Institute of the City of Hope
2 New York University
* To whom correspondence should be addressed. E-mail: nvaidehi{at}coh.org.
Submitted on August 7, 2007
Revised on September 18, 2007
Accepted on 7 April 2008
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Abstract |
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DNA based 2D and 3D arrays have been used as templates for synthesis of functional polymers and proteins. Hydrophobic or amphiphilic DNA arrays would be useful for the synthesis of hydrophobic molecules. The objective of this study is to design modified amphiphilic double crossover DX-DNA molecule that would insert into water-chloroform interface thus showing amphiphilic character. Since experiments for such design are tedious, we have used molecular dynamics simulations to identify and optimize the functional groups to modify the DNA backbone, that would enable insertion into the water-chloroform interface, prior to synthesis. By methylating the phosphates of the backbone, to make phosphonates, combined with placing a benzyl group at the 2' position of the deoxyribose rings in the backbone, we observed that the simple B-DNA structure was able to insert into the water-chloroform interface. We find that the transfer free energy of the methylated benzylated DNA is better than either just methylated or benzylated DNA. The driving force for this insertion comes from entropic contribution to the free energy and the favorable van der Waals interaction of the chloroform molecules with the methyl and benzyl groups of the DNA.
Key Words:
DNA nanostructures, Molecular dynamics, hydrophobic interface, modified nucleotide, permeability, water chloroform interface
