Structure and Dynamics of DNA-Dendrimer Complexation: Role of Counterions, Water, and Base Pair Sequence

Mait, Prabal K and Bagchi, Biman (2006) Structure and Dynamics of DNA-Dendrimer Complexation: Role of Counterions, Water, and Base Pair Sequence. In: Nano Letters, 6 (11). pp. 2478-2485.

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Abstract

We study sequence-dependent complexation between oligonucleotides (single-strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination. Simulations reveal formation of a stable complex and provide a detailed molecular level understanding of the structure and dynamics of such a complexation. The reaction free energy surface in the initial stage is found to be funnel-like, with a significant barrier arising in the late stage due to the occurrence of misfolded states of DNA. Complexation shows surprisingly strong sensitivity to the ssDNA sequence, which is found to arise from a competition between enthalpic versus entropic rigidity of ssDNA.

Item Type:	Journal Article
Publication:	Nano Letters
Publisher:	American Chemical Society
Additional Information:	Copyright of this article belongs to American Chemical Society.
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit Division of Physical & Mathematical Sciences > Physics
Date Deposited:	29 May 2008
Last Modified:	19 Sep 2010 04:45
URI:	http://eprints.iisc.ac.in/id/eprint/14096

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