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Understanding DNA based Nanostructures

Maiti, Prabal K. and Pascal, Tod A. and Vaidehi, Nagarajan and Goddard, William A., III (2007) Understanding DNA based Nanostructures. Journal of Nanoscience and Nanotechnology, 7 (6). pp. 1712-1720. ISSN 1533-4880. https://resolver.caltech.edu/CaltechAUTHORS:MAIjnn07

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Abstract

We use molecular dynamics (MD) simulations to understand the structure, and stability of various Paranemic crossover (PX) DNA molecules and their topoisomer JX molecules, synthesized recently by Seeman and coworkers at New York University (NYU). Our studies include all atoms (4432 to 6215) of the PX structures with an explicit description of solvent and ions (for a total of up to 42,000 atoms) with periodic boundary conditions. We report the effect of divalent counterions Mg(+2) on the structural and thermodynamic properties of these molecules and compare them to our previously reported results in presence of monovalent Na+ ions. The dynamic structures averaged over the 3-nanosecond simulations preserves the Watson-Crick hydrogen bonding as well as the helical structure. We find that PX65 is the most stable structure both in Na+ and Mg(+2) in accordance with the experimental results. PX65 has helical twist and other helical structural parameters close to the values for normal B-DNA of similar length and sequence. Our strain energy calculations demonstrate that stability of the crossover structure increases with the increase in crossover points.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1166/jnn.2007.704DOIUNSPECIFIED
ORCID:
AuthorORCID
Maiti, Prabal K.0000-0002-9956-1136
Pascal, Tod A.0000-0003-2096-1143
Goddard, William A., III0000-0003-0097-5716
Additional Information:Authors' final manuscript. Published version, Copyright © 2007 American Scientific Publishers. We thank Prof. Nadrian Seeman (NYU) for useful discussions on this subject and sharing his experimental data with us prior to publication. We also thank Mr. Gene Carter for collaborating with us in making changes to his Namot2 code to facilitate building of PX crossover points. PKM thanks SERC, IISc, Bangalore, for computational facility, where some of the computations have been carried out. This research was funded partially from NSF (NIRT-005-610 and CTS-0548774).
Funders:
Funding AgencyGrant Number
NSFDMR-005610
NSFCTS-0548774
Issue or Number:6
Record Number:CaltechAUTHORS:MAIjnn07
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:MAIjnn07
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8598
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:22 Aug 2007
Last Modified:07 Apr 2020 16:47

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