@article{ISI:000245790100006,
 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.},
 author = {Maiti, Prabal K. and Pascal, Tod A. and Vaidehi, Nagarajan and Goddard,
III, William A.},
 doi = {10.1166/jnn.2007.704},
 issn = {1533-4880},
 journal = {JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY},
 month = {JUN},
 note = {International Conference on Nano Science and Technology (ICONSAT 2006),
New Delhi, INDIA, MAR 16-18, 2006},
 number = {6, SI},
 orcid-numbers = {Maiti, Prabal/0000-0002-9956-1136},
 pages = {1712-1720},
 researcherid-numbers = {Maiti, Prabal/B-6335-2009},
 times-cited = {15},
 title = {Understanding DNA based nanostructures},
 unique-id = {ISI:000245790100006},
 volume = {7},
 year = {2007}
}