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Comparing Ion Distributions around RNA and DNA Helical and Loop-loop Motifs

Published online by Cambridge University Press:  01 February 2011

Andrey V Semichaevsky
Affiliation:
avsemych@ncsu.edu, North Carolina State University, Materials Science and Engineering, Raleigh, North Carolina, United States
Ashley E Marlowe
Affiliation:
aemarlow@ncsu.edu, North Carolina State University, Materials Science and Engineering, Raleigh, North Carolina, United States
Yaroslava G Yingling
Affiliation:
yara_yingling@ncsu.edu, North Carolina State University, Materials Science and Engineering, Raleigh, North Carolina, United States
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Abstract

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this paper we use explicit molecular dynamics simulations to examine the variations in cationic distributions around DNA and RNA helices and loop-loop interactions with identical sequence except for Thymine to Uracil substitution. Our simulations show that the ionic distributions are different around RNA and DNA motifs which could be related to the discrepancy in stability of loop-loop complexes.

Type
Research Article
Copyright
Copyright © Materials Research Society 2009

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References

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