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Nucleic Acids Research 2005 33(19):6361-6371; doi:10.1093/nar/gki936
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Published online 10 November 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution

J. Zhou, S. Krueger1 and S. K. Gregurick*

Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 100 Hilltop Circle, Baltimore, MD 21250, USA 1NIST Center for Neutron Research, National Institute of Standards and Technology 100 Bureau Drive, Stop 8562, Gaithersburg, MD 20899-8562, USA

*To whom correspondence should be addressed. Email: greguric{at}umbc.edu

Received August 2, 2005. Revised September 19, 2005. Accepted October 12, 2005.

We present a theoretical method to calculate the small angle neutron scattering profile of nucleic acid structures in solution. Our approach is sensitive to the sequence and the structure of the nucleic acid. In order to test our approach, we apply this method to the calculation of the experimental scattered intensity of the decamer d(CCAACGTTGG)2 in H2O. This sequence was specifically chosen for this study as it is believed to adopt a canonical B-form structure in 0.3 M NaCl. We find that not only will our methodology reproduce the experimental scattered intensity for this sequence, but our method will also discriminate between B-, A- and Z-form DNA. By studying the scattering profile of this structure in 0.5 and 1.0 M NaCl, we are also able to identify tetraplex and other similar oligomers formation and to model the complex using the experimental scattering data in conjunction with our methodology.

The authors wish it to be known that, in their opinion, the last two authors should be regarded as joint First Authors


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