A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution
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...
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| Format: | Online |
| Language: | English |
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Oxford University Press
2005
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1283524/ |
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pubmed-1283524 |
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pubmed-12835242005-11-16 A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution Zhou, J. Krueger, S. Gregurick, S. K. Article 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. Oxford University Press 2005 2005-11-10 /pmc/articles/PMC1283524/ /pubmed/16282586 http://dx.doi.org/10.1093/nar/gki936 Text en © The Author 2005. Published by Oxford University Press. All rights reserved |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Zhou, J. Krueger, S. Gregurick, S. K. |
| spellingShingle |
Zhou, J. Krueger, S. Gregurick, S. K. A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution |
| author_facet |
Zhou, J. Krueger, S. Gregurick, S. K. |
| author_sort |
Zhou, J. |
| title |
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution |
| title_short |
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution |
| title_full |
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution |
| title_fullStr |
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution |
| title_full_unstemmed |
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution |
| title_sort |
coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution |
| description |
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. |
| publisher |
Oxford University Press |
| publishDate |
2005 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1283524/ |
| _version_ |
1611379362408431616 |