| Prediction of molecular alignment of nucleic acids in aligned media. | |
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MedLine Citation:
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PMID: 16718586 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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We demonstrate--using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined--that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request. |
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Authors:
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Bin Wu; Michael Petersen; Frederic Girard; Marco Tessari; Sybren S Wijmenga |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2006-05-23 |
Journal Detail:
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Title: Journal of biomolecular NMR Volume: 35 ISSN: 0925-2738 ISO Abbreviation: J. Biomol. NMR Publication Date: 2006 Jun |
Date Detail:
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Created Date: 2006-07-04 Completed Date: 2007-03-26 Revised Date: 2008-11-21 |
Medline Journal Info:
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Nlm Unique ID: 9110829 Medline TA: J Biomol NMR Country: Netherlands |
Other Details:
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Languages: eng Pagination: 103-15 Citation Subset: IM |
Affiliation:
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Laboratory of Physical Chemistry-Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6225ED, Nijmegen, The Netherlands. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Bacteriophage Pf1
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chemistry DNA / chemistry* Mathematics Nucleic Acid Conformation RNA / chemistry* Static Electricity |
| Chemical | |
Reg. No./Substance:
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63231-63-0/RNA; 9007-49-2/DNA |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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