Document Detail


Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations.
MedLine Citation:
PMID:  14747307     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Hydrodynamic properties of small single-stranded RNA homopolymers with three and six nucleotides in free solution are determined from molecular dynamics simulations in explicit solvent. We find that the electrophoretic mobility increases with increasing RNA length, consistent with experiment. Diffusion coefficients of RNA, corrected for finite-size effects and solvent viscosity, agree well with those estimated from experiments and hydrodynamic calculations. The diffusion coefficients and electrophoretic mobilities satisfy a Nernst-Einstein relation in which the effective charge of RNA is reduced by the charge of transiently bound counterions. Fluctuations in the counterion atmosphere are shown to enhance the diffusive spread of RNA molecules drifting along the direction of the external electric field. As a consequence, apparent diffusion coefficients measured by capillary zone electrophoresis can be significantly larger than the actual values at certain experimental conditions.
Authors:
In-Chul Yeh; Gerhard Hummer
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Publication Detail:
Type:  Comparative Study; Evaluation Studies; Journal Article; Validation Studies    
Journal Detail:
Title:  Biophysical journal     Volume:  86     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  2004 Feb 
Date Detail:
Created Date:  2004-01-28     Completed Date:  2004-09-20     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  681-9     Citation Subset:  IM    
Affiliation:
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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MeSH Terms
Descriptor/Qualifier:
Computer Simulation
Diffusion
Electrochemistry / methods
Electromagnetic Fields
Electrophoresis, Capillary / methods*
Models, Chemical*
Models, Molecular*
Motion
Nucleic Acid Conformation
RNA / chemistry*,  radiation effects*
Solutions
Chemical
Reg. No./Substance:
0/Solutions; 63231-63-0/RNA
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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