Document Detail


Global analysis of non-specific protein-nucleic interactions by sedimentation equilibrium.
MedLine Citation:
PMID:  15043926     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Protein-nucleic acid interactions govern a variety of processes, including replication, transcription, recombination and repair. These interactions take place in both sequence-specific and non-specific modes, and the latter occur in many biologically significant contexts. Analytical ultracentrifugation is a useful method for the detailed characterization of the stoichiometry and affinity of macromolecular interactions in free solution. There has been a resurgence of interest in the application of sedimentation equilibrium methods to protein-nucleic acid interactions. However, these studies have been generally focused on sequence-specific interactions. Here we describe an approach to analyze non-specific interactions using sedimentation equilibrium. We have adapted an existing model for non-specific interaction of proteins with finite, one-dimensional nucleic acid lattices for global fitting of multiwavelength sedimentation equilibrium data. The model is extended to accommodate protein binding to multiple faces of the nucleic acid, resulting in overlap of consecutive ligands along the sequence of the RNA or DNA. The approach is illustrated in a sedimentation equilibrium analysis of the interaction of the double-stranded RNA binding motif of protein kinase R with a 20-basepair RNA construct.
Authors:
Jason W Ucci; James L Cole
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Biophysical chemistry     Volume:  108     ISSN:  0301-4622     ISO Abbreviation:  Biophys. Chem.     Publication Date:  2004 Mar 
Date Detail:
Created Date:  2004-03-26     Completed Date:  2004-09-09     Revised Date:  2011-08-15    
Medline Journal Info:
Nlm Unique ID:  0403171     Medline TA:  Biophys Chem     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  127-40     Citation Subset:  IM    
Affiliation:
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA.
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MeSH Terms
Descriptor/Qualifier:
Base Pairing
Ligands
Macromolecular Substances
Nucleic Acids / chemistry*,  metabolism
Protein Binding
Protein Kinases / metabolism
Proteins / chemistry*,  metabolism
RNA, Double-Stranded / chemistry,  metabolism
Solutions
Ultracentrifugation / methods*
Grant Support
ID/Acronym/Agency:
R01 AI053615-01A1/AI/NIAID NIH HHS
Chemical
Reg. No./Substance:
0/Ligands; 0/Macromolecular Substances; 0/Nucleic Acids; 0/Proteins; 0/RNA, Double-Stranded; 0/Solutions; EC 2.7.-/Protein Kinases
Comments/Corrections

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