| Global analysis of non-specific protein-nucleic interactions by sedimentation equilibrium. | |
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MedLine Citation:
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PMID: 15043926 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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. |
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Authors:
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Jason W Ucci; James L Cole |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Biophysical chemistry Volume: 108 ISSN: 0301-4622 ISO Abbreviation: Biophys. Chem. Publication Date: 2004 Mar |
Date Detail:
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Created Date: 2004-03-26 Completed Date: 2004-09-09 Revised Date: 2011-08-15 |
Medline Journal Info:
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Nlm Unique ID: 0403171 Medline TA: Biophys Chem Country: Netherlands |
Other Details:
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Languages: eng Pagination: 127-40 Citation Subset: IM |
Affiliation:
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Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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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:
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R01 AI053615-01A1/AI/NIAID NIH HHS |
| Chemical | |
Reg. No./Substance:
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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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