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Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA.
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MedLine Citation:
PMID:  7063404     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We present extensive calculations of the secondary structure of mRNA which point to its insensitivity to small changes in the free energy assignments of single stranded regions. Truncating the free energies of hairpin loops, bulges, internal loops and multibranched junctions to two significant digits yields structures nearly identical to those generated using three digit values. The results show that one can safely use truncated values in RNA folding calculations. The implementation of these results enabled us to carry out secondary structure calculations on 2600 nucleotides in a single computer run.
Authors:
R Nussinov; I Tinoco; A B Jacobson
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Nucleic acids research     Volume:  10     ISSN:  0305-1048     ISO Abbreviation:  Nucleic Acids Res.     Publication Date:  1982 Jan 
Date Detail:
Created Date:  1982-05-21     Completed Date:  1982-05-21     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  0411011     Medline TA:  Nucleic Acids Res     Country:  ENGLAND    
Other Details:
Languages:  eng     Pagination:  341-9     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Base Composition
Base Sequence*
Computers
Methods
Nucleic Acid Conformation*
RNA, Messenger*
Thermodynamics
Grant Support
ID/Acronym/Agency:
AI 15273/AI/NIAID NIH HHS; GM 10840/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/RNA, Messenger
Comments/Corrections

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

Full Text
Journal Information
Journal ID (nlm-ta): Nucleic Acids Res
ISSN: 0305-1048
ISSN: 1362-4962
Article Information
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Print publication date: Day: 11 Month: 1 Year: 1982
Volume: 10 Issue: 1
First Page: 341 Last Page: 349
ID: 326137
PubMed Id: 7063404

Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA.
R Nussinov
I Tinoco, Jr
A B Jacobson



Article Categories:
  • Research Article


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