1QES

TANDEM GU MISMATCHES IN RNA, NMR, 30 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 30 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2.

McDowell, J.A.He, L.Chen, X.Turner, D.H.

(1997) Biochemistry 36: 8030-8038

  • DOI: 10.1021/bi970122c
  • Primary Citation of Related Structures:  
    1QES, 1QET

  • PubMed Abstract: 
  • The symmetric, tandem GU mismatch motifs, and , which only differ in the mismatch order, have an average difference in thermodynamic stability of 2 kcal/mol at 37 degrees C. Thermodynamic studies of duplexes containing these motifs indicate the effect is largely localized to the mismatches and adjacent base pairs ...

    The symmetric, tandem GU mismatch motifs, and , which only differ in the mismatch order, have an average difference in thermodynamic stability of 2 kcal/mol at 37 degrees C. Thermodynamic studies of duplexes containing these motifs indicate the effect is largely localized to the mismatches and adjacent base pairs. The three-dimensional structures of two representative duplexes, (rGGAGUUCC)2 and (rGGAUGUCC)2, were determined by two-dimensional NMR and a simulated annealing protocol. Local deviations are similar to other intrahelical GU mismatches with little effect on backbone torsion angles and a slight overtwisting between the base pair 5' of the G of the mismatch and the mismatch itself. Comparisons of the resulting stacking patterns along with electrostatic potential maps suggest that interactions between highly negative electrostatic regions between base pairs may play a role in the observed thermodynamic differences.


    Organizational Affiliation

    Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*GP*AP*GP*UP*UP*CP*C)-3')A, B 8N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 30 
  • OLDERADO: 1QES Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-06-05
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations, Other