1EFS

CONFORMATION OF A DNA-RNA HYBRID

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum, structures with the least restraint violations, structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Solution conformation of an RNA--DNA hybrid duplex containing a pyrimidine RNA strand and a purine DNA strand.

Hantz, E., Larue, V., Ladam, P., Le Moyec, L., Gouyette, C., Huynh Dinh, T.

(2001) Int J Biol Macromol 28: 273-284

  • DOI: 10.1016/s0141-8130(01)00123-4
  • Primary Citation of Related Structures:  
    1EFS

  • PubMed Abstract: 

    • RNA--DNA hybrid duplexes are involved in transcription, replication and reverse transcription of nucleic acids. Information on such duplexes may shed some light on the mechanism of these processes. For this purpose, the influence of base composition on the structure of a polypyrimidine--polypurine RNA--DNA duplex r(cucuccuucucuu) ...

    RNA--DNA hybrid duplexes are involved in transcription, replication and reverse transcription of nucleic acids. Information on such duplexes may shed some light on the mechanism of these processes. For this purpose, the influence of base composition on the structure of a polypyrimidine--polypurine RNA--DNA duplex r(cucuccuucucuu). d(GAGAGGAAGAGAA) has been studied using 1H, 31P and 13C NMR experiments, molecular modeling (JUMNA program) and NOE back-calculation methods. The resulting structure of the 13-mer hybrid duplex shows that the RNA strand is in the expected A-type conformation while the DNA strand is in a very flexible conformation. In the DNA strand, the desoxyribose sugars retain the C2'-endo B-type conformation. The duplex helical parameters (such as inclination, twist and displacement of the bases) are close to the A-type conformation. No bending was observed for the global axis curvature. The major groove width is close to the B-form value and the minor groove width is intermediate between standard values for A and B-forms. These results are in favour of the independence of minor groove size (where RNase H interacts) and the base composition of the hybrid duplexes.

    Organizational Affiliation: 

    Laboratoire de Chimie Structurale et Spectroscopie Biomoléculaire CSSB, UFR SMBH, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France. hantz@smbh.univ-paris13.fr



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*GP*AP*A)-3')A 13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*UP*UP*CP*UP*CP*UP*UP*CP*CP*UP*CP*UP*C)-3')B 13N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum, structures with the least restraint violations, structures with the lowest energy 
  • OLDERADO: 1EFS Olderado

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2000-02-10 
  • Released Date: 2000-03-06 
    • Deposition Author(s): Larue, V., Hantz, E.

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance