1JRV

SOLUTION STRUCTURE OF DAATAA DNA BULGE

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 15 
  • Selection Criteria: target function 

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This is version 1.3 of the entry. See complete history. 


Literature

Solution structure of dAATAA and dAAUAA DNA bulges.

Gollmick, F.A., Lorenz, M., Dornberger, U., von Langen, J., Diekmann, S., Fritzsche, H.

(2002) Nucleic Acids Res 30: 2669-2677

  • DOI: 10.1093/nar/gkf375
  • Primary Citation of Related Structures:  
    1JRV, 1JRW, 1JS5, 1JS7

  • PubMed Abstract: 

    • The NMR structure analysis is described for two DNA molecules of identical stem sequences with a five base loop containing a pyrimidine, thymin or uracil, in between purines. These five unpaired nucleotides are bulged out and are known to induce a kink in the duplex structure ...

    The NMR structure analysis is described for two DNA molecules of identical stem sequences with a five base loop containing a pyrimidine, thymin or uracil, in between purines. These five unpaired nucleotides are bulged out and are known to induce a kink in the duplex structure. The dAATAA bulge DNA is kinked between the third and the fourth nucleotide. This contrasts with the previously studied dAAAAA bulge DNA where we found a kink between the fourth and fifth nucleotide. The total kinking angle is approximately 104 degrees for the dAATAA bulge. The findings were supported by electrophoretic data and fluorescence resonance energy transfer measurements of a similar DNA molecule end-labeled by suitable fluorescent dyes. For the dAAUAA bulge the NMR data result in a similar structure as reported for the dAATAA bulge with a kinking angle of approximately 87 degrees. The results are discussed in comparison with a rAAUAA RNA bulge found in a group I intron. Generally, the sequence-dependent structure of bulges is important to understand the role of DNA bulges in protein recognition.

    Organizational Affiliation: 

    Institut für Molekularbiologie, Friedrich-Schiller-Universität, Winzerlaer Strasse 10, D-07745 Jena, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*TP*AP*AP*GP*CP*TP*AP*CP*G)-3'A 17N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3'B 12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 15 
  • Selection Criteria: target function 
  • OLDERADO: 1JRV Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations