6FFR

DNA-RNA Hybrid Quadruplex with Flipped Tetrad


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA-RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies.

Haase, L.Dickerhoff, J.Weisz, K.

(2018) Chemistry 24: 15365-15371

  • DOI: 10.1002/chem.201803367
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A DNA G-quadruplex adopting a (3+1)-hybrid structure was substituted at its 5'-tetrad by riboguanosine (rG) analogs. Incorporation of anti-favoring rG at appropriate syn-positions of the 5'-outer tetrad induced conformational rearrangements to yield ...

    A DNA G-quadruplex adopting a (3+1)-hybrid structure was substituted at its 5'-tetrad by riboguanosine (rG) analogs. Incorporation of anti-favoring rG at appropriate syn-positions of the 5'-outer tetrad induced conformational rearrangements to yield a quadruplex featuring a 5'-tetrad with reversed polarity. A high-resolution structure of a disubstituted quadruplex variant as well as direct NMR experimental evidence reveals a non-conventional C-H⋅⋅⋅O hydrogen bond in a medium groove between the 2'-OH of an rG residue adopting a C2'-endo sugar pucker and H8 of a 3'-neighboring anti-G residue. In contrast, a C3'-endo sugar conformation for another guanine ribonucleotide prevents formation of a corresponding hydrogen bond but relocates its 2'-OH substituent from the quadruplex narrow groove into a medium groove. Both the formation of favorable CHO hydrogen bridges and unfavorable interactions of the 2'-hydroxyl group in a narrow groove will promote RNA folding into a parallel topology featuring all-anti core residues and four grooves of medium size.


    Organizational Affiliation

    Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany.



Macromolecules

Find similar nucleic acids by:   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')A22synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 
  • OLDERADO: 6FFR Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection