284D

THE BI-LOOP, A NEW GENERAL FOUR-STRANDED DNA MOTIF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The bi-loop, a new general four-stranded DNA motif.

Salisbury, S.A.Wilson, S.E.Powell, H.R.Kennard, O.Lubini, P.Sheldrick, G.M.Escaja, N.Alazzouzi, E.Grandas, A.Pedroso, E.

(1997) Proc.Natl.Acad.Sci.USA 94: 5515-5518


  • PubMed Abstract: 
  • The crystal structure of the cyclic octanucleotide d<pATTCATTC> contains two independent molecules that form a novel quadruplex by means of intermolecular Watson-Crick A.T pairs and base stacking. A virtually identical quadruplex composed of G.C pair ...

    The crystal structure of the cyclic octanucleotide d contains two independent molecules that form a novel quadruplex by means of intermolecular Watson-Crick A.T pairs and base stacking. A virtually identical quadruplex composed of G.C pairs was found by earlier x-ray analysis of the linear heptamer d(GCATGCT), when the DNA was looped in the crystal. The close correspondence between these two structures of markedly dissimilar oligonucleotides suggests that they are both examples of a previously unrecognized motif. Their nucleotide sequences have little in common except for two separated 5'-purine-pyrimidine dinucleotides forming the quadruplex, and by implication these so-called "bi-loops" could occur widely in natural DNA. Such structures provide a mechanism for noncovalent linking of polynucleotides in vivo. Their capacity to associate by base stacking, demonstrated in the crystal structure of d(GCATGCT), creates a compact molecular framework made up of four DNA chains within which strand exchange could take place.


    Organizational Affiliation

    Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3')A,B8N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

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Download CCD File 
A, B
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 22.844α = 90.00
b = 27.676β = 90.00
c = 55.370γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-96refinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-06-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance