1RSB

X-ray study of the DNA oligomer d(ATATAT) in P65 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA.

Abrescia, N.G.Gonzalez, C.Gouyette, C.Subirana, J.A.

(2004) Biochemistry 43: 4092-4100

  • DOI: 10.1021/bi0355140

  • PubMed Abstract: 
  • We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex ...

    We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex in which base pairing is of the Hoogsteen type. The double helix is apparently very similar to the standard B-form of DNA, with about 10 base pairs per turn. However, the adenines in the duplex are flipped over; as a result, the physicochemical features of both grooves of the helix are changed. In particular, the minor groove is narrow and hydrophobic. On the other hand, d(ATATAT) displays a propensity to adopt the B conformation in solution. These results confirm the polymorphism of AT-rich sequences in DNA. Furthermore, we show that extrahelical adenines and thymines can be minor groove binders in Hoogsteen DNA.


    Related Citations: 
    • When pseudosymmetry and merohedral twinning came across: thecase of the d(ATATAT) oligonucleotide in a hexagonal lattice
      Abrescia, N.G.A.,Subirana, J.A.
      (2002) Acta Crystallogr.,Sect.D 58: 2205
    • Theoretical Study of a New DNA structure: The antiparallel Hoogsteen Duplex
      Cubero, E.,Abrescia, N.G.A.,Subirana, J.A.,Luque, J.F.,Orozco, M.
      (2003) J.Am.Chem.Soc. 125: 14603
    • Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing
      Abrescia, N.G.A.,Thompson, A.,Huynh-Dinh, T.,Subirana, J.A.
      (2002) Proc.Natl.Acad.Sci.USA 99: 2806


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Av. Diagonal 647, E-08028 Barcelona, Spain. nicola@strubi.ox.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*TP*AP*TP*AP*T)-3'A,B,C,D6N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.218 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 32.313α = 90.00
b = 32.313β = 90.00
c = 117.779γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance