4J2I

Multiple crystal structures of an all-AT DNA dodecamer stabilized by weak interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Polymorphic crystal structures of an all-AT DNA dodecamer.

Acosta-Reyes, F.J.Subirana, J.A.Pous, J.Sanchez-Giraldo, R.Condom, N.Baldini, R.Malinina, L.Campos, J.L.

(2015) Biopolymers 103: 123-133

  • DOI: 10.1002/bip.22565
  • Primary Citation of Related Structures:  
    4HW1, 4J2I

  • PubMed Abstract: 
  • In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms ...

    In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, 08028, Barcelona, Spain.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.4α = 90
b = 27.945β = 103.1
c = 159.715γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references