1KXS

NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 256 
  • Conformers Submitted: 
  • Selection Criteria: Fit with NMR constraints and energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies.

Boulard, Y.Fazakerley, G.V.Sowers, L.C.

(2002) Nucleic Acids Res. 30: 1371-1378


  • PubMed Abstract: 
  • Determination of the solution structure of the duplex d(GCAAGTC(HE)AAAACG)*d(CGTTTTAGACTTGC) containing a 3-(2-hydroxyethyl)-2'-deoxyuridine*deoxyadenine (HE*A) base pair is reported. The three-dimensional solution structure, determined starting from ...

    Determination of the solution structure of the duplex d(GCAAGTC(HE)AAAACG)*d(CGTTTTAGACTTGC) containing a 3-(2-hydroxyethyl)-2'-deoxyuridine*deoxyadenine (HE*A) base pair is reported. The three-dimensional solution structure, determined starting from 512 models via restrained molecular mechanics using inter-proton distances and torsion angles, converged to two final families of structures. For both families the HE and the opposite A residues are intrahelical and in the anti conformation. The hydroxyethyl chain lies close to the helix axis and for one family the hydroxyl group is above the HE*A plane and in the other case it is below. These two models were used to start molecular dynamic calculations with explicit solvent to explore the hydrogen bonding possibilities of the HE*A base pair. The dynamics calculations converge finally to one model structure in which two hydrogen bonds are formed. The first is formed all the time and is between HEO4 and the amino group of A, and the second, an intermittent one, is between the hydroxyl group and the N1 of A. When this second hydrogen bond is not formed a weak interaction CH...N is possible between HEC7H2 and N1A21. All the best structures show an increase in the C1'-C1' distance relative to a Watson-Crick base pair.


    Organizational Affiliation

    CEA, Service de Biochimie et de Génétique Moléculaire, Bâtiment 142, Département de Biologie Joliot Curie, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France. yboulard@cea.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*AP*AP*GP*TP*CP*(HEU)P*AP*AP*AP*AP*CP*G)-3'A14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*TP*TP*TP*AP*GP*AP*CP*TP*TP*GP*C)-3'B14N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HEU
Query on HEU
A
DNA LINKINGC11 H17 N2 O9 PDU
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 256 
  • Conformers Submitted: 
  • Selection Criteria: Fit with NMR constraints and energy 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance