204D

THE SOLUTION STRUCTURES OF PSORALEN MONOADDUCTED AND CROSSLINKED DNA OLIGOMERS BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 40 

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This is version 1.2 of the entry. See complete history

Literature

Solution structures of psoralen monoadducted and cross-linked DNA oligomers by NMR spectroscopy and restrained molecular dynamics.

Spielmann, H.P.Dwyer, T.J.Hearst, J.E.Wemmer, D.E.

(1995) Biochemistry 34: 12937-12953

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have used two-dimensional 1H NMR spectroscopy to determine the solution structures of the 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) furanside monoadducted (MAf) and the photoisomeric HMT interstrand cross-linked (XL) DNA oligonucleotide d( ...

    We have used two-dimensional 1H NMR spectroscopy to determine the solution structures of the 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) furanside monoadducted (MAf) and the photoisomeric HMT interstrand cross-linked (XL) DNA oligonucleotide d(5'-GCGTACGC-3')2. The determination of the structure was based on total relaxation matrix analysis of the NOESY cross-peak intensities using the program MARDIGRAS. Improved procedures to consider the experimental "noise" in NOESY spectra during these calculations have been employed. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for both the MAf and XL from both A-form and B-form dsDNA starting structures. The root-mean-square (rms) deviations of the coordinates for the 40 structures for the MAf and XL were 1.12 and 1.10 A, respectively. The rmsd of the MAf with respect to the XL is 2.20 A. The local DNA structure is distorted in both adducts, with the helix unwound by 34 degrees and 25 degrees for the MAf and XL, respectively, and an overall helical repeat of 11 base pairs, caused by intercalation of the HMT. The MAf is a photochemical intermediate on the path to interstrand XL. Considerable local structural distortion is induced by both adducts, but the DNA returns to B-form structure within three base pairs of the damage site. There is no significant bend in the helix axis of either the MAf or the XL. We have evaluated the accuracy of the two major methods of converting NOESY data into interproton distances, the isolated spin-pair approximation (ISPA) and the complete relaxation rate matrix analysis (RMA). Both methods were evaluated by comparing the resulting calculated interproton distances generated to known covalently fixed distances in the HMT. The overall structures were evaluated by checking their agreement with biophysical evidence from non-NMR techniques. Only the modified RMA method gave correct interproton distances.


    Related Citations: 
    • DNA Structural Reorganization Upon Conversion of a Psoralen Furanside Monoadduct to an Interstrand Cross-Link: Implications for DNA Repair
      Spielmann, H.P.,Dwyer, T.J.,Sastry, S.S.,Hearst, J.E.,Wemmer, D.E.
      (1995) Proc.Natl.Acad.Sci.USA 92: 2345


    Organizational Affiliation

    Structural Biology Division, Lawrence Berkeley Laboratory, University of California, Berkeley 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
B
4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN
C15 H14 O4
RGJSDHXSAKMPNM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 40 
Software Package:
Software NamePurpose
AMBERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-09-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance