1ON5

SOLUTION STRUCTURE OF A CHOLIC ACID-CAPPED DNA DUPLEX

  • Classification: DNA

  • Deposited: 2003-02-27 Released: 2003-08-05 
  • Deposition Author(s): Tuma, J., Richert, C.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution Structure of a Steroid-DNA Complex with Cholic Acid Residues Sealing the Termini of a Watson-Crick Duplex

Tuma, J.Richert, C.

(2003) Biochemistry 42: 8957-8965

  • DOI: 10.1021/bi030056g

  • PubMed Abstract: 
  • The three-dimensional structure of a covalent hybrid between cholic acid and the self-complementary DNA hexamer 5'-TGCGCA-3' was solved via two-dimensional NMR and restrained torsion angle molecular dynamics. In the complex, refined to a pairwise rms ...

    The three-dimensional structure of a covalent hybrid between cholic acid and the self-complementary DNA hexamer 5'-TGCGCA-3' was solved via two-dimensional NMR and restrained torsion angle molecular dynamics. In the complex, refined to a pairwise rmsd of 0.64 A, the steroid binds to the terminal T:A base pairs via extensive van der Waals contacts but without any hydrogen bonds or detectable dipole-dipole interactions. The contacts involve the methyl groups as well as one edge of the streoid's sterane skeleton and both nucleobases and the deoxyriboses of the terminal base pair of the DNA. The surprising shape complementarity between steroid and the undisturbed DNA termini explains the increase in fidelity and affinity observed for hybridization probes bearing bile acid residues. Since the hydroxyl groups of the steroid do not contribute to the binding of the DNA, they may be derivatized, potentially giving access to a new class of specific binders for blunt ends of Watson-Crick duplexes.


    Organizational Affiliation

    Department of Chemistry, Universit├Ąt Konstanz, D-78457 Konstanz, Germany.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
Steroid-DNA hybridA,B6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHD
Query on CHD

Download SDF File 
Download CCD File 
A, B
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5AT
Query on 5AT
A, B
DNA LINKINGC10 H15 N3 O4DT
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-02-27 
  • Released Date: 2003-08-05 
  • Deposition Author(s): Tuma, J., Richert, C.

Revision History 

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance