177D

SOLUTION STRUCTURE AND HYDRATION PATTERNS OF A PYRIMIDINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING A NOVEL T(DOT)CG TRIPLE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple.

Radhakrishnan, I.Patel, D.J.

(1994) J Mol Biol 241: 600-619

  • DOI: 10.1006/jmbi.1994.1534
  • Primary Citation of Related Structures:  
    177D

  • PubMed Abstract: 
  • The solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple has been determined via two and three-dimensional NMR spectroscopy and restrained molecular dynamics simulations incorporating explicit solvent and counter-ions ...

    The solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple has been determined via two and three-dimensional NMR spectroscopy and restrained molecular dynamics simulations incorporating explicit solvent and counter-ions. The T.CG triple, which expands the triplex code, is stabilized by a single hydrogen bond between the O-2 atom of thymine and the free amino proton of cytosine in the Watson-Crick C.G base-pair. This hydrogen bonding alignment produces large variations in helical twist at the dinucleotide steps involving the thymine residue. Localized structural perturbations in the purine-rich strand of the molecule are observed around the cytosine residue in the T.CG triple. Globally, the triplex resembles the solution structure of a previously solved pyrimidine.purine.pyrimidine DNA triplex containing an unusual G.TA triple. Also conserved are the sites and patterns of hydration in the two triplexes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons of Columbia University, New York, NY 10032.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*AP*CP*AP*GP*GP*TP*TP*TP*TP*T*CP*CP*TP*GP*TP*TP*CP*TP*TP*TP*TP*T*CP*TP*TP*TP*TP*CP*C)-3')A31N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Database references, Derived calculations, Other