1K8J

NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB

Volk, D.E.Yang, X.Fennewald, S.M.King, D.J.Bassett, S.E.Venkitachalam, S.Herzog, N.Luxon, B.A.Gorenstein, D.G.

(2002) Bioorg Chem 30: 396-419

  • DOI: https://doi.org/10.1016/s0045-2068(02)00510-2
  • Primary Citation of Related Structures:  
    1K8J, 1K8L, 1K8N

  • PubMed Abstract: 

    A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone.


  • Organizational Affiliation

    Department of Human Biological Chemistry and Genetics, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1157, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
FIRST STRAND OF CK14 DNA DUPLEX14N/A
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
SECOND STRAND OF CK14 DNA DUPLEX14N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations