6FY7

Concerted dynamics of metallo-base pairs in an A/B-form helical transition (minor species)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Concerted dynamics of metallo-base pairs in an A/B-form helical transition.

Schmidt, O.P.Jurt, S.Johannsen, S.Karimi, A.Sigel, R.K.O.Luedtke, N.W.

(2019) Nat Commun 10: 4818-4818

  • DOI: 10.1038/s41467-019-12440-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-Hg <sup>II </sup>-T metallo base pairs separated by six canonical base ...

    Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-Hg II -T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-Hg II -(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-Hg II -(N4)C base pairs and greater A-form characteristics. Ten-fold different 1 J coupling constants ( 15 N, 199 Hg) are observed for (N3)C-Hg II (114 Hz) versus (N4)C-Hg II (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-Hg II -T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding Hg II , demonstrating that C-Hg II -T has unique switching potential in DNA-based materials and devices.


    Organizational Affiliation

    Department of Chemistry, University of Zurich, Zurich, Switzerland.,Department of Chemistry, University of Zurich, Zurich, Switzerland. nathan.luedtke@chem.uzh.ch.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_minorA,B14synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland165949

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Database references