6RLS

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

• PDB DOI: https://doi.org/10.2210/pdb6RLS/pdb
• NAKB: 6RLS
• BMRB: 34398

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2019-05-02 Released: 2019-10-09 
• Deposition Author(s): Schmidt, O.P., Jurt, S., Johannsen, S., Karimi, A., Sigel, R.K.O., Luedtke, N.W.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

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

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

• PubMed: 31645548 
• DOI: https://doi.org/10.1038/s41467-019-12440-x
• Primary Citation of Related Structures:  
  6FY6, 6FY7, 6RLS


• 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 ^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.

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Organizational Affiliation: 

Department of Chemistry, University of Zurich, Zurich, Switzerland.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 8.51 kDa 
• Atom Count: 564 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_apo	A, B	14	synthetic construct

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Schmidt, O.P., Jurt, S., Johannsen, S., Karimi, A., Sigel, R.K.O., Luedtke, N.W.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	165949

Revision History  

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