6M6J | pdb_00006m6j

NMR solution structure of a DNA minidumbbell containing an abasic bulge between two CTTG repeats

• PDB DOI: https://doi.org/10.2210/pdb6M6J/pdb
• NAKB: 6M6J

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2020-03-15 Released: 2020-07-29 
• Deposition Author(s): Wan, L., Lam, S.L., Guo, P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest total energy 

Literature

Rational design of a reversible Mg2+/EDTA-controlled molecular switch based on a DNA minidumbbell.

Wan, L., Lam, S.L., Lee, H.K., Guo, P.

(2020) Chem Commun (Camb) 56: 10127-10130

• PubMed: 32870195 
• DOI: https://doi.org/10.1039/d0cc03774e
• Primary Citation Related Structures: 
  6M6J, 6M6K


• PubMed Abstract: 
  

  Here we report that incorporation of an abasic site to DNA minidumbbells formed by natural sequences can lead to significant enhancements in their thermodynamic stability. Based on these stable minidumbbells, the first metal ion-controlled molecular switch which can regulate instant and reversible DNA duplex formation and dissociation has been constructed.

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Organizational Affiliation: 
• Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China. [e-mail].
School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.77 kDa 
• Atom Count: 178 
• Modeled Residue Count: 9 
• Deposited Residue Count: 9 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*TP*GP*(3DR)P*CP*TP*TP*G)-3')	A	9	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest total energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Wan, L., Lam, S.L., Guo, P.

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references