7E4E | pdb_00007e4e

NMR solution structures of DNA minidumbbell containing a N1-methyladenine

• PDB DOI: https://doi.org/10.2210/pdb7E4E/pdb
• NAKB: 7E4E

• Classification: DNA
• Organism(s): Staphylococcus aureus
• Mutation(s): No 


• Deposited: 2021-02-11 Released: 2021-04-07 
• Deposition Author(s): Wan, L., Guo, P., Lam, S.L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 5 
• Selection Criteria: structures with the least restraint violations 

Literature

Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell.

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

(2021) Int J Mol Sci 22

• PubMed: 33807305 
• DOI: https://doi.org/10.3390/ijms22073633
• Primary Citation Related Structures: 
  7E4E


• PubMed Abstract: 
  

  DNA methylation is a prevalent regulatory modification in prokaryotes and eukaryotes. N ¹ -methyladenine (m ¹ A) and N ⁶ -methyladenine (m ⁶ A) have been found to be capable of altering DNA structures via disturbing Watson-Crick base pairing. However, little has been known about their influences on non-B DNA structures, which are associated with genetic instabilities. In this work, we investigated the effects of m ¹ A and m ⁶ A on both the structure and thermodynamic stability of a newly reported DNA minidumbbell formed by two TTTA tetranucleotide repeats. As revealed by the results of nuclear magnetic resonance spectroscopic studies, both m ¹ A and m ⁶ A favored the formation of a T·m ¹ A and T·m ⁶ A Hoogsteen base pair, respectively. More intriguingly, the m ¹ A and m ⁶ A modifications brought about stabilization and destabilization effects on the DNA minidumbbell, respectively. This work provides new biophysical insights into the effects of adenine methylation on the structure and thermodynamic stability of DNA.

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Organizational Affiliation: 
• MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR 999077, China.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.56 kDa 
• Atom Count: 166 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*(MA7)P*TP*TP*TP*A)-3')	A	8	Staphylococcus aureus

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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 5 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Wan, L., Guo, P., Lam, S.L.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2021-04-21
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references