7VM9 | pdb_00007vm9

Solution NMR structures of DNA minidumbbell formed with two regular CTTTG pentaloops

• PDB DOI: https://doi.org/10.2210/pdb7VM9/pdb
• NAKB: 7VM9

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


• Deposited: 2021-10-08 Released: 2022-02-16 
• Deposition Author(s): Ngai, C.K., Guo, P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

A purine and a backbone discontinuous site alter the structure and thermal stability of DNA minidumbbells containing two pentaloops.

Ngai, C.K., Lam, S.L., Lee, H.K., Guo, P.

(2022) FEBS Lett 596: 826-840

• PubMed: 35060128 
• DOI: https://doi.org/10.1002/1873-3468.14293
• Primary Citation of Related Structures:  
  7VM9


• PubMed Abstract: 
  

  Minidumbbell (MDB) is a noncanonical DNA structure found to form in several pyrimidine-rich short tandem repeats associated with neurodegenerative diseases. The most recently reported MDB contains two pentaloops formed by ATTCT repeats. Here, we studied the effects of a purine residue and a backbone discontinuous site on the structure and thermal stability of MDBs containing two pentaloops. It was found that a purine as the fourth loop residue improved the thermal stability of MDBs containing two regular pentaloops, while a backbone discontinuous site between the third and fourth, or between the fourth and fifth loop residues enhanced the thermal stability of MDBs containing a regular and a quasi pentaloops. The results of this study provide new insights into the sequence criteria and structural basis of MDBs.

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Organizational Affiliation: 
• Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China.
School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.22 kDa 
• Atom Count: 208 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*TP*TP*GP*CP*TP*TP*TP*G)-3')	A	10	synthetic construct

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], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Ngai, C.K., Guo, P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references