5J05

DIY G-Quadruplexes: Solution structure of d(GGGTTTGGGTTTTGGGAGGG) in sodium

• PDB DOI: https://doi.org/10.2210/pdb5J05/pdb
• BMRB: 30045
• NAKB: 5J05

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


• Deposited: 2016-03-27 Released: 2017-04-05 
• Deposition Author(s): Dvorkin, S.A., Karsisiotis, A.I., Webba da Silva, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Encoding canonical DNA quadruplex structure.

Dvorkin, S.A., Karsisiotis, A.I., Webba da Silva, M.

(2018) Sci Adv 4: eaat3007-eaat3007

• PubMed: 30182059 
• DOI: https://doi.org/10.1126/sciadv.aat3007
• Primary Citation of Related Structures:  
  2M6V, 2M6W, 5J05, 5J4P, 5J4W, 5J6U


• PubMed Abstract: 
  

  The main challenge in DNA quadruplex design is to encode a three-dimensional structure into the primary sequence, despite its multiple, repetitive guanine segments. We identify and detail structural elements describing all 14 feasible canonical quadruplex scaffolds and demonstrate their use in control of design. This work outlines a new roadmap for implementation of targeted design of quadruplexes for material, biotechnological, and therapeutic applications.

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Organizational Affiliation: 

School of Pharmacy and Pharmaceutical Sciences, Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, UK.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 6.35 kDa 
• Atom Count: 422 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')	A	20	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Dvorkin, S.A., Karsisiotis, A.I., Webba da Silva, M.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Database references
• Version 1.2: 2019-05-08
  Changes: Data collection
• Version 1.3: 2019-10-23
  Changes: Data collection, Derived calculations, Experimental preparation