7O5E | pdb_00007o5e

The structure of an i-motif/duplex junction at neutral pH

• PDB DOI: https://doi.org/10.2210/pdb7O5E/pdb
• NAKB: 7O5E
• BMRB: 34616

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


• Deposited: 2021-04-08 Released: 2021-09-01 
• Deposition Author(s): Serrano-Chacon, I., Mir, B., Escaja, N., Gonzalez, C.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 15 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of i-Motif/Duplex Junctions at Neutral pH.

Serrano-Chacon, I., Mir, B., Escaja, N., Gonzalez, C.

(2021) J Am Chem Soc 143: 12919-12923

• PubMed: 34370473 
• DOI: https://doi.org/10.1021/jacs.1c04679
• Primary Citation of Related Structures:  
  7O5E


• PubMed Abstract: 
  

  We report here the three-dimensional structure of an i-motif/duplex junction, determined by NMR methods at neutral pH. By including a minor groove tetrad at one side of the C:C ⁺ stack of a monomeric i-motif, and a stem/loop hairpin at the other side, we have designed stable DNA constructs in which i-DNA and B-DNA regions coexist in a wide range of experimental conditions. This study demonstrates that i- and B-DNA are structurally compatible, giving rise to a distinctive fold with peculiar groove shapes. The effect of different residues at the i-motif/duplex interface has been explored. We also show that these constructs can be adapted to sequences of biological relevance, like that found in the promoter region of the KRAS oncogene.

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Organizational Affiliation: 
• Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain.
Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
BIOESTRAN associated unit UB-CSIC, 08028 Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.58 kDa 
• Atom Count: 699 
• Modeled Residue Count: 35 
• Deposited Residue Count: 35 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
I-motif/duplex junction (IDJ)	A	35	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 15 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Serrano-Chacon, I., Mir, B., Escaja, N., Gonzalez, C.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BES-2015-073917
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-52864-R
Spanish Ministry of Science, Innovation, and Universities	Spain	BFU2017-89707-P

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2021-09-29
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Other
• Version 1.3: 2024-06-19
  Changes: Data collection, Database references