5NIP | pdb_00005nip

An i-motif containing the neutral cytidine protonated analogue pseudoisocytidine

• PDB DOI: https://doi.org/10.2210/pdb5NIP/pdb
• BMRB: 34118
• NAKB: 5NIP

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


• Deposited: 2017-03-24 Released: 2017-06-28 
• Deposition Author(s): Mir, B., Soles, X., Gonzalez, C., Escaja, N.
• Funding Organization(s): MINECO

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Literature

The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures.

Mir, B., Soles, X., Gonzalez, C., Escaja, N.

(2017) Sci Rep 7: 2772-2772

• PubMed: 28584239 
• DOI: https://doi.org/10.1038/s41598-017-02723-y
• Primary Citation Related Structures: 
  5NIP


• PubMed Abstract: 
  

  Incorporation of pseudoisocytidine (psC), a neutral analogue of protonated cytidine, in i-motifs has been studied by spectroscopic methods. Our results show that neutral psC:C base pairs can stabilize i-motifs at neutral pH, but the stabilization only occurs when psC:C base pairs are located at the ends of intercalated C:C ⁺ stacks. When psC occupies central positions, the resulting i-motifs are only observed at low pH and psC:C ⁺ or psC:psC ⁺ hemiprotonated base pairs are formed instead of their neutral analogs. Overall, our results suggest that positively charged base pairs are necessary to stabilize this non-canonical DNA structure.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 6.58 kDa 
• Atom Count: 434 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*(DCP)P*CP*GP*TP*TP*TP*CP*(PSC)P*GP*T)-3')	A, B	11	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Mir, B., Soles, X., Gonzalez, C., Escaja, N.

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Funding Organization	Location	Grant Number
MINECO	Spain	BFU2014-52864-R
MINECO	Spain	CTQ2014-52658-R

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection
• Version 2.0: 2019-05-15
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
• Version 2.1: 2024-05-15
  Changes: Data collection, Database references