ISDA

Deposition Date 2017-03-24

Release Date 2017-06-28

Last Version Date 2024-05-15

Entry Detail

PDB ID:

5NIP

Keywords:

DNA

Title:

An i-motif containing the neutral cytidine protonated analogue pseudoisocytidine

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)

Method Details:

Experimental Method:

SOLUTION NMR

Conformers Calculated:

Conformers Submitted:

Selection Criteria:

all calculated structures submitted

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*(DCP)P*CP*GP*TP*TP*TP*CP*(PSC)P*GP*T)-3')
Chain IDs:A, B
Chain Length:11
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

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

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

Sci Rep 7 2772 2772 (2017)

PMID: 28584239 DOI: 10.1038/s41598-017-02723-y

Abstact

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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Primary Citation of related structures