PDBsum entry 5nip

DNA

PDB id: 5nip

Contents

DNA/RNA

PDB id:

5nip

Name:

DNA

Title:

An i-motif containing the neutral cytidine protonated analogue pseudoisocytidine

Structure:

DNA (5'-d( Tp (Dcp)p Cp Gp Tp Tp Tp Cp (Psc)p Gp T)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630

NMR struc:

10 models

Authors:

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

Key ref:

B.Mir et al. (2017). The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures. Sci Rep, 7, 2772. PubMed id: 28584239

Date:

24-Mar-17 Release date: 28-Jun-17

DNA/RNA chains

T-C-C-G-T-T-T-C-8YN-G-T 11 bases

T-C-C-G-T-T-T-C-8YN-G-T 11 bases

Sci Rep 7:2772 (2017)

PubMed id: 28584239

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

B.Mir, X.Solés, C.González, N.Escaja.

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.