8BV6

An i-motif domain able to undergo pH-dependent conformational transitions (neutral structure)

Summary for 8BV6

• Entry DOI: 10.2210/pdb8bv6/pdb
• Related: 8BQY
• NMR Information: BMRB: 34774
• Descriptor: DNA (5'-D(*CP*(DNR)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*CP*GP*T)-3') (1 entity in total)
• Functional Keywords: dna structure, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 6629.26

Authors

Serrano-Chacon, I.,Mir, B.,Cupellini, L.,Colizzi, F.,Orozco, M.,Escaja, N.,Gonzalez, C. (deposition date: 2022-12-01, release date: 2023-02-22, Last modification date: 2024-06-19)

Primary citation

Serrano-Chacon, I.,Mir, B.,Cupellini, L.,Colizzi, F.,Orozco, M.,Escaja, N.,Gonzalez, C.
pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs.
J.Am.Chem.Soc., 145:3696-3705, 2023

PubMed Abstract: We study here a DNA oligonucleotide having the ability to form two different i-motif structures whose relative stability depends on pH and temperature. The major species at neutral pH is stabilized by two C:C base pairs capped by two minor groove G:C:G:C tetrads. The high pH and thermal stability of this structure are mainly due to the favorable effect of the minor groove tetrads on their adjacent positively charged C:C base pairs. At pH 5, we observe a more elongated i-motif structure consisting of four C:C base pairs capped by two G:T:G:T tetrads. Molecular dynamics calculations show that the conformational transition between the two structures is driven by the protonation state of key cytosines. In spite of large conformational differences, the transition between the acidic and neutral structures can occur without unfolding of the i-motif. These results represent the first case of a conformational switch between two different i-motif structures and illustrate the dramatic pH-dependent plasticity of this fascinating DNA motif.

PubMed: 36745195
DOI: 10.1021/jacs.2c13043

Experimental method

SOLUTION NMR