8OFC

Structure of an i-motif domain with the cytosine analog 1,3-diaza-2-oxophenoxacione (tC) at neutral pH

Summary for 8OFC

• Entry DOI: 10.2210/pdb8ofc/pdb
• NMR Information: BMRB: 34798
• Descriptor: DNA (5'-D(*CP*(YCO)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*(DNR)P*GP*T)-3') (1 entity in total)
• Functional Keywords: i-motif, fluorescent, non-canonical dna, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 6719.34

Authors

Mir, B.,Serrano-Chacon, I.,Terrazas, M.,Gandioso, A.,Garavis, M.,Orozco, M.,Escaja, N.,Gonzalez, C. (deposition date: 2023-03-15, release date: 2024-02-07, Last modification date: 2024-04-24)

Primary citation

Mir, B.,Serrano-Chacon, I.,Medina, P.,Macaluso, V.,Terrazas, M.,Gandioso, A.,Garavis, M.,Orozco, M.,Escaja, N.,Gonzalez, C.
Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells.
Nucleic Acids Res., 52:3375-3389, 2024

PubMed Abstract: The i-motif is an intriguing non-canonical DNA structure, whose role in the cell is still controversial. Development of methods to study i-motif formation under physiological conditions in living cells is necessary to study its potential biological functions. The cytosine analog 1,3-diaza-2-oxophenoxazine (tCO) is a fluorescent nucleobase able to form either hemiprotonated base pairs with cytosine residues, or neutral base pairs with guanines. We show here that when tCO is incorporated in the proximity of a G:C:G:C minor groove tetrad, it induces a strong thermal and pH stabilization, resulting in i-motifs with Tm of 39ºC at neutral pH. The structural determination by NMR methods reveals that the enhanced stability is due to a large stacking interaction between the guanines of the tetrad with the tCO nucleobase, which forms a tCO:C+ in the folded structure at unusually-high pHs, leading to an increased quenching in its fluorescence at neutral conditions. This quenching is much lower when tCO is base-paired to guanines and totally disappears when the oligonucleotide is unfolded. By taking profit of this property, we have been able to monitor i-motif folding in cells.

PubMed: 38366792
DOI: 10.1093/nar/gkae106

Experimental method

SOLUTION NMR