A) Hemi‐protonated C⋅C+ base pair. B) Example of a sequence prone to form intramolecular i‐DNA. C) Possible loop arrangements in an i‐DNA structure; Simplified diagram of two linking directions between strands: Central loop can across either major (left, conformation I) or minor (right, conformation II) groove.
Jun-Jie Zhu Research Group
Recent studies indicate that i‐DNA, a four‐stranded cytosine‐rich DNA also known as the i‐motif, is actually formed in vivo; however, a systematic study on sequence effects on stability has been missing. Herein, an unprecedented number of different sequences (271) bearing four runs of 3–6 cytosines with different spacer lengths has been tested. While i‐DNA stability is nearly independent on total spacer length, the central spacer plays a special role on stability. Stability also depends on the length of the C‐tracts at both acidic and neutral pHs. This study provides a global picture on i‐DNA stability thanks to the large size of the introduced data set; it reveals unexpected features and allows to conclude that determinants of i‐DNA stability do not mirror those of G‐quadruplexes. Our results illustrate the structural roles of loops and C‐tracts on i‐DNA stability, confirm its formation in cells, and allow establishing rules to predict its stability.
Cheng, MP; Qiu, DH; Tamon, L; Istvankova, E; Viskova, P; Amrane, S; Guedin, A; Chen, JL; Lacroix, L; Ju, HX; Trantirek, L; Sahakyan, AB; Zhou, J; and Mergny, JL: Thermal and pH Stabilities of i-DNA: Confronting in vitro Experiments with Models and In-Cell NMR Data Angew. Chem. Int. Ed. on linehttps://doi.org/10.1002/anie.202016801