Time-Resolved NMR-Studies of DNA I-Motif Formation Reveal Kinetic Partitioning Mechanism

Abstract

Beside the well known double helix conformation DNA is able to build structures stabilized by non-Watson-Crick base pairs like G-quadruplexes[1] and i-motifs.[2] Those structures can be formed by guanosine- and cytidine-rich strands. These sequences are found e.g. in telomeres, the ends of eukaryotic chromosomes.[3] They present a good targets for cancer therapy. Quarduplex structures are also found in the field of nanodevice applications.[4] The cytidine-rich strand forms its intercalated structure in slightly acid environment.[2] The so-called i-motif is stabilized by fully intercalated hemiprotonated C.C+ base pairs.We investigate structural changes and the kinetics of pH-induced folding of various i-motif structures at atomic resolution. For this, we used a rapid-mixing device which allows us to mix two solutions at a defined time directly inside of the NMR-spectrometer.[5] We could show that after induction of the folding with acid, competitive i-motif structures with different intercalation topology are formed.[6] Depending on the species of the loop-forming nucleotides equilibrium between build conformations can be changed.