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Quantification of Chemical and Mechanical Effects on the Formation of G-quadruplex and i-Motif in Duplex DNA.

Research paper by Sangeetha S Selvam, Shankar S Mandal, Hanbin H Mao

Indexed on: 25 Jul '17Published on: 25 Jul '17Published in: Biochemistry



Abstract

Formation of biologically significant tetraplex DNA species, such as G-quadruplexes and i-motifs, is affected by chemical (ions and pH) and mechanical (superhelicity [σ] and molecular crowding) factors. Due to the extremely challenging experimental conditions, relative im-portance of these factors on tetraplex folding is unknown. In this work, we quantitatively evalu-ated the chemical and mechanical effects on the population dynamics of DNA tetraplexes in In-sulin Linked Polymorphic Region using magneto-optical tweezers. By mechanically unfolding individual tetraplexes, we found that ions and pH have the largest effects on the formation of G-quadruplex and i-motif, respectively. Interestingly, superhelicity has the second largest effect fol-lowed by molecular crowding condition. While chemical effects are specific to tetraplex species, mechanical factors show generic influences. The predominant effect of chemical factors can be attributed to the fact that they directly change the stability of a specific tetraplex whereas the mechanical factors, superhelicity in particular, reduce the stability of the competing species by changing the kinetics of the melting and annealing of the duplex DNA template in a non-specific manner. The substantial dependence of tetraplexes on superhelicity provides strong support that DNA tetraplexes can serve as topological sensors to modulate fundamental cellular processes such as transcription.