posted on 2017-07-24, 00:00authored bySangeetha Selvam, Shankar Mandal, Hanbin Mao
The
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. Because of the extremely challenging experimental conditions,
the relative importance of these factors on tetraplex folding is unknown.
In this work, we quantitatively evaluated the chemical and mechanical
effects on the population dynamics of DNA tetraplexes in the insulin-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 the G-quadruplex and i-motif,
respectively. Interestingly, superhelicity has the second largest
effect followed by molecular crowding conditions. While chemical effects
are specific to tetraplex species, mechanical factors have 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 nonspecific
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.