Folding Dynamics of Parallel and Antiparallel G-Triplexes under the Influence of Proximal DNA

The G-triplex is a kind of DNA structure formed by G-rich sequences. Previous studies have shown that it is an intermediate for the folding of G-quadruplex and has an antiparallel structure. The folding dynamics of this G-triplex structure, however, have not been well studied until now. In addition, whether a parallel G-triplex structure exists, remains unknown. In this study, by using single-molecule fluorescence resonance energy transfer and circular dichroism spectroscopy methods, we have studied the folding dynamics of the G-triplex and revealed at the single-molecule level, for the first time, that G-triplexes have both parallel and antiparallel structures. Moreover, we have investigated the effects of proximal DNA on G-triplex folding. We have found that both single-stranded TTA and double-stranded DNA at either end of a G-triplex sequence can reduce its folding speed. More interestingly, when located at the 5' end of a G-triplex sequence, the proximal DNA will favor the folding of parallel over antiparallel G-triplex structures. As G-triplex is an intermediate for G-quadruplex folding, the present results may also shed new light on the folding properties of G-quadruplex structures, in terms of dynamics, stability, and the effects of proximal DNA.