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J Phys Chem B. 2018 Oct 18;122(41):9499-9506. doi: 10.1021/acs.jpcb.8b08110. Epub 2018 Oct 8.

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

Lu XM1,2, Li H1,2, You J1,2, Li W1,2, Wang PY1,2, Li M1,2, Dou SX1,2, Xi XG3,4.

Author information

1
Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics , Chinese Academy of Sciences , Beijing 100190 , China.
2
School of Physical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China.
3
College of Life Sciences , Northwest A&F University , Yangling, Shaanxi 712100 , China.
4
LBPA, IDA, ENS Cachan, CNRS, Université Paris-Saclay , Cachan F-94235 , France.

Abstract

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.

PMID:
30269502
DOI:
10.1021/acs.jpcb.8b08110

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