Center for Molecular Spectroscopy and Dynamics

ICAMD 2017

Triple helical DNA (DNA triplex) is an exotic conformation of DNA, which is known to exist for special sequences under specific pH and salt conditions. In vivo formation of DNA triplex is thought to be responsible for a certain genetic disease such as Friedreich Ataxia. This conformation has also drawn much attention over decades because of its potential for sequence-specific DNA targeting. 

Here we aim at directly monitoring triplex formation between a duplex and a single-stranded oligonucleotide in real time via single-molecule FRET technique. This technique not only enables us to detect triplex formation but also provides detailed information about relative orientation of these DNA strands, which further confirms the geometry of DNA triplex. We also investigate the effect of pH, salt, and molecular stoichiometry on dynamics of triplex formation. The results obtained here would provide crucial insight into nucleic acid interactions and molecular design for triplex-based nano-device and reporters.

Fig. 1. DNA triplex and its detection by FRET

(D: donor, A: acceptor,

*: Hoogsteen basepair)