Direct observation of the formation of DNA triplexes by single-molecule FRET measurements

In this report we investigated the effects of various biological and chemical factors (DNA sequence, pH, ions, and molecularity) on the formation of DNA triplexes through single-molecule FRET technique. Using this method, we determined how the third strand bound to a DNA duplex and how stable the triplex structure was under various conditions. From this study, we not only verified a variety of well-known features of DNA triplex but also discovered or experimentally supported several interesting behaviors: at neutral pH, a pyrimidine-motif triplex can be formed; the parallel arrangement was not only possible but also dominant over the antiparallel arrangement for a purine-motif triplex. We demonstrated that our method is a versatile analytical tool in studying structural aspects of nucleic acids, particularly non-classical DNA structures, and provides insights into physical mechanism of such structures.