Site-specific dynamics in TAT triplex DNA as revealed by time-domain fluorescence of 2-aminopurine

Triple helices of DNA are finding increasing level of applications in several areas, including antigene therapy and gene regulation. We have probed site-specific dynamic aspects of TAT triple helices of DNA by using steady-state and time-domain fluorescence of 2-aminopurine (2-AP), a fluorescent analog of adenine. TAT triplexes were formed from repeats of adenine and thymine with 2-AP incorporated at various locations in the polyadenine strand. We find an overall decrease in the level of near-neighbor base-stacking interaction in the TAT triplex when compared to AT duplex as reported by fluorescence decay kinetics of 2-AP. More strikingly, we have observed a stark asymmetry in both the level of base stacking and motional dynamics of the bases in the two ends of TAT triplexes, namely, the 5' end having a higher level of base stacking and segmental dynamics when compared to the 3' end. The possible implications of this asymmetry, which reflects the asymmetry in the strength of Hoogstein base-pairing with the 3' end having stronger Hoogstein pairing when compared to the 5' end, is discussed.