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.
Department of Chemical Science, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
T
T
Ramreddy
Mamata
M
Kombrabail
G
G
Krishnamoorthy
B J
BJ
Rao
D015075:2-Aminopurine / Q000737:chemistry*; D020029:Base Pairing; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005453:Fluorescence; D005454:Fluorescence Polarization; D009068:Movement; D013997:Time Factors
C051802:triplex DNA; D015075:2-Aminopurine; D004247:DNA