Kinetics of transient end-to-end contact of single-stranded DNAs.

The formation of the pyrene (Py) dimer radical cation (Py(2)(+)) was used to measure the kinetics of the intrastrand end-to-end contact rates of single-stranded DNAs (ssDNAs) in the 10 nanoseconds to the tens of microseconds time range. ssDNAs labeled with Py at both ends with the lengths of 3, 6, and 9 mer were synthesized, and the two-photon ionization method was employed to generate a Py(+), which enables the measurements of the end-to-end contact rates from 10 ns. The formation rate of Py(2)(+) depended on the length and the sequence of the ssDNAs, and about 1 order of magnitude faster rates were observed for the T-rich ssDNAs compared to those for the corresponding length of A-rich ssDNAs, showing that ssDNA made from adenines is much more rigid than that composed of thymidines. As for the T-rich ssDNAs, the formation of Py(2)(+) attributed to the misfolded structures was also observed, which is consistent with the configurational diffusion model suggested by Ansari and co-workers.