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.
Kawai
Kiyohiko
K
The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Ibaraki, Osaka 567-0047, Japan. kiyohiko@sanken.oskak-u.ac.jp
Yoshida
Hiroko
H
Sugimoto
Akira
A
Fujitsuka
Mamoru
M
Majima
Tetsuro
T
D002412:Cations / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000138:chemical synthesis / Q000737:chemistry*; D019281:Dimerization; D005609:Free Radicals / Q000737:chemistry; D007700:Kinetics; D015394:Molecular Structure; D010084:Oxidation-Reduction; D011721:Pyrenes / Q000138:chemical synthesis / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013997:Time Factors
D002412:Cations; D004277:DNA, Single-Stranded; D005609:Free Radicals; D011721:Pyrenes; C030984:pyrene