| Abstract
| - A novel fluorescence-based method, which entails contact quenching of the long-lived fluorescentstate of 2,3-diazabicyclo[2.2.2]-oct-2-ene (DBO), was employed to measure the kinetics of end-to-endcollision in short single-stranded oligodeoxyribonucleotides of the type 5‘-DBO−(X)n-dG with X = dA, dC,dT, or dU and n = 2 or 4. The fluorophore was covalently attached to the 5‘ end and dG was introducedas an efficient intrinsic quencher at the 3‘ terminus. The end-to-end collision rates, which can be directlyrelated to the efficiency of intramolecular fluorescence quenching, ranged from 0.1 to 9.0 × 106 s-1. Theywere strongly dependent on the strand length, the base sequence, as well as the temperature.Oligonucleotides containing dA in the backbone displayed much slower collision rates and significantlyhigher positive activation energies than strands composed of pyrimidine bases, suggesting a higher intrinsicrigidity of oligoadenylate. Comparison of the measured collision rates in short single-stranded oligodeoxyribonucleotides with the previously reported kinetics of hairpin formation indicates that the intramolecularcollision is significantly faster than the nucleation step of hairpin closing. This is consistent with theconfigurational diffusion model suggested by Ansari et al. (Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc.Natl. Acad. Sci. USA2001, 98, 7771−7776), in which the formation of misfolded loops is thought to slowhairpin formation.
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