Kinetics of End-to-End Collision in Short Single-Stranded Nucleic Acids

• Published in: Journal of the American Chemical Society Vol. 126; no. 3; pp. 808 - 813
• Main Authors: Wang, Xiaojuan, Nau, Werner M
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 28.01.2004; Amer Chemical Soc
• Subjects: Biological and medical sciences; Bridged Bicyclo Compounds, Heterocyclic - chemistry; Chemistry; Chemistry, Multidisciplinary; Fluorescence; Fluorescent Dyes - chemical synthesis; Fluorescent Dyes - chemistry; Fundamental and applied biological sciences. Psychology; Kinetics; Molecular biophysics; Oligodeoxyribonucleotides - chemical synthesis; Oligodeoxyribonucleotides - chemistry; Organophosphorus Compounds - chemical synthesis; Organophosphorus Compounds - chemistry; Photochemistry. Photosynthesis. Bioluminescence; Physical Sciences; Radiation-biomolecule interaction; Science & Technology; FLUCTUATION; DNA-BINDING; INTRAMOLECULAR CONTACT FORMATION; FLUORESCENCE; FLEXIBILITY; TRANSCRIPTIONAL REPRESSION; DYNAMICS; DIFFUSION; MODEL; DEPENDENCE; Nitrogen heterocycle; Luminescence quenching; Bicyclic compound; Single stranded DNA; Radiative lifetimes; Quantum yield; Fluorescence spectrometry; Molecule collision; Luminescence decay
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja038263r

A novel fluorescence-based method, which entails contact quenching of the long-lived fluorescent state of 2,3-diazabicyclo[2.2.2]-oct-2-ene (DBO), was employed to measure the kinetics of end-to-end collision 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 introduced as an efficient intrinsic quencher at the 3‘ terminus. The end-to-end collision rates, which can be directly related to the efficiency of intramolecular fluorescence quenching, ranged from 0.1 to 9.0 × 106 s-1. They were 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 significantly higher positive activation energies than strands composed of pyrimidine bases, suggesting a higher intrinsic rigidity of oligoadenylate. Comparison of the measured collision rates in short single-stranded oligodeoxyribonucleotides with the previously reported kinetics of hairpin formation indicates that the intramolecular collision is significantly faster than the nucleation step of hairpin closing. This is consistent with the configurational diffusion model suggested by Ansari et al. (Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc. Natl. Acad. Sci. USA 2001, 98, 7771−7776), in which the formation of misfolded loops is thought to slow hairpin formation.