Nanosecond to submillisecond dynamics in dye-labeled single-stranded DNA, as revealed by ensemble measurements and photon statistics at single-molecule level.
Single-molecule and ensemble time-resolved fluorescence measurements were applied for the investigation of the conformational dynamics of single-stranded DNA, ssDNA, connected with a fluorescein dye by a C6 linker, where the motions both of DNA and the C6 linker affect the geometry of the system. From the ensemble measurement of the fluorescence quenching via photoinduced electron transfer with a guanine base in the DNA sequence, three main conformations were found in aqueous solution: a conformation unaffected by the guanine base in the excited state lifetime of fluorescein, a conformation in which the fluorescence is dynamically quenched in the excited-state lifetime, and a conformation leading to rapid quenching via nonfluorescent complex. The analysis by using the parameters acquired from the ensemble measurements for interphoton time distribution histograms and FCS autocorrelations by the single-molecule measurement revealed that interconversion in these three conformations took place with two characteristic time constants of several hundreds of nanoseconds and tens of microseconds. The advantage of the combination use of the ensemble measurements with the single-molecule detections for rather complex dynamic motions is discussed by integrating the experimental results with those obtained by molecular dynamics simulation.
Division of Frontier Materials Science and Division of Chemistry, Graduate School of Engineering Science and Center for Quantum Materials Science under Extreme Conditions, Osaka University, Machikaneyama1-3, Toyonaka, Osaka 560-8531, Japan.
Takahiro
T
Kaji
Syoji
S
Ito
Shigenori
S
Iwai
Hiroshi
H
Miyasaka
D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004579:Electron Transport; D005456:Fluorescent Dyes / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D017785:Photons; D013050:Spectrometry, Fluorescence; D013997:Time Factors
D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes