Conformational fluctuations in single DNA molecules.

Measurement of fluorescent lifetimes of dye-tagged DNA molecules reveal the existence of different conformations. Conformational fluctuations observed by fluorescence correlation spectroscopy give rise to a relaxation behavior that is described by "stretched" exponentials and indicates the presence of a distribution of transition rates between two conformations. Whether this is an inhomogeneous distribution, where each molecule contributes with its own reaction rate to the overall distribution, or a homogeneous distribution, where the reaction rate of each molecule is time-dependent, is not yet known. We used a tetramethylrhodamine-linked 217-bp DNA oligonucleotide as a probe for conformational fluctuations. Fluorescence fluctuations from single DNA molecules attached to a streptavidin-coated surface directly show the transitions between two conformational states. The conformational fluctuations typical for single molecules are similar to those seen in single ion channels in cell membranes.

[1]  J. Ramstein,et al.  Fluorescence relaxation of proflavin-deoxyribonucleic acid interaction. Kinetic properties of a base-specific reaction. , 1980, Biochemistry.

[2]  Otto S. Wolfbeis,et al.  Fluorescence spectroscopy : new methods and applications , 1992 .

[3]  Jerker Widengren,et al.  Fast interactions between Rh6G and dGTP in water studied by fluorescence correlation spectroscopy , 1997 .

[4]  J. Patlak.  Molecular kinetics of voltage-dependent Na+ channels. , 1991, Physiological reviews.

[5]  A. H. Klahn,et al.  References and Notes , 2022 .

[6]  R N Zare,et al.  Probing individual molecules with confocal fluorescence microscopy. , 1994, Science.

[7]  R. Rigler,et al.  Fluorescence correlation spectroscopy of triplet states in solution: a theoretical and experimental study , 1995 .

[8]  W. P. Ambrose,et al.  Alterations of Single Molecule Fluorescence Lifetimes in Near-Field Optical Microscopy , 1994, Science.

[9]  H Schindler,et al.  Imaging of single molecule diffusion. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Jerker Widengren,et al.  Mechanisms of photobleaching investigated by fluorescence correlation spectroscopy , 1996 .

[11]  Dennis E. Koppel,et al.  Statistical accuracy in fluorescence correlation spectroscopy , 1974 .

[12]  A. Cooper.  Dynamics of Proteins and Nucleic Acids , 1988 .

[13]  Wolynes,et al.  Intermittency of single molecule reaction dynamics in fluctuating environments. , 1995, Physical review letters.

[14]  S. Provencher.  CONTIN: A general purpose constrained regularization program for inverting noisy linear algebraic and integral equations , 1984 .

[15]  D. Marquardt.  An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[16]  H. J. Li,et al.  Relaxation studies of the proflavine-DNA complex: the kinetics of an intercalation reaction. , 1969, Journal of molecular biology.

[17]  Markus Sauer,et al.  NUCLEOBASE-SPECIFIC QUENCHING OF FLUORESCENT DYES. 1. NUCLEOBASE ONE-ELECTRON REDOX POTENTIALS AND THEIR CORRELATION WITH STATIC AND DYNAMIC QUENCHING EFFICIENCIES , 1996 .

[18]  F J Sigworth,et al.  Open channel noise. V. Fluctuating barriers to ion entry in gramicidin A channels. , 1990, Biophysical journal.

[19]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[20]  E. Betzig,et al.  Near-field spectroscopy of single molecules at room temperature , 1994, Nature.

[21]  R. Rigler,et al.  Picosecond Fluorescence Spectroscopy in the Analysis of Structure and Motion of Biopolymers , 1985 .

[22]  Edward S. Yeung,et al.  Differences in the chemical reactivity of individual molecules of an enzyme , 1995, Nature.

[23]  B. Sakmann,et al.  Single-channel currents recorded from membrane of denervated frog muscle fibres , 1976, Nature.

[24]  X. Xie,et al.  Single-Molecule Spectroscopy and Dynamics at Room Temperature , 1996 .

[25]  R. Rigler,et al.  Conformational transitions monitored for single molecules in solution. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[26]  P. Wolynes,et al.  The energy landscapes and motions of proteins. , 1991, Science.

[27]  Louis E. Brus,et al.  Imaging and Time-Resolved Spectroscopy of Single Molecules at an Interface , 1996, Science.