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.