Title: Fluorescence spectroscopy of DNA G-quadruplexes : ensemble and single-molecule measurements
Abstract: Guanine-rich DNA can form structures called G-quadruplexes, which can be biologically important and also have potential applications in different fields including chemistry, nanotechnology and material science.G-quadruplexes are highly polymorphic and the activities of these molecules strongly depend on their structures.This study will focus on conformation and stability as well as excited state dynamics of G-quadruplexes using both ensemble and single-molecule fluorescence measurements, coupled with other techniques such as UV absorption, CD, and NMR spectroscopy.It has been shown that G-quadruplex DNA has stronger intrinsic fluorescence than their less-structured counterparts.We characterize and compare fluorescence properties of various well-defined G-quadruplex structures.We show that the increase of intrinsic fluorescence of G-rich DNA sequences when they form Gquadruplexes can be used to monitor the folding and unfolding of G-quadruplexes as a function of cations and temperature.The temperature-dependent fluorescence spectra of different G-quadruplexes also exhibit characteristic patterns.We demonstrate that the stability and possibly also the structure of G-quadruplexes can be characterized and distinguished by their intrinsic fluorescence spectra.Excited states created in DNA under UV light have recently received much attention of the scientific community in efforts to understand the photoreactions behind the genetic damage induced by UV light.We report the observation of excimer formation by stacking of two G-quadruplex blocks based on the spectroscopic signatures of this excimer: no change in absorption, red shifted fluorescence emission and lifetime decay in the order of nanoseconds.This is also the first time that fluorescence and NMR experiments are performed concurrently on identical samples, in order to maintain the high-resolution NMR structural information, when studying excimer emission.We show that for the formation of the geometryoptimized excimers, the specific base-stacking overlap at the G-quadruplex interface is critical.This specific overlap pattern has not been observed in B-DNA or G-