Structure of Human Telomeric DNA G-Quadruplexes in a Model Cell-Like Confined Environment Using a Fluorescent Nucleoside Probe

Abstract

Nucleic acids play a central role in carrying genetic information, and also have the ability to catalyze biochemical reactions and regulate gene expression in the cell. Their functions often involve conformational changes while interacting with other nucleic acids, proteins and small molecule metabolites. Several biophysical tools have been developed which report these conformation changes in vitro. In particular, microenvironment-sensitive fluorescent nucleoside analogues have afforded effective biophysical tools to understand the structure, dynamics and function of nucleic acids. However, their use has been limited to in vitro studies because of low quantum yield when incorporated into oligonucleotides and or their excitation maximum in the UV region. Self-assembling systems like reverse micelles, which are UV transparent, have been reported to have the similar physical properties in their aqueous core as observed in the cellular environment and provide necessary macromolecular crowding effects, thus making them as useful cell mimicking systems. In this context, here we report the photophysical studies of environment-sensitive fluorescent nucleoside analogue, 5-(benzofuran-2-yl)-2’-deoxyuridine (BFdU), in micellar and reverse micellar systems. The nucleoside analogue senses the change in the microenvironment of micelles and in the core of reverse micelles. Furthermore, we have used the environment-sensitivity of nucleoside in studying the structure of human telomeric DNA sequence in reverse micelles, which served as a model cell-like confined environment. Steady-state fluorescence and lifetime studies suggest that the nucleoside analogue incorporated into telomeric DNA repeat successfully senses the changes in the metal ion dependent conformational changes in buffer systems and in AOT reverse micellar systems. Also it can photo physically distinguish between G-quadruplexes and corresponding duplexes in AOT reverse micelles. Hence it can be used as a non-invasive robust tool for the detection and conformational studies of G-quadruplex structures.