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Pure Appl. Chem., 2011, Vol. 83, No. 1, pp. 213-232

Published online 2010-12-01

Fluorescent ribonucleoside analogues as probes for investigating RNA structure and function*

Seergazhi G. Srivatsan* and Anupam A. Sawant

Indian Institute of Science Education and Research, Sai Trinity Building, Pashan, Pune 411021, India

Abstract: Numerous biophysical tools based on fluorescence have been developed to advance the understanding of RNA–nucleic acid, RNA–protein, and RNA–small molecule inter-actions. In this regard, fluorescent ribonucleoside analogues that are sensitive to their local environment provide sensitive probes for investigating RNA structure, dynamics, and recognition. Most of these analogues closely resemble the native ribonucleosides with respect to their overall dimension and have the ability to form canonical Watson–Crick (WC) base pairs. Therefore, it is possible to place these probes near the point of interaction in a target nucleic acid with minimum structural perturbations and gain insight into the intricacies of conformational changes taking place in and around the interaction site. Here, we provide a concise background on the development and recent advances in the applications of base-modified fluorescent ribonucleoside analogue probes. We first present various base-modified fluorescent ribonucleoside analogues, their photophysical properties, and methods to incorporate these analogues into oligoribonucleotides. We then discuss the established spectroscopic techniques, which make use of the fluorescence properties of these emissive ribonucleoside analogues. Finally, we present the applications of base-modified fluorescent ribonucleoside analogues used as probes incorporated into oligoribonucleotides in investigating RNA structures and functions.
*Pure Appl. Chem. 83, 1–252 (2011). A collection of invited, peer-reviewed articles by former winners of the IUPAC Prize for Young Chemists, in celebration of the International Year of Chemistry 2011.