Fluorescent ribonucleoside analogues as probes for investigating RNA structure and function

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.

Excited-State Proton Transfer and Phototautomerism in Nucleobase and Nucleoside Analogs: A Mini-Review

“…[1][2][3][4] Although the number of such compounds is expanding rapidly, [3][4][5][6][7][8] their spectral behavior is not always fully understood, especially in relation to tautomerism, protonation and deprotonation sites, and excited-state acid-base reactions. Correct interpretation of the fluorescence experiments in biological systems in many instances requires resolution of the above problems, as illustrated by our FIGURE 1 Structure of some of the purine analogs discussed in this article.…”

FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids

“…The well-defined transition dipole position and orientation at the timescale of energy transfer is a considerable advantage of these FRET probes offering the potential to retrieve distance and orientational information from FRET measurements. Furthermore, the ability to position the reporters inside the very site of interest is an attractive, if not vital, feature in a majority of studies (17,18). However, the technical and theoretical challenges involved in the simulation and quantitative analysis of these probes have up till now posed serious limitations in the design and analysis of base–base FRET experiments.…”

Phosphine‐Free Stille–Migita Chemistry for the Mild and Orthogonal Modification of DNA and RNA

“…R f = 0.26 (DCM/MeOH 95:5);1 H NMR (500 MHz, [D 6 ]DMSO): d = 8.07 (s, 1 H, H6), 6.34(d, J = 15.7 Hz, 1 H, H7), 6.15 (t, J = 6.5 Hz, 1 H, H1'), 5.86 (dt, J = 15.7 Hz, 6.9 Hz, 1 H, H8), 5.19(d, NMR (202 MHz, D 2 O, 10 mm phosphate buffer pD = 7.0 (d = 2.35 ppm)): d = À7.37 (d, J = 17.6 Hz, Pg), À10.41 (d, J = 19.7 Hz, Pa), À21.35 ppm (t, J = 18.5 Hz, Pb); HR-ESI-TOF-MS: m/z calcd for [MÀH À ] C 13 H 20 N 6 O 13 P 3 561.0307, found 561.0326.…”