Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels.

Benoît Y Michel,Alexander P Demchenko,Dmytro Dziuba,Rachid Benhida,Alain Burger

doi:10.3389/fchem.2020.00112

Abstract

Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).

Highlights

Rapid progress in genomics, transcriptomics, and epigenomics are driving a strong demand for reliable fluorescence-based tools for studying the structural and conformational polymorphisms of nucleic acids (NAs), their variability and internal dynamics, their interactions with proteins, metabolites, NA-targeting drugs, water molecules, and ions at sub-molecular and atomic levels (Wilhelmsson and Tor, 2016)
Despite significant progress and the large number of Fluorescent Nucleoside Analogs (FNAs) reported to date, new efforts continue and further developments in this field are expected (Manna et al, 2018; Sabale et al, 2018)
As the reader may have noticed, the intensity-based probes are over-represented in the literature, whereas less attention has been paid to FNAs that exploit other reporting principles

Summary

Introduction

Transcriptomics, and epigenomics are driving a strong demand for reliable fluorescence-based tools for studying the structural and conformational polymorphisms of nucleic acids (NAs), their variability and internal dynamics, their interactions with proteins, metabolites, NA-targeting drugs, water molecules, and ions at sub-molecular and atomic levels (Wilhelmsson and Tor, 2016). Fluorescence methods based on single fluorescent nucleosides site-selectively incorporated into NAs have found applications for NA visualization within cells, genotyping, detection of single-nucleotide polymorphisms (SNP), studies of structures, thermodynamics, dynamics of NAs and their interactions with proteins, and small molecules targeting NAs. How do these techniques work, where are we and what are the prospects for this booming research area? These DNA-based structures are covalently labeled with a single type of fluorophore and it is possible to attach the probe, to a specific NA sequence, and to position it in the structure in non-perturbing manner.

Results

Conclusion