RNA G-quadruplexes (G4s) play important roles in translational regulation, mRNA processing events and gene expression. Therefore, a fluorescent probe that is capable of efficiently recognizing RNA G-quadruplex structures among other RNA forms is highly desirable. In this study, a water-soluble fluorogenic dye (i.e., Thioflavin T (ThT)) was employed to recognize RNA G-quadruplex structures using UV-Vis absorption spectra, fluorescence spectra and emission lifetime experiments. By stacking on the G-tetrad, the ThT probe exhibited highly specific recognition of RNA G-quadruplex structures with striking fluorescence enhancement compared with other RNA forms. The specific binding demonstrates that ThT is an efficient fluorescence sensor that can distinguish G4 and non-G4 RNA structures.One of the most important types of nucleic acid structure is the G-quadruplex (G4), which is formed from four guanine bases by stacking of Hoogsteen bonded G-quartets 1 . The G-quadruplexes play a vital role in the human genome and transcriptome 2,3 . The DNA or RNA G-quadruplexes that are formed in cells are associated with many important cellular processes 4-8 . G-quadruplexes have been viewed as emerging therapeutic targets due to their correlation with human diseases [8][9][10][11][12] . Most of the early studies of G-quadruplexes focused on DNA strands, and few studies focused on RNA G-quadruplexes. Recently, RNA G-quadruplexes have been associated with many biological processes, such as telomere maintenance, pre-mRNA splicing and polyadenylation, RNA turnover, mRNA targeting and translation 13 . Therefore, the development of techniques that could efficiently recognize RNA G-quadruplexes structures and investigate their biological functions and impacts is highly desirable. Many techniques including X-ray crystallography and NMR experiments have been utilized to identify high-resolution structures of RNA G-quadruplexes 14,15 . However, these techniques are more suitable for comprehensively studying targeted RNA G-quadruplex structures. Additionally, circular dichroism (CD) has been extensively used to monitor G-quadruplex formation because the positive band at 264 nm and the negative band at 240 nm indicate the formation of parallel-type G-quadruplex structures 16 . However, it is difficult to interpret the G-quadruplex type in the presence of different forms of nucleic acids. Because the probe recognition sites in RNA G-quadruplexes are different from those in other RNA motifs, small molecules that selectively bind to RNA G-quadruplexes and emit fluorescence may be used as RNA G-quadruplex detectors. Our previous study revealed a cyanine dye (CyT) that was able to selectively recognize RNA G-quadruplex structures with ~2000-fold fluorescence enhancement 17 . Due to the important biological functions of RNA G-quadruplex, the development of a multiband probe that can selectively recognize RNA G-quadruplex structures is needed to further expand the application of RNA G-quadruplexes, which have been recognized as significant molecular...
The G-quadruplex ligands database (G4LDB, http://www.g4ldb.org) provides a unique collection of reported G-quadruplex ligands to streamline ligand/drug discovery targeting G-quadruplexes. G-quadruplexes are guanine-rich nucleic acid sequences in human telomeres and gene promoter regions. There is a growing recognition for their profound roles in a wide spectrum of diseases, such as cancer, diabetes and cardiovascular disease. Ligands that affect the structure and activity of G-quadruplexes can shed light on the search for G-quadruplex-targeting drugs. Therefore, we built the G4LDB to (i) compile a data set covering various physical properties and 3D structure of G-quadruplex ligands; (ii) provide Web-based tools for G-quadruplex ligand design; and (iii) to facilitate the discovery of novel therapeutic and diagnostic agents targeting G-quadruplexes. G4LDB currently contains >800 G-quadruplex ligands with ∼4000 activity records, which, to our knowledge, is the most extensive collection of its kind. It offers a user friendly interface that can meet a variety of data inquiries from researchers. For example, ligands can be searched for by name, molecular properties, structures, ligand activities and so on. Building on the reported data, the database also provides an online ligand design module that can predict ligand binding affinity in real time.
G-quadruplex DNA has been viewed as a prospective anti-cancer target owing to its potential biological relevance. Real-time monitoring of DNA G-quadruplex structures in living cells can provide valuable insights into the relationship between G-quadruplex formation and its cellular consequences. However, the probes capable of detecting DNA G-quadruplexes in living cells are still very limited. Herein, we reported a new fluorescent probe, IMT, for real-time visualization of DNA G-quadruplex structures in living cells. Using IMT as a fluorescent indicator, the quantity changes of DNA G-quadruplex at different points in time during continuous cellular progression responding to Aphidicolin and Hydroxyurea treatment have been directly visualized. Our data demonstrate that IMT will be a valuable tool for exploring DNA G-quadruplexes in live cells. Further application of IMT in fluorescence imaging may reveal more information on the roles of DNA G-quadruplexes in biological systems.
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