Structural isomers and binding sites of guanine-rich quadruplexes investigated by induced circular dichroism of thionin: loops and tails

Ligand binding to G-quadruplex DNA: new insights from ultraviolet resonance Raman spectroscopy

G-Quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of several biological processes of many organisms. The rational design of G4-targeting molecules developed as potential anticancer and antiviral therapeutics is a complex problem intrinsically due to the structural polymorphism of these peculiar DNA structures. The aim of the present work is to show how Ultraviolet Resonance Raman (UVRR) spectroscopy can complement other techniques in providing valuable information about ligand/G4 interactions in solution. Here, the binding of BRACO-19 and Pyridostatin - two of the most potent ligands - to selected biologically relevant G4s was investigated by polarized UVRR scattering at 266 nm. The results give new insights into the binding mode of these ligands to G4s having different sequences and topologies by performing an accurate analysis of peaks assigned to specific groups and their changes upon binding. Indeed, the UVRR data not only show that BRACO-19 and Pyridostatin interact with different G4 sites, but also shed light on the ligand and G4 chemical groups really involved in the interaction. In addition, UVRR results complemented by circular dichroism data clearly indicate that the binding mode of a ligand can also depend on the conformation(s) of the target G4. Overall, these findings demonstrate the utility of using UVRR spectroscopy in the investigation of G4s and G4-ligand interactions in solution.

Biscarbazolylmethane-based cyanine: a two-photon excited fluorescent probe for DNA and selective cell imaging

We report a novel biscarbazole-based cyanine with a large Stokes shift and TPA cross-section as a light-up probe for DNA and selective TPEF cell imaging.

Detection of G-quadruplexes in cells and investigation of G-quadruplex structure of d(T2AG3)4 in K+ solution by a carbazole derivative: BMVC

Verification of the existence of quadruplex structure in native human telomeres and determination of the major structure of d(T(2)AG(3))(4) (H24) in K(+) solution are the major questions regarding the structure of human telomeres. We have synthesized a fluorescent probe of 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC) that has a very high binding affinity for G-quadruplex H24. BMVC stabilizes quadruplex structures and acts as a sensitive probe to the local environment. Although the circular dichroism patterns of H24 are different in Na(+) and K(+) solutions, similar binding behaviors of BMVC to H24 in these solutions led us to suggest that the major G-quadruplex structure of H24 in K(+) solution is very likely similar to that in Na(+) solution. Of particular interest is the fluorescent band detected at -575 nm in quadruplex H24 and at -545 nm in duplex DNA. In addition, the intensity of BMVC fluorescence increases by two orders of magnitudes upon interaction with either duplex or G-quadruplex DNA. BMVC has a greater binding preference for G-quadruplex H24 than for duplex DNA. Analyzing the BMVC fluorescence at the ends of metaphase chromosomes and other regions of chromosomes allowed us to verify the presence of G-quadruplex structure in human telomeres for the first time. Using fluorescence lifetime imaging microscopy, the longer decay time of BMVC in G-quadruplex H24 than in duplex DNA allowed us to map the G-quadruplex structure in human metaphase chromosomes.

G-quadruplexes: targets in anticancer drug design

G-quadruplexes are special secondary structures adopted in some guanine-rich DNA sequences. As guanine-rich sequences are present in important regions of the eukaryotic genome, such as telomeres and the regulatory regions of many genes, such structures may play important roles in the regulation of biological events in the body. G-quadruplexes have become valid targets for new anticancer drugs in the past few decades. Many leading compounds that target these structures have been reported, and a few of them have entered preclinical or clinical trials. Nonetheless, the selectivity of this kind of antitumor compound has yet to be improved in order to suppress the side effects caused by nonselective binding. As drug design targets, the topology and structural characteristics of quadruplexes, their possible biological roles, and the modes and sites of small-ligand binding to these structures should be understood clearly. Herein we provide a summary of published research that has set out to address the above problem to provide useful information on the design of small ligands that target G-quadruplexes. This review also covers research methodologies that have been developed to study the binding of ligands to G-quadruplexes.

Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule

We have introduced a G-quadruplex-binding ligand, 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC), to verify the major structure of d(T2AG3)4 (H24) in potassium solution and examine the structural conversion of H24 in sodium solution upon potassium titration. The studies of circular dichroism, induced circular dichroism, spectral titration and gel competition have allowed us to determine the binding mode and binding ratio of BMVC to the H24 in solution and eliminate the parallel form as the major G-quadruplex structure. Although the mixed-type form could not be eliminated as a main component, the basket and chair forms are more likely the main components of H24 in potassium solution. In addition, the circular dichroism spectra and the job plots reveal that a longer telomeric sequence d(T2AG3)13 (H78) could form two units of G4 structure both in sodium or potassium solutions. Of particular interest is that no appreciable change on the induced circular dichroism spectra of BMVC is found during the change of the circular dichroism patterns of H24 upon potassium titration. Considering similar spectral conversion detected for H24 and a long sequence H78 together with the G4 structure stabilized by BMVC, it is therefore unlikely that the rapid spectral conversion of H24 and H78 is due to structural change between different types of the G4 structures. With reference to the circular dichroism spectra of d(GAA)7 and d(GAAA)5, we suggest that the spectral conversion of H24 upon potassium titration is attributed to fast ion exchange resulting in different loop base interaction and various hydrogen bonding effects.

A fluorescent carbazole derivative: high sensitivity for quadruplex DNA

We have synthesized a novel molecule, 3,6-bis(1-methyl-4-vinylpyridium)carbazole diiodide (BMVC), for recognizing specific quadruplex structures, particularly the quadruplex of human telomeric sequence d(T(2)AG(3))(4). The fluorescence intensity of the BMVC molecule increases from 1 to almost 2 orders of magnitude upon interacting with various DNAs. At a concentration of BMVC of 10 microM, fluorescence bands with different colors of BMVC in electrophoresis gels of various DNAs can be observed. The fluorescence of BMVC can be used to discriminate between duplex and quadruplex DNAs. At the low concentration of 0.1 microM BMVC in prestained gels, the fluorescence is observed in the presence of quadruplexes with anti-anti-anti-anti and anti-anti-syn-syn arrangements. However, no fluorescence band is detected upon interacting with duplexes and quadruplexes with anti-syn-anti-syn arrangement. Moreover, the sensitivity assays show that as little as 0.2 pmol of quadruplex of d(T(2)AG(3))(4) can be revealed by BMVC.