Specific Recognition of Promoter G-Quadruplex DNAs by Small Molecule Ligands and Light-up Probes

G-Quadruplexes (G4s) are four-stranded nucleic acid structures whose underlying G-rich sequences are present across the chromosome and transcriptome. These highly structured elements are known to regulate many key biological functions such as replication, transcription, translation, and genomic stability, thereby providing an additional layer of gene regulation. G4s are structurally dynamic and diverse, and they can fold into numerous topologies. They are potential targets for small molecules, which can modulate their functions. To this end, myriad classes of small molecules have been developed and studied for their ability to bind and stabilize these unique structures. Though many of them can selectively target G4s over duplex DNA, only a few of them can distinguish one G4 topology from others. Design and development of G4-specific ligands are challenging owing to the subtle structural variations among G4 structures. However, screening assays and computational methods have identified a few classes of ligands that preferentially or specifically target the G4 topology of interest over others. This review focuses on the small molecules and fluorescent probes that specifically target human promoter G4s associated with oncogenes. Targeting promoter G4s could circumvent the issues such as undruggability and development of drug resistance associated with the protein targets. The ligands discussed here highlight that development of G4-specific ligands is an achievable goal in spite of the limited structural data available. The future goal is to pursue the development of G4-specific ligands endowed with drug-like properties for G4-based therapeutics and diagnostics

Gas-Phase Synthesis for Label-Free Biosensors: Zinc-Oxide Nanowires Functionalized with Gold Nanoparticles

Metal oxide semiconductor nanowires have important applications in label-free biosensing due to their ease of fabrication and ultralow detection limits. Typically, chemical functionalization of the oxide surface is necessary for specific biological analyte detection. We instead demonstrate the use of gas-phase synthesis of gold nanoparticles (Au NPs) to decorate zinc oxide nanowire (ZnO NW) devices for biosensing applications. Uniform ZnO NW devices were fabricated using a vapor-solid-liquid method in a chemical vapor deposition (CVD) furnace. Magnetron-sputtering of a Au target combined with a quadrupole mass filter for cluster size selection was used to deposit Au NPs on the ZnO NWs. Without additional functionalization, we electrically detect DNA binding on the nanowire at sub-nanomolar concentrations and visualize individual DNA strands using atomic force microscopy (AFM). By attaching a DNA aptamer for streptavidin to the biosensor, we detect both streptavidin and the complementary DNA strand at sub-nanomolar concentrations. Au NP decoration also enables sub-nanomolar DNA detection in passivated ZnO NWs that are resilient to dissolution in aqueous solutions. This novel method of biosensor functionalization can be applied to many semiconductor materials for highly sensitive and label-free detection of a wide range of biomolecules

Efficiency of Organelle Capture by Microtubules as a Function of Centrosome Nucleation Capacity: General Theory and the Special Case of Polyspermia

Transport of organelles along microtubules is essential for the cell metabolism and morphogenesis. The presented analysis derives the probability that an organelle of a given size comes in contact with the microtubule aster. The question is asked how this measure of functionality of the microtubule aster is controlled by the centrosome. A quantitative model is developed to address this question. It is shown that for the given set of cellular parameters, such as size and total tubulin content, a centrosome nucleation capacity exists that maximizes the probability of the organelle capture. The developed general model is then applied to the capture of the female pronucleus by microtubules assembled on the sperm centrosome, following physiologically polyspermic fertilization. This application highlights an unintuitive reflection of nonlinearity of the nucleated polymerization of the cellular pool of tubulin. The prediction that the sperm centrosome should lower its nucleation capacity in the face of the competition from the other sperm is a stark illustration of the new optimality principle. Overall, the model calls attention to the capabilities of the centrosomal pathway of regulation of the transport-related functionality of the microtubule cytoskeleton. It establishes a quantitative and conceptual framework that can guide experiment design and interpretation

Qualitative SERS analysis of G-quadruplex DNAs using selective stabilising ligands

Nucleic acids are of key biological importance due to their range of functions and ability to form various different structures, with an example of emerging significance being quadruplexes formed by guanine-rich sequences. These guanine rich sequences are found in different regions of the genome such as telomeres, gene promoters and introns and UTRs of mRNAs. Here a new approach has been developed that utilises surface enhanced Raman scattering (SERS) for the detection of the formation of G-quadruplexes. Three G-quadruplex stabilising ligands that each have their own unique SERS response were used in this study and their ability to act as reporters assessed. A SERS response was only obtained from the ligands in the absence of G-quadruplex formation. This resulted in an "on/off" method which was successfully used to qualitatively detect the formation of G-quadruplex using quadruplex-forming sequences such as human telomeric and C-MYC promoter DNAs. The unique SERS spectra of each stabilising ligand offer the potential for use of SERS to study higher order DNA structures. This work shows that the ligands used can act simultaneously as a potential therapeutic stabilising agent and a SERS reporter, therefore allowing the use of SERS as a method of analysis of the formation of G-quadruplex DNAs