Environment-Sensitive Probes Containing a 2,6-Diethynylpyridine Motif for Fluorescence Turn-On Detection and Induction of Nanoarchitectures of Human Telomeric Quadruplex

Triazolyl Dibenzo[a,c]phenazines Stabilize Telomeric G-quadruplex and Inhibit Telomerase

We herein report the synthesis and biophysical evaluation of triazolyl dibenzo[a,c]phenazine derivatives as a novel class of G-quadruplex ligands. The aromatic core facilitates π-π interaction and the flexible, protonatable side chains interact with the phosphate backbone of DNA via electrostatic interactions. Förster resonance energy transfer (FRET) melting assay and isothermal titration calorimetry (ITC) studies suggest that these ligands show binding preference for the hTELO G-quadruplex over G-quadruplexes found in the promoter region of various oncogenes and duplex DNA. The in vitro telomeric repeat amplification protocol (Q-TRAP) assay reveals that these ligands reduce telomerase activity in cancer cells.

Space-confined indicator displacement assay inside a metal-organic framework for fluorescence turn-on sensing

The indicator displacement assay (IDA) is for the first time performed within a metal-organic framework (MOF) to achieve ultrasensitive fluorescence turn-on sensing. A Zr(iv) ion MOF (UiO-67-DQ-PsO) furnished with electron-deficient diquat units (DQ2+, as the receptor) on the wall and electron-rich 1-pyrenesulfonate anions (PsO-, as the fluorescent indicator) in the pores was prepared by postsynthetic anion exchange. The MOF is capable of sensing alkylamines owing to the competing PsO--DQ2+ and alkylamine-DQ2+ charge-transfer interactions, the former interaction causing a fluorescence OFF state and the latter displacing PsO- to trigger its emission. Significant advantages have been demonstrated for the IDA inside the MOF. The turn-on assay exhibits much higher sensitivity and anti-interference than the turn-off sensing using the MOF without indicators (the sensitivity is enhanced by as much as six orders of magnitude to the subnanomolar level). The integration of both the receptor and indicator in the porous solid enables facile regeneration and recyclability of the IDA ensemble. Furthermore, we show that the confined space provided by the MOF significantly enhances the supramolecular interactions to make possible the IDA impossible in solution. This work not only demonstrates a novel conceptual approach to fabricate superior fluorescence turn-on sensors using porous materials but also has important implications for supramolecular chemistry in porous materials.

DNA Quadruple Helices in Nanotechnology

DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.

Target guided synthesis using DNA nano-templates for selectively assembling a G-quadruplex binding c-MYC inhibitor

The development of small molecules is essential to modulate the cellular functions of biological targets in living system. Target Guided Synthesis (TGS) approaches have been used for the identification of potent small molecules for biological targets. We herein demonstrate an innovative example of TGS using DNA nano-templates that promote Huisgen cycloaddition from an array of azide and alkyne fragments. A G-quadruplex and a control duplex DNA nano-template have been prepared by assembling the DNA structures on gold-coated magnetic nanoparticles. The DNA nano-templates facilitate the regioselective formation of 1,4-substituted triazole products, which are easily isolated by magnetic decantation. The G-quadruplex nano-template can be easily recovered and reused for five reaction cycles. The major triazole product, generated by the G-quadruplex inhibits c-MYC expression by directly targeting the c-MYC promoter G-quadruplex. This work highlights that the nano-TGS approach may serve as a valuable strategy to generate target-selective ligands for drug discovery.

Identification of inhibitors can be accelerated by using the target as a template for ligand formation. Here the authors show that DNA-functionalised magnetic nanoparticles guide templating of G-quadruplex binding c-MYC inhibitors from an array of building blocks, and can be isolated by magnetic decanting.

Selective recognition of c-MYC G-quadruplex DNA using prolinamide derivatives

Herein we report the design, synthesis, biophysical and biological evaluation of triazole containing prolinamide derivatives as selectivec-MYCG-quadruplex binding ligands.

A Nucleus-Imaging Probe That Selectively Stabilizes a Minor Conformation of c-MYC G-quadruplex and Down-regulates c-MYC Transcription in Human Cancer Cells

The c-MYC proto-oncogene is a regulator of fundamental cellular processes such as cell cycle progression and apoptosis. The development of novel c-MYC inhibitors that can act by targeting the c-MYC DNA G-quadruplex at the level of transcription would provide potential insight into structure-based design of small molecules and lead to a promising arena for cancer therapy. Herein we report our finding that two simple bis-triazolylcarbazole derivatives can inhibit c-MYC transcription, possibly by stabilizing the c-MYC G-quadruplex. These compounds are prepared using a facile and modular approach based on Cu(I) catalysed azide and alkyne cycloaddition. A carbazole ligand with carboxamide side chains is found to be microenvironment-sensitive and highly selective for "turn-on" detection of c-MYC quadruplex over duplex DNA. This fluorescent probe is applicable to visualize the cellular nucleus in living cells. Interestingly, the ligand binds to c-MYC in an asymmetric fashion and selects the minor-populated conformer via conformational selection.