Analysis of non-canonical three- and four-way DNA junctions

Switching on Supramolecular DNA Junction Binding Using a Human Enzyme

Non-canonical DNA junction structures are important in human disease and in nucleic acid nanoscience and there is a growing interest in how to bind and modulate them. A key next step is to exert "on command" control over such binding. Herein we develop a new metallo-supramolecular triple-helicate cylinder agent that is inert to DNA junction binding until activated by human enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1) and its cofactor nicotinamide adenine dinucleotide phosphate (NADPH). This inactive cylinder bears six flexible arms each with a quinone group at the termini. Reduction by the enzyme leads to all six arms being removed, transforming the inert cylinder into a new and active metallo-supramolecular agent that binds junctions. This gives the ability to "switch-on" DNA junction formation and binding in response to the presence of two external stimuli - a human enzyme overexpressed in many disease states, and NADPH - and absence of inhibitor, giving NAND logic control. Modelling indicates the binding activation originates not in steric unblocking but changes in conformational flexibility. The work provides the foundation for and a route map toward future designs of sophisticated, inert, and supramolecular structures which are transformed by enzymes into new, active, and supramolecular structures for a variety of potential applications.

Supramolecular Recognition of a DNA Four-Way Junction by an M2L4 Metallo-Cage, Inspired by a Simulation-Guided Design Approach

DNA four-way junctions (4WJs) play an important biological role in DNA repair and recombination, and viral regulation, and are attractive therapeutic targets. Compounds that recognise the junction structure are rare; in this work, we describe cationic metallo-supramolecular M2L4 cages as a new type of 4WJ binder with nanomolar affinities. A combination of molecular dynamics (MD) simulations and biophysical experiments show that the size and shape of a compound comprising square planar Pd or Pt and anthracene-based ligands is an excellent fit for the 4WJ cavity. Whilst the cage is also capable of binding to three-way junctions (3WJs) and Y-fork structures, we show that the 4WJ is the preferred DNA target, and that duplex B-DNA is not a competitor. Among 3WJs, T-shape bulged 3WJs are bound more preferably than perfect Y-shaped 3WJs. Whilst previous work studying M2L4 metallo-supramolecular cages has focused on binding inside their structures, this work exploits the external aromatic surfaces of the supramolecule, creating a supramolecular guest that ideally matches the DNA host cavity. This approach allows available structures to be identified as potential junction binders and then screened for their fit to a nucleic acid junction target using simulations. This has potential to significantly accelerate discovery.

Design and in vitro anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease

Copper compounds with artificial metallo-nuclease (AMN) activity are mechanistically unique compared to established metallodrugs. Here, we describe the development of a new dinuclear copper AMN, Cu2-BPL-C6 (BPL-C6 = bis-1,10-phenanthroline-carbon-6), prepared using click chemistry that demonstrates site-specific DNA recognition with low micromolar cleavage activity. The BPL-C6 ligand was designed to force two redox-active copper centres-central for enhancing AMN activity-to bind DNA, via two phenanthroline ligands separated by an aliphatic linker. DNA-binding experiments, involving circular dichroism spectroscopy, agarose gel electrophoresis and fluorescence quenching, revealed a preference for binding with adenine-thymine-rich DNA. The oxidative cleavage mechanism of Cu2-BPL-C6 was then elucidated using in vitro molecular and biophysical assays, including in-liquid atomic force microscopy analysis, revealing potent DNA cleavage mediated via superoxide and hydrogen peroxide oxidative pathways. Single-molecule analysis with peripheral blood mononuclear cells identified upregulated single-strand DNA lesions in Cu2-BPL-C6-treated cells. Using specific base excision repair (BER) enzymes, we showed that Endo IV selectively repairs these lesions indicating that the complex generates apurinic and apyrimidinic adducts. Broad spectrum anticancer evaluation of BPL-C6 was performed by the National Cancer Institute's 60 human cell line screen (NCI-60) and revealed selectivity for certain melanoma, breast, colon and non-small cell lung cancer cell lines.

An ultrasensitive liquid crystal aptasensing chip assisted by three-way junction DNA pockets for acrylamide detection in food samples

Acrylamide, an unsaturated amide found in heat-processed foods, poses serious risks to human health due to its neurotoxicity, carcinogenicity, and genotoxicity. This highlights the importance of quantitative determination of acrylamide in foods and the environments to ensure public health safety. Therefore, there is an urgent need for simple, rapid, and highly sensitive methods to accurately quantify acrylamide. In the present study, a user-friendly aptasensor was designed to quantify ultra-low levels of acrylamide in nuts for the first time. This innovative approach utilizes chemical engineering of a glass slide as a portable sensing platform, which incorporates liquid crystal (LC) molecules and a three-way junction (TWJ) DNA pocket. The immobilized TWJ pocket can disrupt the vertical alignment of LCs, turning the dark polarized background of the aptasensor to a colorful state. The binding of the specific aptamer to acrylamide disrupts the TWJ structure, enabling the LCs to return to their homotropic alignment. This structural change restores the dark polarized view of the sensing platform. The TWJ-engineered LC aptasensor effectively detects ultra-low concentrations of acrylamide in the range of 0.0005 to 50 fmol/L, with a detection limit of 0.106 amol/L. The aptasensor was successfully applied to real roasted nut samples, including peanut, almond, pistachio, and hazelnut, achieving recovery values ranging from 96.84 % to 99.61 %. With its simplicity, portability, ease of use, and cost-effectiveness, this aptasensor is a powerful sensing device for food safety monitoring.

Gene Editing with Artificial DNA Scissors

Artificial metallo-nucleases (AMNs) are small molecule DNA cleavage agents, also known as DNA molecular scissors, and represent an important class of chemotherapeutic with high clinical potential. This review provides a primary level of exploration on the concepts key to this area including an introduction to DNA structure, function, recognition, along with damage and repair mechanisms. Building on this foundation, we describe hybrid molecules where AMNs are covalently attached to directing groups that provide molecular scissors with enhanced or sequence specific DNA damaging capabilities. As this research field continues to evolve, understanding the applications of AMNs along with synthetic conjugation strategies can provide the basis for future innovations, particularly for designing new artificial gene editing systems.

A copper(ii) peptide helicate selectively cleaves DNA replication foci in mammalian cells

The use of copper-based artificial nucleases as potential anticancer agents has been hampered by their poor selectivity in the oxidative DNA cleavage process. An alternative strategy to solve this problem is to design systems capable of selectively damaging noncanonical DNA structures that play crucial roles in the cell cycle. We designed an oligocationic CuII peptide helicate that selectively binds and cleaves DNA three-way junctions (3WJs) and induces oxidative DNA damage via a ROS-mediated pathway both in vitro and in cellulo, specifically at DNA replication foci of the cell nucleus, where this DNA structure is transiently generated. To our knowledge, this is the first example of a targeted chemical nuclease that can discriminate with high selectivity 3WJs from other forms of DNA both in vitro and in mammalian cells. Since the DNA replication process is deregulated in cancer cells, this approach may pave the way for the development of a new class of anticancer agents based on copper-based artificial nucleases.