Single-Molecule Analysis of Human Telomere Sequence Interactions with G-quadruplex Ligand

Nanopore-Based Single-Molecule Investigation of Cation Effect on the i-Motif Structure

The i-motif, a secondary structure of a four-helix formed by cytosine-rich DNA (i-DNA) through C-C+ base pairing, is prevalent in human telomeres and promoters. This structure creates steric hindrance, thereby inhibiting both gene expression and protein coding. The conformation of i-DNA is intricately linked to the intracellular ionic environment. Hence, investigating its conformation under various ion conditions holds significant importance. In this study, we explored the impact of cations on the i-motif structure at the single-molecule level using the α-hemolysin (α-HL) nanochannel. Our findings reveal that the ability of i-DNA to fold into the i-motif structure follows the order Cs+ > Na+ > K+ > Li+ for monovalent cations. Furthermore, we observed the interconversion of single-stranded DNA (ss-DNA) and the i-motif structure at high and low concentrations of Mg2+ and Ba2+ electrolyte solutions. This study not only has the potential to extend the application of i-motif-based sensors in complex solution environments but also provides a new idea for the detection of metal ions.

Application of nanopore sensors for biomolecular interactions and drug discovery

Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.

Split G-Quadruplexes Enhance Nanopore Signals for Simultaneous Identification of Multiple Nucleic Acids

Assembly of DNA structures based on hybridization like split G-quadruplex (GQ) have great potential for the base-pair specific identification of nucleic acid targets. Herein, we combine multiple split G-quadruplex (GQ) assemblies on designed DNA nanostructures (carrier) with a solid-state nanopore sensing platform. The split GQ probes recognize various nucleic acid sequences in a parallel assay that is based on glass nanopore analysis of molecular structures. Specifically, we split a GQ into two asymmetric parts extended with sequences complementary to the target. The longer G-segment is in solution, and the shorter one is on a DNA carrier. If the target is present, the two separate GQ parts will be brought together to facilitate the split GQ formation and enhance the nanopore signal. We demonstrated detection of multiple target sequences from different viruses with low crosstalk. Given the programmability of this DNA based nanopore sensing platform, it is promising in biosensing.

G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands

Noncanonical nucleic acid structures, such as G-quadruplex (G4) and i-Motif (iM), have attracted increasing research interests because of their unique structural and binding properties, as well as their important biological activities. To date, thousands of small molecules that bind to varying G4/iM structures have been designed, synthesized and tested for diverse chemical and biological uses. Because of the huge potential and increasing research interests on G4-targeting ligands, we launched the first G4 ligand database G4LDB in 2013. Here, we report a new version, termed G4LDB 2.2 (http://www.g4ldb.com), with upgrades in both content and function. Currently, G4LDB2.2 contains >3200 G4/iM ligands, ∼28 500 activity entries and 79 G4–ligand docking models. In addition to G4 ligand library, we have also added a brand new iM ligand library to G4LDB 2.2, providing a comprehensive view of quadruplex nucleic acids. To further enhance user experience, we have also redesigned the user interface and optimized the database structure and retrieval mechanism. With these improvements, we anticipate that G4LDB 2.2 will serve as a comprehensive resource and useful research toolkit for researchers across wide scientific communities and accelerate discovering and validating better binders and drug candidates.

Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures

i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3-10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.

Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs)

Mechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using a single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg²⁺ and the key tertiary interactions. The absence of Mg²⁺ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structures in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations in combination with force distribution analysis. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.

A conformational switch-based fluorescent biosensor for homogeneous detection of telomerase activity

As a universal tumor biomarker, research on the activity and inhibition of telomerase is of great importance for cancer diagnosis and therapy. Herein, we demonstrate the conformational switch-based fluorescence detection of telomerase activity using a redesigned RNA aptamer Spinach. Briefly, the original Spinach aptamer was extended at its 5' end and folded into an inactive conformation, where association with the small molecule fluorophore, 5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) was prevented. Only in the presence of telomerase, (TTAGGG)_n repeats were added to the 3' end of the telomerase substrate primer, and the elongation products hybridized with inactive Spinach molecules, triggering its conformational switch and refolding it into the active, DFHBI-binding conformation. Moreover, the fluorescence signal was further amplified through a target recycling circuit, where Ribonuclease H (RNase H) specifically hydrolyzed the phosphodiester bonds of RNA in the DNA-RNA hybrid. The released telomere products could then hybridize to new inactive Spinach molecules and initiate multiple amplification cycles. The proposed fluorescent biosensor presented great performance for telomerase activity detection from 100 to 5 × 10⁴ Hela cells with a detection limit of 100 cells. Besides, this new assay offers a good biosensing platform for differentiation of cancer cell lines from normal cell line and evaluation the inhibition efficiency of telomere-binding ligand, which is of great importance for telomerase-related cancer diagnosis and therapy.

Single-molecule counting of oxidative DNA damage in telomeres from cancer cells

We demonstrate for the first time the single-molecule counting of oxidative DNA damage in telomeres from cancer cells.

Integrated Solid-State Nanopore Electrochemistry Array for Sensitive, Specific, and Label-Free Biodetection

Nanopore ionic current measurement is currently a prevailing readout and offers considerable opportunities for bioassays. Extending conventional electrochemistry to nanoscale space, albeit noteworthy, remains challenging. Here, we report a versatile electrochemistry array established on a nanofluidic platform by controllably depositing gold layers on the two outer sides of anodic aluminum oxide (AAO) nanopores, leading to form an electrochemical microdevice capable of performing amperometry in a label-free manner. Electroactive species ferricyanide ions passing through gold-decorated nanopores act as electrochemical indicator to generate electrolytic current signal. The electroactive species flux that dominates current signal response is closely related to the nanopore permeability. Such well-characteristic electrolytic current-species flux correlation lays a premise for quantitative electrochemical analysis. As a proof-of-concept demonstration, we preliminarily verify the analytical utility by detection of nucleic acid and protein at picomolar concentration levels. Universal surface modification and molecule assembly, specific target recognition and reliable signal output in nanopore enable direct electrochemical detection of biomolecules without the need of cumbersome probe labeling and signal amplification.

Insight into How Telomeric G-Quadruplexes Enhance the Peroxidase Activity of Cellular Hemin

The toxic oxidative damage of G-quadruplexes (G4), linked to neurodegenerative diseases, may arise from their ability to bind and oxidatively activate cellular hemin. However, there have been no precise studies on how telomeric G4 enhances the low intrinsic peroxidase activity of hemin. Herein, a label-free and nanopore-based strategy was developed to explore the enhancement mechanism of peroxidase activity of hemin induced by telomeric G4 (d(TTAGGG)n ). The nanopore-based strategy demonstrated that there were simultaneously two different binding modes of telomere G4 to hemin. At the single-molecule level, it was found that the hybrid structural telomeric G4 directly binds to hemin (the affinity constant (Ka )≈106  m-1 ) to form a tight complex, and some of them underwent a topological change to a parallel structure with an enhancement of Ka to approximately 107  m-1 . Through detailed analysis of the topology and peroxidase activity and molecular modeling investigations, the parallel telomere G4/hemin DNAzyme structure was proven to be preferable for high peroxidase activity. Upon strong π-π stacking, the parallel structural telomere G4 supplied a key axial ligand to the hemin iron, which accelerated the intermediate compound formation with H2 O2 in the catalytic cycle. Our studies developed a label-free and single-molecule strategy to fundamentally understand the catalytic activity and mechanism of telomeric DNAzyme, which provides some support for utilizing the toxic, oxidative-damage property in cellular oxidative disease and anticancer therapeutics.

Nanopore biosensor for sensitive and label-free nucleic acid detection based on hybridization chain reaction amplification

A label-free nanopore biosensor for detection of DNA target is proposed utilizing hybridization chain reaction (HCR) strategy for signal amplification. The DNA target triggered HCR to form large DNA nanostructure inside the nanopore and out the nanopore membrane, which inducing the ionic current decrease effectively due to the blockage of the nanopore. The developed method achieves a desirable sensitivity of 30fM with a wide linear dynamic range from 0.1 to 10pM and demonstrated good application for real sample analysis. This work has great potential to be applied in the early diagnosis of gene-related diseases and provide a new paradigm for label-free nucleic acid amplification strategy in ultrasensitive nanopore biosensor.

Label-Free Nanopore Biosensor for Rapid and Highly Sensitive Cocaine Detection in Complex Biological Fluids

Detection of very low amounts of illicit drugs such as cocaine in clinical fluids like serum continues to be important for many areas in the fight against drug trafficking. Herein, we constructed a label-free nanopore biosensor for rapid and highly sensitive detection of cocaine in human serum and saliva samples based on target-induced strand release strategy. In this bioassay, an aptamer for cocaine was prehybridized with a short complementary DNA. Owing to cocaine specific binding with aptamer, the short DNA strand was displaced from aptamer and translocation of this output DNA through α-hemolysin nanopore generated distinct spike-like current blockages. When plotted in double-logarithmic scale, a linear relationship between target cocaine concentration and output DNA event frequency was obtained in a wide concentration range from 50 nM to 100 μM of cocaine, with the limit of detection down to 50 nM. In addition, this aptamer-based sensor method was successfully applied for cocaine detection in complex biological fluids like human saliva and serum samples with great selectivity. Simple preparation, low cost, rapid, label-free, and real sample detection are the motivating factors for practical application of the proposed biosensor.