Nannan Liu

Two-Way Nanopore Sensing of Sequence-Specific Oligonucleotides and Small-Molecule Targets in Complex Matrices Using Integrated DNA Supersandwich Structures†

Recent advances in molecular science and nanotechnology offer unprecedented opportunities to miniaturize chemical analysis systems into nanofluidic devices that mimic ion channels and have single-molecule sensitivity, target-specific selectivity, and reduced consumption of materials. When analytes are present in the nanofluidic sensing system, they temporarily or permanently block the pathway for ion conduction, yielding characteristic changes in background current that serves as a signature for target identification, or concentration qualification. Although the sensitivity approaches a relatively high level, this technique is still challenging for treating multi-component or complex clinic samples. In recent years, the sequence-specific and label-free detection of DNA targets associated with many crucial pathogenic diseases has attracted a broad interest. To meet the requirements of this application, these nanofluidic devices have been endowed with chemical selectivity by integration with nucleic-acid-based sensing elements. For example, simple-structured DNA components were used for oligonucleotide detection using the hybridization technique. Intermolecular DNA duplexes, forming T-Hg-T structures, have been used for nanopore-based sensing of mercury. We used DNA molecular motors, showing a conformational change in response to external stimuli, to construct adaptive DNA-nanopore switches. In conventional DNA-based nanopore sensors, a single capture DNA hybridizes to a single target strand or binds to a single molecular target (Figure 1, insert), which restricts their performance. On the

Real-Time, Quantitative Lighting-up Detection of Telomerase in Urines of Bladder Cancer Patients by AIEgens

As a biomarker for early cancer diagnosis, telomerase are one of the promising targets for cancer therapeutics. Inspired by the fluorescent emission principle of aggregation-induced emission fluorogens, we creatively designed an AIE-based turn-on method to detect telomerase activity from cell extracts. A positively charged fluorogen (TPE-Z) is not fluorescent when freely diffused in solution. The fluorescence of TPE-Z is enhanced with the elongation of the DNA strand which could light up telomere elongation process. By exploitation of it, we can detect telomerase activity from different cell lines (E-J, HeLa, MCF-7, and HLF) with high sensitivity and specificity. Moreover, our method is successfully employed to demonstrate the applications in bladder cancer diagnosis (41 urine specimens from bladder cancer patients and 15 urine specimens from normal people are detected). The AIE-based method provides a simple one-pot technique for quantification and monitoring of the telomerase activity and shows great potential for future use in clinical tests.

Target-Specific 3D DNA Gatekeepers for Biomimetic Nanopores

3D cross-linked DNA superstructures switch off the ionic flux through solid-state nanopores with extremely high ON-OFF ratios of 10(3) -10(5) . This gating mechanism can be generally applicable in a wide range of nanopores with opening diameters up to 650 nm. The 3D bio-supramolecular gatekeepers outperform previous low-dimensional or simple-structured DNA functional components.

Electrochemical biocomputing: a new class of molecular-electronic logic devices

Biocomputing, a subarea of unconventional chemical computing, is performed by DNA, protein/enzymes, and other living organisms. Recently, various biomolecular logic gates employing optical changes or PAGE measurements have been studied intensively using various inputs. However, the low detection speed, which is an inherent characteristic of the PAGE method, has prevented it from being developed technologically. Most of the biomolecular logic gates reported to date are mainly based on fluorescence, phosphorescence, or colorimetric outputs, which are laborious, time-consuming, and unsuitable for directly detecting subtle structures. They also suffer the limitations of cumbersomely interfacing the optical outputs with nonmolecular-based technologies. In this context, biomolecular assisted electrochemistry is one of the most popular techniques due to the combined advantages of high sensitivity, specificity, small volume requirements, low cost, and the possibility of mass production via the microelectronic industry. In addition, it is necessary that the future of molecular logic gates elements is strongly related to the successful linkage of molecules onto a conductive or semiconductive support. In this highlight, we will focus on the bioelectronic computing devices based on DNA, enzymes, and biofuel cells.

Regulation of DNA self-assembly and DNA hybridization by chiral molecules with corresponding biosensor applications.

Chirality is one of the fundamental biochemical properties in a living system, and a lot of biological and physiological processes are greatly influenced by the chirality of molecules. Inspired by this phenomenon, we study the covalent assembly of DNA on chiral molecule modified surfaces and further discuss the hybridization of DNA on chiral surfaces with nucleic acids. Take methylene blue (MB) modified DNA as a model molecule, we show that the peak current of the L-NIBC (NIBC, N-isobutyryl-L(D)-cysteine) modified gold surface (L-surface) is larger than the D-surface because of a stronger interaction between short-chain DNA and the L-surface; however, the D-surface has a higher hybridization efficiency than the L-surface. Moreover, we apply this result to actual application by choosing an electrochemical DNA (E-DNA) sensor as a potential platform. Furthermore, we further amplify the difference of hybridization efficiency using the supersandwich assay. More importantly, our findings are successfully employed to program the sensitivity and limit of detection.

Imparting biomolecules to a metal-organic framework material by controlled DNA tetrahedron encapsulation

Recently, the incorporation of biomolecules in Metal-organic frameworks (MOFs) attracts many attentions because of controlling the functions, properties and stability of trapped molecules. Although there are few reports on protein/MOFs composites and their applications, none of DNA/MOFs composite is reported, as far as we know. Here, we report a new composite material which is self-assembled from 3D DNA (guest) and pre-synthesized MOFs (host) by electrostatic interactions and hydrophilic interactions in a well-dispersed fashion. Its biophysical characterization is well analyzed by fluorescence spectroscopy, quartz crystal microbalance (QCM) and transmission electron microscopy (TEM). This new composite material keeps 3D DNA nanostructure more stable than only 3D DNA nanostructure in DI water at room temperature, and stores amounts of genetic information. It will make DNA as a guest for MOFs and MOFs become a new platform for the development of DNA nanotechnology.

Nanopore-Based DNA-Probe Sequence-Evolution Method Unveiling Characteristics of Protein–DNA Binding Phenomena in a Nanoscale Confined Space

Almost all of the important functions of DNA are realized by proteins which interact with specific DNA, which actually happens in a limited space. However, most of the studies about the protein-DNA binding are in an unconfined space. Here, we propose a new method, nanopore-based DNA-probe sequence-evolution (NDPSE), which includes up to 6 different DNA-probe systems successively designed in a nanoscale confined space which unveil the more realistic characteristics of protein-DNA binding phenomena. There are several features; for example, first, the edge-hindrance and core-hindrance contribute differently for the binding events, and second, there is an equilibrium between protein-DNA binding and DNA-DNA hybridization.

DNA hybridization chain reaction and DNA supersandwich self-assembly for ultrasensitive detection

The fabrication of sensitive sensors with high selectivity is highly desirable for the detection of some important biomarkers, such as nucleic acids, proteins, small molecules and ions. DNA hybridization chain reaction (HCR) and DNA supersandwich self-assembly (SSA) are two prevalent enzyme-free signal amplification strategies to improve sensitivity of the sensors. In this review, we firstly describe the characteristics about DNA HCR and DNA SSA, and then summarize the advances in the one-dimensional DNA nanostructures assisted by HCR and SSA. This review has been divided into three parts according to the two signal amplification methods and highlights recent progress in these two strategies to improve the detection sensitivity of proteins, nucleic acids, small molecules and ions.