Ruixue Duan

Lab in a tube: ultrasensitive detection of microRNAs at the single-cell level and in breast cancer patients using quadratic isothermal amplification.

Through rational design of a functional molecular probe with high sequence specificity that takes advantage of sensitive isothermal amplification with simple operation, we developed a one-pot hairpin-mediated quadratic enzymatic amplification strategy for microRNA (miRNA) detection. Our method exhibits ultrahigh sensitivity toward miR-21 with detection limits of 10 fM at 37 °C and 1 aM at 4 °C, which corresponds to nine strands of miR-21 in a 15 μL sample, and it is capable of distinguishing among miRNA family members. More importantly, the proposed approach is also sensitive and selective when applied to crude extractions from MCF-7 and PC3 cell lines and even patient tissues from intraductal carcinoma and invasive ductal carcinoma of the breast.

Sensitive and Bidirectional Detection of Urine Telomerase Based on the Four Detection-Color States of Difunctional Gold Nanoparticle Probe

Telomerase, a valuable biomarker, is highly correlated with the development of most of human cancers. Here, we develop a bidirectional strategy for telomerase activity detection and bladder cancer diagnosis based on four detection-color states of difunctional gold nanoparticle (GNP) probes such as blue, purple, red, and precipitate. Specifically, we define the red GNP probe as origin, which represents urine extracts with inactive telomerase and implies normal individuals. The forward direction is corresponding to the detection of a relatively high concentration of active telomerase, in which system GNP probes assemble obviously and precipitate, predicting bladder cancer samples. The negative direction is corresponding to extracts with a relatively low concentration (purple) and without any telomerase (blue), which can be differentiated by naked eyes or UV-vis spectrum, indicating bladder cancer and normal individuals, respectively. More importantly, this noninvasive strategy shows great sensitivity and selectivity when tested by 18 urine specimens from bladder cancer patients, inflammation, and normal individuals.

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.

Combining Protein and miRNA Quantification for Bladder Cancer Analysis

We combine the telomerase extension reaction and microRNA (miRNA)-induced rolling circle amplification, followed by graphene oxide (GO) and nicking enzyme-assisted signal amplification as a method to analyze telomerase and miRNA-21 in urine samples with the following merits. First, it is a binary assay and can simultaneously output double signals that correspond to the quantities of telomerase and miRNA, respectively. Second, telomerase activity is enhanced by using a DNA molecular beacon probe to inhibit the formation of G-quadruplex. Third, background noise is decreased significantly via introduction of GO. Fourth, performance tests on about 258 urine samples demonstrate that this binary assay can distinguish between urine from bladder cancer patients, those with cystitis, and normal individuals. Finally, this strategy also shows great potential in distinguishing between muscle-invasive bladder cancers and non-muscle-invasive bladder cancers. The proposed strategy will greatly contribute to clinical decision-making and individualized treatments.