Performance of nano-assembly logic gates with a DNA multi-hairpin motif

Designing a CRISPR/Cas12a- and Au-Nanobeacon-Based Diagnostic Biosensor Enabling Direct, Rapid, and Sensitive miRNA Detection

Direct, rapid, sensitive, and selective detection of nucleic acids in complex biological fluids is crucial for medical early diagnosis. We herein combine the trans-cleavage ability of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a with Au-nanobeacon to establish a CRISPR-based biosensor, providing rapid miRNA detection with high speed and attomolar sensitivity. In this strategy, we first report that the trans-cleavage activity of CRISPR/cas12a, which was previously reported to be triggered only by target ssDNA or dsDNA, can be activated by the target miRNA directly. Therefore, this method is direct, i.e., does not need the conversion of miRNA into its complementary DNA (cDNA). Meanwhile, as compared to the traditional ssDNA reporters and molecular beacon (MB) reporters, the Au-nanobeacon reporters exhibit improved reaction kinetics and sensitivity. In this assay, the miRNA-21 could be detected with very high sensitivity in only 5 min. Finally, the proposed strategy enables rapid, sensitive, and selective miRNA determination in complex biological samples, providing a potential tool for medical early diagnosis.

Design and Realization of Triple dsDNA Nanocomputing Circuits in Microfluidic Chips

DNA logic gates, nanocomputing circuits, have already implemented basic computations and shown great signal potential for nano logic material application. However, the reaction temperature and computing speed still limit its development. Performing complicated computations requires a more stable component and a better computing platform. We proposed a more stable design of logic gates based on a triple, double-stranded, DNA (T-dsDNA) structure. We demonstrated a half adder and a full adder using these DNA nanocircuits and performed the computations in a microfluidic chip device at room temperature. When the solutions were mixed in the device, we obtained the expected results in real time, which suggested that the T-dsDNA combined microfluidic chip provides a concise strategy for large DNA nanocircuits.

Small RNA Biosensor Design Strategy To Mitigate Off-Analyte Response

Several bottlenecks in the design of current sensor technologies for small noncoding RNA must be addressed. The small size of the sensors and the large number of other nucleotides that may have sequence similarity makes selectivity a real concern. Many of the current sensors have one strand with an exposed region called a toehold. The toehold serves as a place for the analyte nucleic acid strand to bind and initiate competitive displacement of sensors' secondary strands. Since the toehold region is not protected, any endogenous oligonucleotide sequences that are similar or only different by a few nucleic acids will interact with the toehold and cause false signals. To address sensor selectivity, we investigated how the toehold location in the sensor impacts the sensitivity and selectivity for the analyte of interest. We will discuss the differences in sensitivity and selectivity for a miR-146a-5p biosensor in the presence of different naturally occurring mismatch sequences. We found that altering the toehold location lowered the rate of the false signal from off-analyte microRNA by upward of 20 percentage points. Detection limits as low as 56 pM were observed when the sensor concentration was 5 nM. The findings herein are broadly applicable to other small and large RNAs as well as other types of sensing platforms.

Adjusting Linking Strands to Form Size-Controllable DNA Origami Rings

DNA origami is a powerful tool in nanotechnology that can be used to construct arbitrary structures for several nanoengineering applications. Generally, the more complex and sophisticated the construction, the greater is the number of origamis and connection strands that will be needed. Therefore, developing an effective and low-cost method for multiform DNA architecture is important in nanoengineering. Here, we adopted an oblique linking strategy to connect cross-shaped DNA origami with a controlled curing angle. The size of the DNA rings ranged from four blocks of approximately 200 nm to eleven blocks of c.a. 600 nm. We observed that the minimum size of the DNA ring structure was limited by the width of a single block. The largest rings were negatively affected by thermodynamic randomness, and thus, DNA rings consisting of more than eleven blocks were not observed. This strategy facilitates the generation of various DNA origami rings, whose size can be controlled by adjusting the length of the connection strands.

Fluorescent miRNA analysis enhanced by mesopore effects of polydopamine nanoquenchers

The combination of fluorophore-labelled single-strand DNA probes and nanomaterial quenchers has shown great potential in miRNA detection. The development of advanced detection systems by understanding and controlling the fluorescence quenching/recovery via nanoquenchers' microstructures and local morphologies is an attractive area warranting further investigations. Inspired by nanopore sequencing, we present a novel miRNA sensing strategy using fluorophore-labeled DNA as probes and a type of large-pore-sized mesoporous polydopamine nanoparticles (MPDA-L, 70 nm in diameter) as fluorescence quenchers. It is revealed that the quenching efficiency of MPDA-L towards the fluorophore labelled on the probe, reached more than 99% at a relatively low particle concentration. Moreover, the mesopores effectively protected the probe DNA from cleavage by DNase I which was used for signal amplification. Sensitive detection of miRNA with a low detection limit of 32-40 pM, as well as a linear detection range of up to 5 nM, was realized by the mesopore effects via a greatly improved differential affinity of ssDNA and the probe-miRNA heteroduplex toward the surface of nanoquenchers. Interestingly, enhanced DLVO (Derjaguin-Landau-Verwey-Overbeek) repulsion generated inside the pore surface by the negative surface-curvature effect correlates with the improved duplex detachment and fluorescence recovery. The developed strategy can be successfully applied to quantify down-regulated let-7a and up-regulated miRNA-21 in different types of cancer cells by using total RNA samples from cell lysate. These findings are expected to inspire strategies and pave a way for utilizing porous nanomaterials for constructing miRNA detection systems.

More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing

Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.

A chemical/molecular 4-input/2-output keypad lock with easy resettability based on red-emission carbon dots-Prussian blue composite film electrodes

In this work, a resettable 4-input/2-output keypad lock system based on red-emission carbon dots (rCDs) and Prussian blue (PB) modified electrodes was developed. Electrochromic PB layers were first electrochemically deposited on the indium tin oxide (ITO) electrode surface. An admixture of rCDs and chitosan (Chi) was then cast on the surface of PB layers, forming rCDs-Chi/PB film electrodes. UV-vis absorption of the films was sensitive to the applied potential since the blue PB constituent of the films would be transformed to nearly colorless Prussian white (PW) at the reduction potential of -0.2 V and then from PW back to PB at the oxidation potential of 0.4 V, and the transformation between PB and PW would also influence the fluorescence emission of the rCD constituent in the films. The addition of cysteine (Cys) in the testing solution could reduce the PB in the films into PW and generate an amperometric electrocatalytic current at 0.4 V. Meanwhile, the addition of Fe3+ in solution could greatly quench the fluorescence from the rCD component in the films. Thus, the responses of UV-vis absorbance, fluorescence emission and amperometric current of the rCDs-Chi/PB film electrode system exhibited potential-, Cys- and Fe3+-responsive switching properties. Based on the aforementioned work, a combinational logic gate circuit with 3 inputs and 3 outputs was established. In particular, on the same platform, a novel chemical/molecular 4-input/2-output keypad lock with easy resettability was elaborately designed with amperometric current and fluorescence peak intensity as two different types of outputs, so that a higher security level could be achieved.

Target-initiated labeling for the dual-amplified detection of multiple microRNAs

Herein we exploited a novel target-initiated labeling strategy for the multiplex detection of microRNAs (miRNAs) by coupling duplex-specific nuclease (DSN) with terminal deoxynucleotidyl transferase (TdT). In the presence of target miRNA, the immobilized and 3'-blocked capture probes hybridized with target and thus the formed DNA-RNA hybrid was recognized by DSN. DSN mediated the digestion of 3'-phosphated capture probes (CPs) in the hybrids and synchronously target was released and recycled for another round of hybridization and cleavage. The cleaved CP fragments with a free 3'-OH were then elongated and labeled with multiple biotin-dUTP nucleotides by TdT. Fluorescence reporter streptavidin-phycoerythin was finally added to react with the immobilized biotins and render fluorescence signals. This dual-amplification labeling strategy was successfully demonstrated to sensitively detect multiple miRNAs, taking advantage of DSN-mediated target recycling and TdT-catalyzed multiple signal modification with analysis by a commercial Luminex xMAP array platform. Our experimental results showed the simultaneous quantitative measurement of three sequence-specific miRNAs at concentrations from 1 pM to 2.5 nM. Attempts were also made to directly detect miRNAs in total RNA extracted from cancer cells. The dual-amplification labeling strategy reported here shows a great potential for the development of a method for the multiplexed, sensitive, selective, and simple analysis of multiple miRNAs in tissues or cells for biomedical research and clinical early diagnosis.

Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR

Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.

Controllable Photodynamic Therapy Implemented by Regulating Singlet Oxygen Efficiency

With singlet oxygen (1O2) as the active agent, photodynamic therapy (PDT) is a promising technique for the treatment of various tumors and cancers. But it is hampered by the poor selectivity of most traditional photosensitizers (PS). In this review, we present a summary of controllable PDT implemented by regulating singlet oxygen efficiency. Herein, various controllable PDT strategies based on different initiating conditions (such as pH, light, H2O2 and so on) have been summarized and introduced. More importantly, the action mechanisms of controllable PDT strategies, such as photoinduced electron transfer (PET), fluorescence resonance energy transfer (FRET), intramolecular charge transfer (ICT) and some physical/chemical means (e.g. captivity and release), are described as a key point in the article. This review provide a general overview of designing novel PS or strategies for effective and controllable PDT.