Jinbo Zhu

Photoinduced electron transfer of DNA/Ag nanoclusters modulated by G-quadruplex/hemin complex for the construction of versatile biosensors.

Photoinduced electron transfer (PET) has been observed for the first time between DNA/Ag fluorescent nanoclusters (NCs) and G-quadruplex/hemin complexes, accompanied by a decrease in the fluorescence of the DNA/Ag NCs. In this PET process, a parallel G-quadruplex and the sensing sequences are blocked by a duplex. The specific combination of targets with the sensing sequence triggers the release of the G-quadruplex and allows it to fold properly and bind hemin to form a stable G-quadruplex/hemin complex. The complex proves favorable for PET because it makes the G-quadruplex bind hemin tightly, which promotes the electron transfer from the DNA/Ag NCs to the hemin Fe(III) center, thus resulting in a decrease in the fluorescence intensity of the DNA/Ag NCs. This novel PET system enables the specific and versatile detection of target biomolecules such as DNA and ATP with high sensitivity based on the choices of different target sequences.

Graphene-Based Aptamer Logic Gates and Their Application to Multiplex Detection

In this work, a GO/aptamer system was constructed to create multiplex logic operations and enable sensing of multiplex targets. 6-Carboxyfluorescein (FAM)-labeled adenosine triphosphate binding aptamer (ABA) and FAM-labeled thrombin binding aptamer (TBA) were first adsorbed onto graphene oxide (GO) to form a GO/aptamer complex, leading to the quenching of the fluorescence of FAM. We demonstrated that the unique GO/aptamer interaction and the specific aptamer-target recognition in the target/GO/aptamer system were programmable and could be utilized to regulate the fluorescence of FAM via OR and INHIBIT logic gates. The fluorescence changed according to different input combinations, and the integration of OR and INHIBIT logic gates provided an interesting approach for logic sensing applications where multiple target molecules were present. High-throughput fluorescence imagings that enabled the simultaneous processing of many samples by using the combinatorial logic gates were realized. The developed logic gates may find applications in further development of DNA circuits and advanced sensors for the identification of multiple targets in complex chemical environments.

Enzyme‐Free Unlabeled DNA Logic Circuits Based on Toehold‐Mediated Strand Displacement and Split G‐Quadruplex Enhanced Fluorescence

Adopting fluorescence of PPIX enhanced by a split G-quadruplex and toehold mediated strand displacement reaction, a series of unlabeled fluorescent logic gates is set up and some of them are cascaded into circuits. Controlled release of PPIX, which is also a photosensitizer in photodynamic diagnosis and therapy, is realized by this circuit, making it a wise choice for DNA computing.

Simple and Sensitive Fluorescent and Electrochemical Trinitrotoluene Sensors Based on Aqueous Carbon Dots

Aqueous N-rich carbon dots (CDs), prepared by the microwave-assisted pyrolysis method, are applied as a dual sensing platform for both the fluorescent and electrochemical detection of 2,4,6-trinitrotoluene (TNT). The fluorescent sensing platform is established on the strong TNT-amino interaction which can quench the photoluminescence of amino functionalized CDs through charge transfer. The resultant linear detection ranges from 10 nM to 1.5 μM with a fast response time of 30 s. Glassy carbon electrode modified with CDs exhibits a fine capability for TNT reduction with the linear range from 5 nM to 30 μM, better than that obtained by the fluorescent method. Moreover, the minimum distinguishable response concentration with respect to these two methods is down to the nanomolar level with a high specificity and sensitivity.

G-quadruplex DNAzyme based molecular catalytic beacon for label-free colorimetric logic gates

Efficient and economic DNA nanomaterials that can work as logic components are necessary for the development of DNA computers with high speed and outstanding data storage capacity. A new molecular catalytic beacon (MCB) and a series of label-free colorimetric logic gates based on the formation and dissociation of G-quadruplex DNAzyme were established in this work. These logic gates (NOT, NOR, IMPLICATION, AND, OR and INHIBIT) were realized by the interaction between the special designed oligonucleotide hairpins and the short input single strand complementary DNA. We were able to recognize the logic output signals effortlessly by our naked eyes. It is a simple, economic and safe approach for the design of complex multiple input DNA logic molecular device.

A new approach to light up DNA/Ag nanocluster-based beacons for bioanalysis

Dynamic DNA assembly, operated in an autonomous and reconfigurable manner by controlling the kinetics of strand displacement reactions (SDR), is an ideal approach to amplify the fluorescent signals for molecular diagnostic and imaging. Herein, we for the first time have demonstrated an enhancement of fluorescence intensity of DNA/Ag nanocluster-based beacons by the modulation of SDR. This is a new DNA/Ag NCs fluorescence light-up system through the use of the enhancer of G-rich overhang. Such a sensing system can be used to develop a DNA/Ag nanocluster-based beacon for the fluorescent detection of nucleic acid and thrombin with high selectivity and sensitivity, in which the detection sensitivity could be further enhanced through additional Exo III based amplification.

Four-Way Junction-Driven DNA Strand Displacement and Its Application in Building Majority Logic Circuit

We introduced a four-way DNA junction-driven toehold-mediated strand displacement method. Separation of the different functional domains on different strands in the four-way junction structure and usage of glue strand to recombine them for different logic gates make the design more flexible. On the basis of this mechanism, a majority logic circuit fabricated by DNA strands was designed and constructed by assembling three AND gates and one OR gate together. The output strand drew the G-rich segments together to form a split G-quadruplex, which could specifically bind PPIX and enhance its fluorescence. Just like a poll with three voters, the high fluorescence signal would be given off only when two or three voters vote in favor. Upon slight modification, the majority circuit was utilized to select the composite number from 0 to 9 represented by excess-three code. It is a successful attempt to integrate the logic gates into a circuit and to achieve desired functions.

Label-free G-quadruplex-specific fluorescent probe for sensitive detection of copper(II) ion.

An effective G-quadruplex-based probe has been constructed for rapid and sensitive detection of Cu(2+). In this probe, an anionic porphyrin, protoporphyrin IX (PPIX) served as a reference signal, which binds to G-quadruplex specifically and the fluorescence intensity increases sharply. While, in the presence of Cu(2+), the G-quadruplex can catalyze the related Cu(2+) insertion into the protoporphyrin, the fluorescent intensity is decreased. The fluorescence of the response ligand could be selectively quenched in the presence of Cu(2+) and not interfered by other metal ions. The probe provided an effective platform for reliable detection of Cu(2+) with a detection limit as low as 3.0nM, the high sensitivity was attributed to the strong metalation of PPIX with Cu(2+) catalyzed by G-quadruplex (PS5.M). Linear correlations were obtained over the logarithm of copper ion concentration in the range from 8×10(-9)M to 2×10(-6)M (R=0.998). The G-quadruplex-based probe also could be used to detect Cu(2+) in real water samples. Additionally, these striking properties endow the G-quadruplex-ligand with a great promise for analytical applications.

Aptamer-Based Sensing Platform Using Three-Way DNA Junction-Driven Strand Displacement and Its Application in DNA Logic Circuit

We proposed a new three-way DNA junction-driven strand displacement mode and fabricated an aptamer-based label-free fluorescent sensing platform on the basis of this mechanism. Assembling the aptamer sequence into the three-way DNA junction makes the platform sensitive to the target of the aptamer. A label-free signal readout method, split G-quadruplex enhanced fluorescence of protoporphyrin IX (PPIX), was used to report the final signal. Here, adenosine triphosphatase (ATP) was taken as a model and detected through this approach, and DNA strand could also be detected by it. The mechanism was investigated by native polyacrylamide gel electrophoresis. Furthermore, on the basis of this molecular platform, we built a logic circuit with ATP and DNA strands as input. Aptamer played an important role in mediating the small molecule ATP to tune the DNA logic gate. Through altering the aptamer sequence, this molecular platform will be sensitive to various stimuli and applied in a wide field.

Molecular aptamer beacon tuned DNA strand displacement to transform small molecules into DNA logic outputs

A molecular aptamer beacon tuned DNA strand displacement reaction was introduced in this work. This strand displacement mode can be used to transform the adenosine triphosphate (ATP) input into a DNA strand output signal for the downstream gates to process. A simple logic circuit was built on the basis of this mechanism.