Re-engineering Electrochemical Aptamer-Based Biosensors to Tune Their Useful Dynamic Range via Distal-Site Mutation and Allosteric Inhibition

DNA Tile and Invading Stacking Primer-Assisted CRISPR-Cas12a Multiple Amplification System for Entropy-Driven Electrochemical Detection of MicroRNA with Tunable Sensitivity

Conventional electrochemical detection of microRNA (miRNA) encounters issues of poor sensitivity and fixed dynamic range. Here, we report a DNA tile and invading stacking primer-assisted CRISPR-Cas12a multiple amplification strategy to construct an entropy-controlled electrochemical biosensor for the detection of miRNA with tunable sensitivity and dynamic range. To amplify the signal, a cascade amplification of the CRISPR-Cas12a system along with invading stacking primer signal amplification (ISPSA) was designed to detect trace amounts of miRNA-31 (miR-31). The target miR-31 could activate ISPSA and produce numerous DNAs, triggering the cleavage of the single-stranded linker probe (LP) that connects a methylene blue-labeled DNA tile with a DNA tetrahedron to form a Y-shaped DNA scaffold on the electrode. Based on the decrease of current, miR-31 can be accurately and efficiently detected. Impressively, by changing the loop length of the LP, it is possible to finely tune the entropic contribution while keeping the enthalpic contribution constant. This strategy has shown a tunable limit of detection for miRNA from 0.31 fM to 0.56 pM, as well as a dynamic range from ∼2200-fold to ∼270,000-fold. Moreover, it demonstrated satisfactory results in identifying cancer cells with a high expression of miR-31. Our strategy broadens the application of conventional electrochemical biosensing and provides a tunable strategy for detecting miRNAs at varying concentrations.

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

Programming the dynamic range of nanobiosensors with engineering poly-adenine-mediated spherical nucleic acid

Spherical nucleic acid (SNA) conjugates consisting of gold cores functionalized with a densely packed DNA shells are of great significance in the field of medical detection and intracellular imaging. Especially, poly adenine (polyA)-mediated SNAs can improve the controllability and reproducibility of DNA assembly on the nanointerface, showing the tunable hybridization ability. However, due to the physics of single-site binding, the biosensor based on SNA usually exhibits a dynamic range spanning a fixed 81-fold change in target concentration, which limits its application in disease monitoring. To address this problem, we report a tri-block DNA-based approach to assemble SNA for nucleic acid detection based on structure-switching mechanism with programmable dynamic range. The tri-block DNA is a FAM-labeled stem-loop structure, which contains three blocks: polyA block as an anchoring block for tunable surface density, stem block with different GC base pair content for varying the structure stability, and the fixed loop block for target recognition. We find that varying the polyA block, the reaction temperature, and the GC base pair, SNA shows different target binding affinity and detection limit but with normally 81-fold dynamic range. We can extend the dynamic range to 1000-fold by using the combination of two SNAs with different affinity, and narrow the dynamic range to 5-fold by sequestration mechanism. Furthermore, the tunable SNA enables sensitive detection of mRNA in cells. Given its tunable dynamic range, such nanobiosensor based on SNA offers new possibility for various biomedical and clinical applications.

An enzyme-responsive electrochemical DNA biosensor achieving various dynamic range by using only-one immobilization probe

Developing a simple and easy-to-operate biosensor with tunable dynamic range would provide enormous opportunities to promote the diagnostic applications. Herein, an enzyme-responsive electrochemical DNA biosensor is developed by using only-one immobilization probe. The immobilization probe was designed with a two-loop hairpin-like structure that contained the mutually independent target recognition and enzyme (EcoRI restriction endonuclease) responsive domains. The target recognition was based on a toehold-mediated strand displacement reaction strategy. The toehold region was initially caged in the loop of the immobilization probe and showed a relatively low binding affinity with target, which was improved via EcoRI cleavage of immobilization probe to liberate the toehold region. The EcoRI cleavage operation for immobilization probe demonstrated the well regulation ability in detection performance. It showed a largely extended dynamic range, a significantly lowered detection limit and better discrimination ability toward the mismatched sequences whether in two buffers (with high or low salt concentrations) or in the serum system. The advantages also includes simplicity in probe design, and facile biosensor fabrication and operation. It thus opens a new avenue for the development of the modulated DNA biosensor and hold a great potential for the diagnostic applications and drug monitoring.

Recent progress and perspectives of continuous in vivo testing device

Devices for continuous in-vivo testing (CIVT) can detect target substances in real time, thus providing a valuable window into a patient's condition, their response to therapeutics, metabolic activities, and neurotransmitter transmission in the brain. Therefore, CIVT devices have received increased attention because they are expected to greatly assist disease diagnosis and treatment and research on human pathogenesis. However, CIVT has been achieved for only a few markers, and it remains challenging to detect many key markers. Therefore, it is important to summarize the key technologies and methodologies of CIVT, and to examine the direction of future development of CIVT. We review recent progress in the development of CIVT devices, with consideration of the structure of these devices, principles governing continuous detection, and nanomaterials used for electrode modification. This detailed and comprehensive review of CIVT devices serves three purposes: (1) to summarize the advantages and disadvantages of existing devices, (2) to provide a reference for development of CIVT equipment to detect additional important markers, and (3) to discuss future prospects with emphasis on problems that must be overcome for further development of CIVT equipment. This review aims to promote progress in research on CIVT devices and contribute to future innovation in personalized medical treatments.

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A detailed and comprehensive review of continuous in vivo testing device.

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The nanomaterials, delicate structures and detection principles of the works are discussed.

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The achievements and shortcomings of the existing devices are summarized.

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The problems that should be solved in the further development of the devices and the future prospects are put forward.

An orthogonal dual-regulation strategy for sensitive biosensing applications

Biosensing systems based on controllable motion behaviors of droplets have attracted extensive attention, but still face challenges of insufficient sensitivity and uncontrollable dynamic range due to imprecise manipulation of droplet motion on the surfaces. Here, we report an orthogonal dual-regulation strategy for precise motion control of droplets and we demonstrate its utility as a sensitive sensing system with controllable dynamic ranges of sensing for adenosine triphosphate, miRNA, thrombin and kanamycin, as well as discrimination of five kinds of DNA. We endowed a DNA-contained bio-droplet sliding on a lubricant-infused structural surface with micro-grooves to separately adjust the resistance from liquid phase and solid phase. The resistance from liquid phase mainly depended on hydrophobic interaction between DNA and lubricant, which can be finely tuned by different DNA's average chain length. Meanwhile, the resistance from solid surface was determined by the energy barrier from the periodic micro-grooves, which can be adjusted by varying the droplet's sliding direction on the surface. The hydrophobic interaction is conformed to be orthogonal to the micro-grooves' anisotropic resistance by three different methods. This orthogonal dual-regulation strategy thus demonstrated its ability to precisely control bio-droplets' motion behaviors and sensitive detection with adjustable dynamic ranges for various bio-targets. The dual-regulation strategy will provide significant insights for super-wettable biosensors, visual inspection and beyond.

Real-Time Tunable Dynamic Range for Calibration-Free Biomolecular Measurements with a Temperature-Modulated Electrochemical Aptamer-Based Sensor in an Unprocessed Actual Sample

The sensing technologies for monitoring molecular analytes in biological fluids with high frequency and in real time could enable a broad range of applications in personalized healthcare and clinical diagnosis. However, due to the limited dynamic range (less than 81-fold), real-time analysis of biomolecular concentration varying over multiple orders of magnitude is a severe challenge faced by this class of analytical platforms. For the first time, we describe here that temperature-modulated electrochemical aptamer-based sensors with a dynamically adjustable calibration-free detection window could enable continuous, real-time, and accurate response for the several-hundredfold target concentration changes in unprocessed actual samples. Specifically, we could regulate the electrode surface temperature of sensors to obtain the corresponding dynamic range because of the temperature-dependent affinity variations. This temperature modulation method relies on an alternate hot and cold electrode reported by our group, whose surface could actively be heated and cooled without the need for altering ambient temperature, thus likewise applying for the flowing system. We then performed dual-frequency calibration-free measurements at different interface temperatures, thus achieving an extended detection window from 25 to 2500 μM for procaine in undiluted urine, 1-500 μM for adenosine triphosphate, and 5-2000 μM for adenosine in undiluted serum. The resulting sensor architecture could drastically expand the real-time response range accessible to these continuous, reagent-less biosensors.

Electrochemical strategies for the detection of cTnI

Acute myocardial infarction (AMI) is the main cause of death from cardiovascular diseases. Thus, early diagnosis of AMI is essential for the treatment of irreversible damage from myocardial infarction. Traditional electrocardiograms (ECG) cannot meet the specific detection of AMI. Cardiac troponin I (cTnI) is the main biomarker for the diagnosis of myocardial infarction, and the detection of cTnI content has become particularly important. In this review, we introduced and compared the advantages and disadvantages of various cTnI detection methods. We focused on the analysis and comparison of the main indicators and limitations of various cTnI biosensors, including the detection range, detection limit, specificity, repeatability, and stability. In particular, we pay more attention to the application and development of electrochemical biosensors in the diagnosis of cardiovascular diseases based on different biological components. The application of electrochemical microfluidic chips for cTnI was also briefly introduced in this review. Finally, this review also briefly discusses the unresolved challenges of electrochemical detection and the expectations for improvement in the detection of cTnI biosensing in the future.

Hybridization Chain Reaction-Amplified Electrochemical DNA-Based Sensors Enable Calibration-Free Measurements of Nucleic Acids Directly in Whole Blood

Hybridization chain reaction (HCR) amplification strategy has been extensively explored for the application of electrochemical DNA-based sensors. Despite the enhancement in its sensitivity using the HCR, such sensor platform exhibited significant sensor-to-sensor variations in current due to variations in probe counts and lengths. To circumvent this, we are developing here a calibration-free "O-N" approach to generate a ratiometric, unitless value that is independent of these variations. Specifically, this approach employs two types of redox reporters, denoted as "One reporter" and "N reporters", with the former attached on the capture DNA and the latter on H1 and H2 strands. By optimizing the attachment sites of these reporters onto DNA strands, we demonstrate a significantly enhanced sensitivity of such sensor platform by four orders of magnitude, achieving accurate, calibration-free measurement of nucleic acids including ctDNA directly in undiluted whole blood without the requirement to calibrate each individual sensor.

A wrinkled structure of gold film greatly improves the signaling of electrochemical aptamer-based biosensors

Electrochemical aptamer-based (E-AB) sensors provide a great opportunity towards the goal of point-of-care and wearable sensing technologies due to their good sensitivity and selectivity. Nevertheless, the output signals from this sensor class remain low when sensors are interrogated via square-wave voltammetry. This low signaling limits the sensor's precision for its capability to detect small changes in target concentrations. To circumvent this, we proposed here the use of a readily shrink-induced, wrinkled Au-coating polyolefin film to immobilize a greater number of DNA probes and thus improve the signaling. Specifically, wrinkled gold film exhibits a 5.5-fold increase of surface area in comparison to the unwrinkled ones. Using these substrates we fabricated a set of E-AB sensors of three biological molecules, including kanamycin, doxorubicin and ATP. We achieved up to 10-fold increase in its current and also good accuracies within ±20% error in the target concentration range across 2 orders of magnitude.

A wrinkled gold substrate greatly improves the signaling of electrochemical aptamer-based biosensors, achieving up to 10-fold increase in signals.