Interfacial DNA Framework-Enhanced Background-to-Signal Transition for Ultrasensitive and Specific Micro-RNA Detection

Abstract

Interfacial DNA self-assembly is fundamental to solid nucleic acid biosensors, whereas how to improve the signal-to-noise ratio has always been a challenge, especially in the charge-based electrochemical DNA sensors because of the large noise from the negatively charged DNA capture probes. Here, we report a DNA framework-reversed signal-gain strategy through background-to-signal transition for ultrasensitive and highly specific electrical detection of microRNAs (miRNAs) in blood. By using a model of enzyme-catalyzed deposition of conductive molecules (polyaniline) targeting to DNA, we observed the highest signal contribution per unit area by the highly charged three-dimensional (3D) tetrahedral DNA framework probe, relative to the modest of two-dimensional (2D) polyA probe and the lowest of one-dimensional (1D) single-stranded (ss)­DNA probe, suggesting the positive correlation of background DNA charge with signal enhancement. Using such an effective signal-transition design, the DNA framework-based electrochemical sensor achieves ultrasensitive miRNAs detection with sensitivity up to 0.29 fM (at least 10-fold higher than that with 1D ssDNA or 2D polyA probes) and high specificity with single-base resolution. More importantly, this high-performance sensor allows for a generalized sandwich detection of tumor-associated miRNAs in the complex matrices (multiple cell lysates and blood serum) and further distinguishes the tumor patients (e.g., breast, lung, and liver cancer) from the normal individuals. These advantages signify the promise of this miRNA sensor as a versatile tool in precision diagnosis.

DNA-Coupled AuNPs@CuMOF for Sensitive Electrochemical Detection of Carcinoembryonic Antigen

“…The designed thiol-modified DNA oligonucleotide probes serve as anchoring blocks to the AuNPs@CuMOFs and carrying CEA aptamer intended for CEA capturing. The selected CEA aptamer with the sequence 5′-ATACCAGCTTATTCAATT-3′ has been first identified by Hashemi Tabar and Smith, then approved with different CEA aptasensor applications. , In this work, the suggested 3D TDNA (ABCD) capture probe is formed through the self-assembling of four oligonucleotides (A, B, C, and D) in a single step. , In brief, each oligonucleotide strand (1 μL, 50 μM) was treated with TCEP in an assembly buffer of 50 mM MgCl 2 and 20 mM Tris-HCl, adjusted to pH 8.0. The resulting mixture underwent an initial heating process at a temperature of 95 °C for 5 min, followed by cooling phases at 37 °C for 30 min and 4 °C for 30 s. The self-assembled structure was characterized using 10% polyacrylamide gel electrophoresis (PAGE) at 150 V for 40 min.…”

“…To date, electrochemical immunoassay has attracted tremendous attention as a promising candidate, considering its high sensitivity, selectivity, portability, and simplicity at cost-effectiveness. − However, the efficiency of such immunosensors strongly depends on how the recognition probes are tethered to the sensing surface. − In other words, the control of capture probe orientation and density streamlines its binding activity with the targets, affecting the stability and sensitivity of the biosensors. Addressing this controversy, three-dimensional tetrahedron DNA structured probes (3D TDNA) were introduced as a new type of DNA structure, providing exceptional mechanical robustness and structural stability. − On the other hand, altering the sensing surface using multiple technologies involving nanomaterial functionalization plays a pivotal role in yielding higher biocompatibility and electron conductivity while mitigating surface fouling. To do so, multiple nanomaterials have been incorporated to fulfill the rising need for heightened sensitivity and early detection capabilities of biomarkers, including carbon nanotubes, quantum dots, metal nanoparticles, graphene, and polymer nanocomposites …”

Signal Amplification-Based Biosensors and Application in RNA Tumor Markers

“…Meanwhile, enzyme amplification technology was used to enhance the output signal and overcome the problems of short size and low abundance in the detection of miRNAs [46]. Guo et al constructed an electrochemical biosensor platform based on the enzyme catalyzed deposition of DNA conducting molecules (polyaniline) and DNA framework electrochemical background signal conversion strategy (etFNA) for ultra-sensitive and specific detection of miRNAs [47]. In the presence of target miRNAs, tFNA probes allow miRNAs and their partially complementary botanized DNA to assemble a sandwich structure through base stacking effects.…”

Sequential logic circuit built onλexonuclease for cross inhibition

“…Besides being the carrier and transmitter of genetic information, DNA is also a significant nanomaterial. With the rapid development of DNA nanotechnology, various self-assembly systems have been designed based on Watson-Crick base pairing for applications in biomedicine, 1,2 DNA computing, [3][4][5][6] and other fields. [7][8][9] Among them, DNA computing, with its advantages of programmable design and high parallelism, 10 has been widely used in areas such as nanomachines, [11][12][13][14] molecular detection, [15][16][17][18][19] and DNA logic circuits.…”