Deoxyribonucleic Acid Probes Research Articles

Dual signal amplification sensor based on imprint-modified DNA for high-sensitivity detection of copper ions

In order to improve the sensitivity of ion imprinted electrochemical (IIE) sensor to detect copper ions, a novel dual signal amplification (DSA) sensor was proposed using deoxyribonucleic acid (DNA) modified IIE sensor. Chitosan (CS) was used as a functional monomer for IIE sensor. The IIE sensor was prepared by mixing copper ion templates with CS and removing the templates. Gold nanoparticles (AuNPs) were electrodeposited onto the surface of IIE sensor to improve their conductivity and provide a connecting platform for DNA probes. And then the DNA probe was fixed on the surface of AuNPs to prepare a DSA sensor. The signal of DSA sensor was significantly amplified by the synergistic effect of IIE sensor and DNA probe. The feasibility, parameter optimization and electrochemical performance were analyzed by experimental comparison, surface micro scanning and kinetic study. The results show that compared with IIE sensor, the sensitivity of DSA sensor is significantly improved, with a value of 1.6712 × 10-6 A·(µM)-1. The exchange current density is 5.9765 × 10-8 A·cm−2. The detection range is 10 nM to 100 nM (R2 = 0.99651) with the detection limit of 4.17 nM (3σ/slope). The recommended method has high sensitivity and selectivity, as well as very high recovery rates in tap water and milk.

Label-free detection of platelet-derived growth factor-BB via liquid crystal/aqueous interface functionalized using a double-stranded DNA probe

A liquid crystal (LC)-filled transmission electron microscopy (TEM) grid cell coated with cationic surfactant octyltrimethylammonium bromide (OTAB) and adsorbed with a double-stranded deoxyribonucleic acid (dsDNA) probe at the LC/aqueous interface (TEMOTAB/DNA) was utilized for the highly specific detection of platelet-derived growth factor (PDGF-BB). Upon adsorption of the OTAB-coated 4-cyano-4′-pentylbiphenyl (5CB) on the TEM grid (TEMOTAB) and subsequent adsorption of the dsDNA probe, a homeotropic orientation was observed. Subsequently, the TEMOTAB/DNA biosensor was exposed to PDGF-BB, which induced a homeotropic-to-planar configurational change in 5CB, as observed using polarized optical microscopy with crossed polarizers. The optimized adsorption density of the dsDNA probe facilitated the detection of 2.63 pg mL−1 PDGF-BB in the detection range of 5–200 pg mL−1. Remarkably, this LC-based biosensor discriminated PDGF-BB from bovine serum albumin, immunoglobulin G, hemoglobin, carcinoembryonic antigen, epidermal growth factor, PDGF-AA, and PDGF-AB. The application potential of this sensor was further demonstrated by its effective performance in detecting PDGF-BB in both human serum and synthetic urine samples. Because of its high specificity, sensitivity, and label-free detection capabilities, this biosensor has potential applications in cancer detection.

Detection of intracellular microRNA-21 for cancer diagnosis by a nanosystem containing a ZnO@polydopamine and DNAzyme probe.

MicroRNAs (miRNAs) are a series of single-stranded non-coding ribonucleic acid (RNA) molecules which associated closely with various human diseases. Efficient strategies for detecting miRNAs are of great significance to cancer diagnosis and prognosis. Here we provide a novel nanosystem that can be applied for the detection of miRNAs. The nanosystem consists of a single-stranded deoxyribonucleic acid (DNA) probe and a probe carrier. The DNA probe was designed based on a deoxyribozyme (DNAzyme) with several necessary functional sequences and two fluorescent dyes labeled at proper sites. The ZnO@polydopamine (ZnO@PDA) nanomaterial serves not only as a probe carrier, but also as a supplier of Zn2+ that can activate the DNAzyme. The DNA probe will undergo a conformation alteration induced by miRNA-21, which then trigger the DNAzyme catalyzed self-cleavage reaction with the assist of Zn2+ provided by ZnO decomposition under weak acid environment. A change of fluorescent color will occur due to the interruption of fluorescence resonance energy transfer between the two fluorescent dyes, and the dissociated miRNA-21 can repeatedly induce the above responses to amplify the fluorescence signal. The feasibility of the whole procedure was demonstrated by various experiments. This nanosystem showed a good selectivity towards miRNA-21, and under the optimal incubation time of 2 hours, a good linear relationship was obtained in a concentration range of 0.01-2.0 nM with a detection limit of 3.8 pM. In in vivo detection, an obvious fluorescence color change from red to green can be observed in the presence of miRNA-21. The results proved that this miRNA detection strategy has a broad application prospect in tumor diagnosis and miRNA related biological studies.

Acinetobacter Baumannii Detection Using A Bio-FET Device: Towards Healthcare Infection Management

Acinetobacter is a group of bacteria commonly found in the environment, like in soil and water. While there are many types, the most common cause of infections is Acinetobacter baumannii, which accounts for most Acinetobacter infections in humans.Acinetobacter baumannii could result in infections in the blood, urinary tract, in wounds of the body or lungs. Traditionally, medical technicians in hospital use the sample from patients (like stool, urine, or sputum) to streak on a plate or do bacteria culture test. It takes too much time and patients cannot wait so long. Therefore, it is vital that a new diagnostic technique can be used to detect Acinetobacter baumannii much faster than the traditional methods.The electrical double layer (EDL)-gated field-effect transistor-based biosensor (BioFET) is a fast and promising diagnostic technique because it is highly sensitive, quickly response, and high selective to the target analyte. Besides, a portable device could help the medical personnel detect the bacteria and treat the patients as early as possible. Here, we used a portable BioFET device from STARX co. (Model II) to detect the complementary Deoxyribonucleic acid (DNA) of Acinetobacter Baumannii via a specific DNA probe we designed. We utilized the portable device to examine the specificity and selectivity in various conditions, such as urine and blood. Thus, the results showed that the system with the portable device could give the hospital personnel a tool to control healthcare associated infection caused by Acinetobacter baumannii. Figure 1

Harnessing single fluorescent probe to image deoxyribonucleic acid and ribonucleic acid in cells

The roles of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in cells are closely related. However, the absence of molecular tools for simultaneous imaging of the two nucleic acids has prevented scientists from elucidating the regulatory mechanisms of nucleic acid interaction. The nucleic acid probes developed in recent years have ignored the regulatory relationship between DNA and RNA. Simultaneously imaging RNA and DNA in cells through a single small-molecule fluorescent probe is important. In this study, we propose a strategy for developing fluorescent probes localized to DNA and RNA to investigate their detection and imaging characteristics. The novel probe Bptp-RD has been successfully used for DNA and RNA imaging in cells. We investigated the detection and imaging characteristics of this nucleic acid probe and discovered the following: 1) the differences in the detection results of this nucleic acid probe for DNA and RNA come from the structural differences of the nucleic acids rather than chemical composition differences; 2) through using small-molecule probes to image a nucleic acid in cells, another nucleic acid can be visualized by reducing the fluorescence signal caused by DNA or RNA; 3) the order of response of the small-molecule fluorescent probe with intercalation and binding mechanisms to the type of nucleic acid structure is single chain, double chain, and ring. This work will help improve the understanding of RNA and DNA probes, and the novel probe has high potential to explore the interaction between RNA and DNA in cells.

Microarray image enhancement techniques by denoising: Current status and future directions

Microarray imaging is a technique for simultaneously detecting the expression of numerous genes. Microarrays are simply a slide with unique Deoxyribonucleic Acid (DNA) probes, often known as gene chips. This paper aims to provide an overview of important contributions to the field of image denoising in the context of microarray imaging. The methodologies discussed in the article include various techniques of transform domain and spatial filtering methods for denoising microarray images that can be used to improve the quality of microarray images. We have identified the strengths and limitations of these techniques and highlights their potential impact. The paper also explores future developments in this area and discusses their potential impact, on microarray imaging.

Lateral flow biosensor based on LAMP-CRISPR/Cas12a for sensitive and visualized detection of Salmonella spp.

Salmonella is a major pathogen that causes serious foodborne diseases in humans and poses a serious threat to food safety and public health worldwide. Its rapid and accurate diagnosis is essential to prevent bacterial contamination of food. This study aimed to develop a lateral flow biosensor (LFB) based on loop-mediated isothermal amplification (LAMP)-clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 12a (Cas12a) that is affordable and can aid in visually detecting Salmonella in a food sample. False positives were prevented by synthesizing CRISPR ribonucleic acid (crRNA) with a selected 21-base pair protospacer that did not overlap with the used LAMP primers. A single-stranded deoxyribonucleic acid (DNA) probe labeled with biotin and 6-Carboxyfluorescein (6-FAM) was used for designing the LFB. The duration of these processes was as follows: DNA extraction (20 min), LAMP (60 min), Cas12a cleavage (5 min), and LFB (5 min). The detection limit was 1.22 × 10° CFU/mL in pure culture. The validity of the LAMP-CRISPR/Cas12a based LFB was verified by detecting Salmonella in onions, melon, and salami. Consequently, the developed LAMP-CRISPR/Cas12a based LFB assay show the potential for rapid on-site detection of Salmonella with high specificity, sensitivity, convenience, mobility, low cost, and affordability. • LFB based on LAMP-CRISPR/Cas12a was developed for detection of Salmonella. • The developed method demonstrated suitability for naked-eye detection of Salmonella. • The detection can be completed within 100 min for on-site detection.

SARS‐CoV‐2 N Gene‐Targeted Anodic Stripping Voltammetry Sensor Using a Novel CoS‐NGQD/Pt@Pd Platform and Au‐DNA‐CdTe QD Probe

AbstractRapid screening of individuals infected with severe acute respiratory syndrome‐coronavirus‐2 (SARS‐CoV‐2) is necessary to contain contagion in a large population. Nucleic acid‐based gold standard assays are time‐consuming, and nucleic acid amplification is mandatory and expensive, impeding the containment of the coronavirus disease 2019 (COVID‐19) outbreak. To overcome the aforementioned disadvantages, this study deals with a specially designed gold (Au)‐deoxyribonucleic acid (DNA)‐cadmium telluride (CdTe) quantum dot (QD) probe to target two sections of the nucleocapsid (N) gene of SARS‐CoV‐2 ribonucleic acid (RNA) of three variants (B.1.1.529, B.1.617.2, and B.1.351). A duplex‐specific nuclease (DSN)‐assisted highly selective release of signaling probes enable higher specificity, and an Au‐supported DNA probe is incorporated to carry many CdTe QD signaling probes. After dissolution, the generated Cd2+ ions are quantified at the novel cobalt sulfide (CoS)‐nitrogen‐doped graphene QD (NGQD)/platinum (Pt)@palladium (Pd) electrode with extraordinary sensitivity through square wave anodic stripping voltammetry (SWASV). The developed sensor exhibits a wide range of detection (10 to 108 copies µL−1) and a lower detection limit (0.12 copies µL−1), without any amplification. The selectivity of the sensor is tested against MERS and HCoV‐NL63, and real‐time detection is performed on heat‐inactivated viral samples, which show excellent selectivity.

Fluorescence In Situ Hybridization (FISH) for the Genotyping of Triticeae Tribe Species and Hybrids.

This chapter is dedicated to using fluorescence in situ hybridization (FISH) for the genotyping of Triticeae tribe species and hybrids. The basic method of FISH on metaphase chromosomes is presented with a discussion on its modifications, and deoxyribonucleic acid (DNA) probes that can be useful for genotyping are proposed.

Fiber-Based Surface Plasmon Resonance Biosensor for Leptospira DNA Detection

Fiber-based surface plasmon resonance (SPR) sensors are the ideal configuration for rapid and label-free biomolecule detection. Gold-coated tapered optical fiber was used to excite the SPR mode that propagates at the metal–dielectric interface. By forming self-assembled monolayers (SAMs) of active chemical functional groups, the deoxyribonucleic acid (DNA) probe targeting the secY gene of Leptospira was immobilized onto the sensor surface. Red shifts in the SPR wavelengths were observed at different concentrations of leptospiral DNA target against the immobilized DNA probe due to the ability of plasmonic interaction to sensitively detect the binding of biomolecules on the sensor area. The developed sensor showed satisfactory linear responses at two target concentration ranges; low (1.0 fM to 1.0 pM) and high (0.1 nM to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.0~\mu \text{M}$ </tex-math></inline-formula> ), with the highest sensitivity of 1.22 nm per log M. The negative control test also revealed high sensor specificity toward the complementary DNA strand. This sensor will represent a significant step toward laboratory-free diagnosis of leptospirosis.

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing.

A recent approach to perform genetic tracing of complex biological problems involves the generation of synthetic deoxyribonucleic acid (DNA) probes that specifically mark cells with a phenotype of interest. These synthetic locus control regions (sLCRs), in turn, drive the expression of a reporter gene, such as fluorescent protein. To build functional and specific sLCRs, it is critical to accurately select multiple bona fide cis-regulatory elements from the target cell phenotype cistrome. This selection occurs by maximizing the number and diversity of transcription factors (TFs) within the sLCR, yet the size of the final sLCR should remain limited. In this work, we discuss how optimization, in particular integer programing, can be used to systematically address the construction of a specific sLCR and optimize pre-defined properties of the sLCR. Our presented instance of a linear optimization problem maximizes the activation potential of the sLCR such that its size is limited to a pre-defined length and a minimum number of all TFs deemed sufficiently characteristic for the phenotype of interest is covered. We generated an sLCR to trace the mesenchymal glioblastoma program in patients by solving our corresponding linear program with the software optimizer Gurobi. Considering the binding strength of transcription factor binding sites (TFBSs) with their TFs as a proxy for activation potential, the optimized sLCR scores similarly to an sLCR experimentally validated in vivo, and is smaller in size while having the same coverage of TFBSs. We provide a Python implementation of the presented framework in the Supplementary Material with which an optimal selection of cis-regulatory elements can be calculated once the target set of TFs and their binding strength with their TFBSs is known. Supplementary data are available at Bioinformatics online.

Fabrication and quantitative performance analysis of a low-cost, flexible CNT network-based DNA sensors using ink-jet printing

This paper reports the design, fabrication and quantitative performance analysis of a low-cost, flexible carbon nanotube (CNT) network-based deoxyribonucleic acid (DNA) sensor. These sensors comprise an array of ink-jet printed silver (Ag) electrodes on a transparent polyethylene terephthalate (PET) flexible substrate, where a CNT network acts as a sensing layer. DNA hybridization is studied by immobilizing single-stranded DNA (ssDNA) probes on the CNT surface; these probes recognize their complementary DNA target. The analytic hierarchy process (AHP) was used to analyze the quantitative performance of flexible CNT biosensors. Various influencing factors (performance indicators) have been identified and quantified in the performance of flexible CNT biosensors (before bending, during bending and after bending). Additionally, the noise and other external factors contributing to the measured real signal have been quantified. The interpretation of the overall outcome will enable the improvement of the performance of flexible biosensors fabricated through large-scale manufacturing for possible commercialization.

Establishment and Application of Ligation Reaction-Based Method for Quantifying MicroR-156b.

Microribonucleic acids (miRNAs) play significant roles in the regulation of biological processes and in responses to biotic or abiotic environmental stresses. Therefore, it is necessary to quantitatively detect miRNAs to understand these complicated biological regulation mechanisms. This study established an ultrasensitive and highly specific method for the quantitative detection of miRNAs using simple operations on the ground of the ligation reaction of ribonucleotide-modified deoxyribonucleic acid (DNA) probes. This method avoids the complex design of conventional reverse transcription. In the developed assay, the target miRNA miR156b was able to directly hybridize the two ribonucleotide-modified DNA probes, and amplification with universal primers was achieved following the ligation reaction. As a result, the target miRNA could be sensitively measured even at a detection limit as low as 0.0001 amol, and differences of only a single base could be detected between miR156 family members. Moreover, the proposed quantitative method demonstrated satisfactory results for overexpression-based genetically modified (GM) soybean. Ligation-based quantitative polymerase chain reaction (PCR) therefore has potential in investigating the biological functions of miRNAs, as well as in supervising activities regarding GM products or organisms.

Critical evaluation of CNA estimators for DNA data using matching confidence masks and WGS technology

A big number of different estimators have been proposed during decades to detect the Copy Number Alterations (CNA) in Deoxyribonucleic Acid (DNA) structures and indicate various diseases, including cancer. Due to the different cost functions and wide variations in DNA probes, the estimates in some cases turn out to be incompatible with each other. Therefore, each DNA profile is often supplied with a ‘gold standard’ provided by medical experts according to their expertise. In this paper, we test various CNAs estimators based on the Whole Genome Sequencing (WGS) and select the best one using probabilistic confidence masks. The masks are created for the segmental Gaussian noise and asymmetric exponential power distribution in the breakpoints. The estimates produced by the algorithms are compared at several probability levels. A complete statistical analysis of the CNA structures is carried out by varying the probability of the breakpoint existence. The best estimator is selected for each of the DNA profiles.

Efficient Determination of PML/RARα Fusion Gene by the Electrochemical DNA Biosensor Based on Carbon Dots/Graphene Oxide Nanocomposites.

PurposeThe PML/RARα fusion gene as a leukemogenesis plays a significant role in clinical diagnosis of the early stage of acute promyelocytic leukemia (APL). Here, we present an electrochemical biosensor for PML/RARα fusion gene detection using carbon dots functionalized graphene oxide (CDs/GO) nanocomposites modified glassy carbon electrode (CDs/GO/GCE).Materials and MethodsIn this work, the CDs/GO nanocomposites are produced through π-π stacking interaction and could be prepared in large quantities by a facile and economical way. The CDs/GO nanocomposites were decorated onto electrode surface to improve the electrochemical activity and as a bio-platform attracted the target deoxyribonucleic acid (DNA) probe simultaneously.ResultsThe CDs/GO/GCE was fabricated successfully and exhibits high electrochemical activity, good biocompatibility, and strong bioaffinity toward the target DNA sequences, compared with only the pristine CDs on GCE or GO on GCE. The DNA biosensor displays excellent sensing performance for detecting the relevant pathogenic DNA of APL with a detection limit of 83 pM (S/N = 3).ConclusionAccording to the several experimental results, we believe that the simple and economical DNA biosensor has the potential to be an effective and powerful tool for detection of pathogenic genes in the clinical diagnosis.

Principles and Applications of Deoxyribonucleic Acid Microarray: A Review

Deoxyribonucleic acid (DNA) microarrays are collections of DNA probes arranged on a base pair and the latest commercialized molecular diagnostic technologies that offer high throughput results, more sensitive and require less time. It is the most reliable and widely accepted tool facilitating the simultaneous identification of thousands of genetic elements even a single gene. Microarrays are powerful new tools for the investigation of global changes in gene expression profiles in cells and tissues. The different types of DNA microarray or DNA chip devices and systems are described along with their methods of fabrication and their use. The DNA microarrays assembly process is automatized and further miniaturized. DNA microarrays are used in the search of various specific genes or in gene polymorphism and expression analysis. They will be widely used to investigate the expression of various genes connected with various diseases in order to find the causes of these diseases and to enable their accurate treatment. Generally, microarray analysis is not only applied for gene expression studies, but also used in immunology, genotyping, diagnostics and sequence analysis. Additionally, microarray technology being developed and applied to new areas of proteomics, cancer research, and cellular analysis.

Ultrasensitive and Selective Detection of SARS-CoV-2 Using Thermotropic Liquid Crystals and Image-Based Machine Learning

Rapid, robust virus-detection techniques with ultrahigh sensitivity and selectivity are required for the outbreak of the pandemic coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Here, we report that the femtomolar concentrations of single-stranded ribonucleic acid (ssRNA) of SARS-CoV-2 trigger ordering transitions in liquid crystal (LC) films decorated with cationic surfactant and complementary 15-mer single-stranded deoxyribonucleic acid (ssDNA) probe. More importantly, the sensitivity of the LC to the SARS ssRNA, with a 3-bp mismatch compared to the SARS-CoV-2 ssRNA, is measured to decrease by seven orders of magnitude, suggesting that the LC ordering transitions depend strongly on the targeted oligonucleotide sequence. Finally, we design a LC-based diagnostic kit and a smartphone-based application (app) to enable automatic detection of SARS-CoV-2 ssRNA, which could be used for reliable self-test of SARS-CoV-2 at home without the need for complex equipment or procedures.

Ultrasensitive and Selective Detection of SARS-CoV-2 Using Thermotropic Liquid Crystals and Image-Based Machine Learning

Rapid, robust virus detection techniques with ultrahigh sensitivity and selectivity are required for the outbreak of the pandemic coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Here, we report that femtomolar concentrations of single-stranded ribonucleic acid (ssRNA) of SARS-CoV-2 trigger ordering transitions in liquid crystal (LC) films decorated with cationic surfactants and complementary 15-mer single-stranded deoxyribonucleic acid (ssDNA) probes. More importantly, the sensitivity of the LC to the severe acute respiratory syndrome (SARS) ssRNA, with a 3 base pair-mismatch compared to the SARS-CoV-2 ssRNA, was measured to decrease by seven orders of magnitude, suggesting that the LC ordering transitions depend strongly on the targeted oligonucleotide sequence. Finally, we designed a LC-based diagnostic kit and a smartphone-based application (App) to enable automatic detection of SARS-CoV-2 ssRNA, which can be used for reliable self-test of SARS-CoV-2 at home without the need for complex equipment or procedures.Funding: J.P. and X.W. thank the funding support by the startup funds of The Ohio State University (OSU) and X.W. thanks OSU Institute for Materials Research Kickstart Facility Grant. X.B. thanks the funding support by the startup funds of Davidson School of Chemical Engineering at Purdue University. S.S. and R.Q. thanks the funding support by Office of Naval Research (ONR Grant N00014-17-1-2928).Conflict of Interest: The Ohio State University has filed a patent application (Application Number 63066000) on the work described in this manuscript. The inventors listed on the patent application are X.W., X.B., Q.R., X.Y. and A.M.R. The authors declare no other competing interests.

Dynamic DNA Assemblies in Biomedical Applications.

Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer‐aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli‐triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.

Deoxyribonucleic-acid-sensitive Polycrystalline Diamond Solution-gate Field-effect Transistor with a Carboxyl-terminated Boron-doped Channel.

This paper describes a deoxyribonucleic-acid-sensitive electrolyte solution-gate field-effect transistor (SGFET) sensor utilizing a partial carboxyl-terminated boron-doped polycrystalline diamond surface as a linker to connect a deoxyribonucleic acid (DNA) probe. A high density of carboxyl termination on the polycrystalline diamond surface that was employed as a FET channel was achieved using a vacuum ultraviolet system with oxygen gas. A single-stranded DNA probe was immobilized on the polycrystalline diamond channel via amino coupling. The current-voltage characteristics of the polycrystalline diamond SGFET sensor was examined with bias voltages within its potential voltage window. The characteristics of the drain-source current verses the drain-source voltage showed a pinch-off, a shift voltage of up to 40 mV with a coefficient of variation of 4 - 11% was obtained between hybridization and denaturation. In addition, a single nucleotide mutation of DNA sequence was selectively recognized by the shift voltage up to ca. 10 mV.