Deoxyribonucleic Acid Hybridization Research Articles

Multiplexed In Situ Imaging of Site-Specific m6A Methylation with Proximity Hybridization Followed by Primer Exchange Amplification (m6A-PHPEA).

Post-transcriptional modification of N6-methyladenosine (m6A) is crucial for ribonucleic acid (RNA) metabolism and cellular function. The ability to visualize site-specific m6A methylation at the single-cell level would markedly enhance our understanding of its pivotal regulatory functions in the field of epitranscriptomics. Despite this, current in situ imaging techniques for site-specific m6A are constrained, posing a significant barrier to epitranscriptomic studies and pathological diagnostics. Capitalizing on the precise targeting capability of deoxyribonucleic acid (DNA) hybridization and the high specificity of the m6A antibody, we present a method, termed proximity hybridization followed by primer exchange amplification (m6A-PHPEA), for the site-specific imaging of m6A methylation within cells. This approach enables high-resolution, single-cell imaging of m6A methylation across various RNA molecules coupled with efficient signal amplification. We successfully imaged three distinct m6A methylation sites concurrently in multiple cell types, revealing cell-to-cell variability in expression levels. This method promises to illuminate the dynamics of m6A-modified RNAs, potentially revolutionizing epitranscriptomic research and the development of advanced pathological diagnosis for chemical modifications.

Dealing with plasmonic crystal biosensors: Sensitivity assessment of nanodisks/nanoholes arrayed plasmonic system for label-free DNA detection

Label-free optical deoxyribonucleic acid (DNA) sensing with arrayed plasmonic nanostructures (plasmonic crystals) is a promising technology for biomedical diagnosis and bioanalytical science. Plasmonic biosensors can detect target biomolecules by utilizing the shift in plasmonic resonance caused by changes in the surrounding refractive index (RI) attributed to the capture of target biomolecules using a recognizer. Conventional explanations for the sensitivity of plasmonic crystals are based on bulk (BRIS) and surface RI sensitivities (SRIS) for basic plasmonic nanoparticles despite their unique properties such as surface lattice resonances (SLRs), wherein localized surface plasmons (LSPs) cooperatively oscillate with their pitch. Therefore, investigating the sensitivity of SLRs is imperative for improving sensing performance. In this study, the sensitivity of adenomatous polyposis coli (APC) gene-related DNA hybridization detection of complementary plasmonic crystals composed of nanodisks (PNDs) on or under plasmonic nanoholes (PNHs) was investigated considering the SLR properties. The BRIS was measured using the conventional definition of the peak wavelength shift per unit RI increment (nm/RIU) followed by the SRIS measurement using the layer-by-layer method. The BRIS and SRIS measurements reflect the practical sensitivity for DNA detection. PNHs had higher sensitivity than PNDs, with a limit of detection of 0.30 nM. Further, only the SLR-based mode responded to localized RI changes because of DNA hybridization, whereas both the LSPs- and SLR-based modes responded to uniform RI changes caused by layer-by-layer coating. Our investigation will open up possibilities and opportunities for plasmonic crystal biosensors.

Self-assembled methodologies for the construction of DNA nanostructures and biological applications.

Over the past decades, deoxyribonucleic acid (DNA), as a versatile building block, has been widely employed to construct functionalized nanostructures. Among the diverse types of materials, DNA related nanostructures have gained growing attention due to their intrinsic programmability, favorable biocompatibility, and strong molecular recognition capability. The conventional construction strategy for building DNA structures is based on Watson-Crick base-pairing rules, which are mainly driven by the hydrogen bonding of bases. However, hydrogen bonding-based DNA nanostructures cannot meet the requirements of specific morphology and multifunctionality. Currently, various functional elements have been introduced to expand the synthetic methodologies for constructing the DNA hybrid nanostructures, including small molecules, peptide polymers, organic ligands and transition metal ions. Besides, the potential applications for these DNA hybrid nanostructures have also been explored. It has been demonstrated that DNA hybrid structures with various properties can be extensively applied in the fields of magnetic resonance, luminescence imaging, biomedical detection, and drug delivery systems. In this review, we highlight the pioneering contributions to the methodologies of DNA-based nanostructure assembly. Furthermore, the recent advances in drug delivery systems and biomedical diagnosis based on DNA hybrid nanostructures are briefly summarized.

Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution.

Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.

Performance Analysis of Electrochemical Detection Platform for DNA Hybridization Using TGN-Based Nanobiosensor

Trilayer graphene nanoribbon (TGN) has great potential in related biomedical applications such as drug and gene delivery and deoxyribonucleic acid (DNA) sensing. The performance of a biosensor based on a liquid gate TGN field effect transistor (Lg-TGNFET) to different DNA cancentrations and adsorption effect on the sensing parameters are analytically investigated in this research. Also, the energy band structure, density of states, carrier concentration, electrical conductance and caused electrical response on TGN as a detection element are studied considering the spin–orbit coupling effect, in which significant current change of the TGN-based biosensor is observed after exposure to DNA different values. DNA concentration as a function of gate voltage is assumed and sensing factor is defined. The results of this research confirm that the current of the biosensor is decreased and Vg-min is obviously left-shifted by increasing value of DNA concentration, suggesting that DNA molecules n-dopes the TGN film. In order to verify the accuracy of the TGN-based biosensor, it is compared with recent analytical and experimental reports on DNA biosensors. The proposed biosensor with high specificity and sensitivity exposes higher current compared to that of monolayer graphene counterpart for analogous ambient conditions.

Synergistic integration of MoOx co-catalyst with oxygen vacancies-engineered on BiVO4 for enhancing the sensitivity of photoelectrochemical DNA biosensing

Photoelectrochemical (PEC) biosensors of deoxyribonucleic acid (DNA) hybridization with simultaneously high signal-to-noise ratio and low limit-of-detection remains greatly challenging owing to the rapid recombination of photogenerated carriers of photoelectrode. Herein, we report an efficient strategy to amplify the photocurrent signal by coupling the MoOx co-catalysts and surface oxygen vacancies (Ov) of BiVO4 as photoelectrode (MoOx/BiVO4-Ov). Using a simple in situ solution impregnation method, non-noble metal MoOx nanoparticles can be grown uniformly onto BiVO4, subsequently, abundant surface Ov of MoOx/BiVO4 is induced by N2-plasma treatment. The coupling of MoOx and surface Ov on BiVO4 can efficiently promote the separation of photogenerated carriers, as a result, the optimized MoOx/BiVO4-Ov shows an excellent photocurrent response of 300.52 μA/cm2 under simulated sunlight illumination, which is 59.6 and 5.4 times higher than that of pristine BiVO4 and MoOx/BiVO4, respectively. Furthermore, the PEC biosensor based on MoOx/BiVO4-Ov demonstrates an excellent sensitivity toward DNA hybridization (10 pM to 10 μM) with a calculated detection limit down to 0.0549 pM. Moreover, this PEC biosensor exhibits specific selectivity as well as high stability. The proposed amplification strategy by the synergistic effect of co-catalysts and defects is valuable for the construction of efficient sensors for the early diagnosis of multiple diseases.

Oral microbial colonization on titanium and polyetheretherketone dental implant healing abutments: An in vitro and in vivo study

Although polyetheretherketone (PEEK) implant healing abutments have become popular because of their esthetic, mechanical, and chemical properties, studies analyzing oral polymicrobial adhesion to PEEK abutments are lacking. The purpose of this in vitro and in vivo study was to evaluate oral microbial adhesion and colonization on titanium (Ti) and PEEK healing abutments. Ti (N=35) and PEEK substrates (N=35) were evaluated in vitro in terms of the initial adhesion (1 hour) or biofilm accumulation (48 hours) of Candida albicans and a polymicrobial inoculum using stimulated human saliva to mimic a diverse oral microbiome. Surface decontamination ability was evaluated after 24 hours of in vitro biofilm formation after exposure to an erbium-doped yttrium aluminum garnet (Er:YAG) laser. Conventional and flowable composite resin veneering on PEEK was also tested for microbial adhesion. In addition, an in vivo model with 3 healthy volunteers was conducted by using a palatal appliance containing the tested materials (3 or 4 specimens of each material per appliance) for 2 days to evaluate the effect of substrate on the microbial profile. Biofilms were evaluated by live cell counts and scanning electron microscopy images, and the microbial profile by Checkerboard deoxyribonucleic acid (DNA)-DNA hybridization. The t test and Mann-Whitney test were used to compare the groups (α=.05). PEEK and Ti materials showed similar fungal adhesion (P>.05). Although the PEEK surface limited the initial in vitro polymicrobial adhesion (approximately 2 times less) compared with Ti (P=.040), after 48 hours of biofilm accumulation, the microbial load was statistically similar (P=.209). Er:YAG laser decontamination was more effective on PEEK than on Ti surfaces, reducing approximately 11 times more microbial accumulation (P=.019). Both composite resins tested showed similar microbial adhesion (1 hour). In vivo, the PEEK material showed reduced levels of 6 bacterial species (P<.05), including the putative pathogen Treponema denticola. Although PEEK and Ti had similar bacterial and fungus biofilm attachment and accumulation, PEEK promoted a host-compatible microbial profile with a significantly reduced T. denticola load.

CMOS Capacitive Sensor for DNA Detection in Undiluted Ionic Solution

Capacitive detection of affinity-bound biomolecules enables rapid and label-free bioassays suitable for point-of-care diagnostic applications. However, direct detection at high ionic strengths is severely limited by the Debye charge-screening effect of the electric double layer on the sensor surface, leading most studies to be performed at diluted ionic strengths. In this study, probe-target deoxyribonucleic acid (DNA) hybridization was successfully measured by modulating the electric field of the interdigitated sensing electrodes to reduce charge screening. The developed 8 × 8 complementary metal oxide semiconductor (CMOS) capacitive sensor array exhibited a sensitivity of 150 fF/log10[DNA] measured at 15 MHz from 10 aM to 100 pM with a response time of approximately 400 seconds. The array also exhibited a pH sensitivity of 354 fF/pH.

A Novel Image Encryption Scheme for DNA Storage Systems Based on DNA Hybridization and Gene Mutation.

With the rapid development of DNA (deoxyribonucleic acid) storage technologies, storing digital images in DNA is feasible. Meanwhile, the information security in DNA storage system is still a problem to solve. Therefore, in this paper, we propose a DNA storage-oriented image encryption algorithm utilizing the information processing mechanisms in molecule biology. The basic idea is to perform pixel replacement by gene hybridization, and implement dual diffusion by pixel diffusion and gene mutation. The ciphertext DNA image can be synthesized and stored in DNA storage system after encryption. Experimental results demonstrate it can resist common attacks, and shows a strong robustness against sequence loss and base substitution errors in the DNA storage channel. A DNA storage-oriented image encryption algorithm based on gene hybridization and gene mutation, First, we scramble rows and columns of the plaintext image by dynamic Josephus traversing. Second, we replace the pixels by gene hybridization. Finally, we diffuse the image matrix in binary domain and encode pixels into 8-base strands which are later further diffused by gene mutation. The ciphertext image can be synthesized according to the mutant gene codes and stored in any DNA storage system.

Comparison of laboratory methods for identifying members of the family Mycobacteriaceae.

The introduction of a method based on matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF mass spectrometry) into the practice of laboratories significantly increased the identification of acid-resistant bacteria (ARB). Seventy-four nontuberculous mycobacteria (NTM) cultures identified by deoxyribonucleic acid (DNA) hybridization, polymerase chain reaction, Sanger sequencing, and MALDI-ToF mass spectrometry. Analysis of the identification results obtained by the methods of DNA hybridization and Sanger sequencing showed a complete match only for 67.6% of samples of the total number of cultures included in the study. The partial match of the identification results was 68.9%. When comparing the results of the identification of 74 samples obtained by MALDI-ToF mass spectrometry to the results obtained by sequencing, full match of identification of Mycobacterium chimaera/Mycobacterium intracelullare, Mycobacterium porcinum/Mycobacterium peregrinum and Mycobacterium tuberculosis complex was found for 90.5% of the samples; the partial match of the results - for 4.1%.. DNA hybridization as a method for identifying NTM showed acceptable sensitivity and specificity; however, for mass spectrometry, a significantly higher sensitivity with comparable specificity was determined. Mass spectrometry is an important element in the modern system of species identification of microorganisms. The optimization of sample preparation protocols and assessment of the impact on the identification of new techniques of cultivation of microorganisms can significantly improve the quality of identification of microorganisms from the ARB group. In this case, accurate species identification and the development of algorithms for its application will improve the diagnosis of diseases caused by ARB.

Optimum Design of Surface Plasmon Resonance (SPR) Tapered Fiber Optic Biosensing Probe With Graphene–MoS2 Over Layers for DNA Hybridization

A novel graphene/MoS2-coated tapered fiber optic surface plasmon resonance (SPR) biosensing probe is presented for the first time to analyze the deoxyribonucleic acid (DNA) hybridization working in the near-infrared region (IR) of the electromagnetic spectrum with improved performance. A proper optimization mechanism is devised to study DNA hybridization concerning the taper ratio. A transfer matrix method (TMM) has been envisaged to study various performance parameters such as the figure of merit (F.O.M.), detection accuracy (D.A.), full width at half maximum (FWHM), and sensitivity. The proposed biosensor is very effectively able to distinguish between DNA hybridization and single-nucleotide polymorphisms (SNPs) by observing a considerable shift in SPR resonance wavelength and transmission dip. Due to the effect of optimized graphene/MoS2 nanostructured and tapering section of fiber, the proposed SPR biosensor work in the near-IR region is very much advantageous for further scope of sensing technology.

Detection of DNA Hybridization Beyond the Debye Screening Length by CMOS Capacitive Sensors

Capacitive sensors are very promising to provide label-free and real-time biological detection for point-of-care diagnostic applications. However, the Debye charge screening effect severely hinders the detection under high ionic strength condition, such as in human serum. Therefore, most measurements are made indirectly in diluted solutions. To solve this problem, electric field modulation between the interdigitated sensing electrodes is applied in this study to increase the Debye length. For DNA (deoxyribonucleic acid) measurements, the two designs operating around 90 and 40 MHz exhibited sensitivities of 2.6 fF/log[DNA] and 10.8 fF/log[DNA] up to 100 fM and a response time of 12 minutes.

Theoretical simulation of DNA hybridization based on cascaded plasmonic V-shaped channel biosensor

A compact biosensor based on specially designed Cascaded V-shaped Channels (CVSChs) for the analysis and detection of Deoxyribonucleic Acid (DNA) hybridization is presented in this paper. The proposed biosensor employs a Gold (Au) nanowire in then CVSChs sensing region and provides more flexibility as far as tailoring the detection range and sensitivity as compared to the single V-shaped channel (VSC). It has been numerically demonstrated that the detection sensitivity of DNA hybridization is significantly dependent on the number of the V shaped channels. A two – dimensional Finite Difference Time Domain (FDTD) analysis with Perfectly Matched Layers (PMLs) is employed to evaluate the sensor performance with different structural parameters. Simulation results indicate that the proposed biosensor can achieve a high sensitivity of 2541 nm / RIU by optimizing the structural parameters. We demonstrate a proof-of-concept hybrid biosensor by monitoring the resonance shift due to the hybridization event. The proposed biosensor will have great impact on early stage detection of infected cells.

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.

Electrochemical sensor based on MoS2 nanosheets and DNA hybridization for trace mercury detection

• Chitosan/GO/MoS 2 /AuNPs and T-Hg 2+ -T base pair were used to form an electrochemical sensor with low detection limit, good repeatability, and specificity. • MoS 2 nanosheets were used as a substrate for the immobilization of DNA and amplified the electrochemical signal produced by the sensor. • A novel electrochemical method for trace Hg 2+ detection in water was developed. Mercury ions (Hg 2+ ) are highly toxic and can cause serious harm to the environment and human health. In this study, we prepared a novel electrochemical sensor based on an electrode coated with chitosan/graphene oxide/molybdenum disulfide/Au nanoparticles (chitosan/GO/MoS 2 /AuNPs) and thymine-Hg 2+ -thymine base pair to detect trace Hg 2+ in water. This method effectively utilized the affinity of MoS 2 to immobilize deoxyribonucleic acid (DNA) on the electrode surface and enabled the amplification of the electrochemical signals detected by the sensor. The specific binding of the thymine-Hg 2+ -thymine base pair and the electrochemical activity of MoS 2 successfully reduced the detection limit of Hg 2+ and rendered it interference resistant. In the presence of Hg 2+ , a double-stranded structure was formed on the electrode after the interaction between Hg 2+ and DNA, which caused the change of the oxidation current signal of the electrode surface. The sensor showed good linearity ranging from 0.01 μg/L to 4 μg/L with a correlation coefficient of 0.991, and the limit of detection was found to be 5.8 ng/L. This portable chitosan/GO/MoS 2 /AuNPs modified electrode showed satisfactory recovery in tap water samples, thus demonstrating its potential for application in trace Hg 2+ detection.

High-performance fiber-optic-based SPR sensor for DNA hybridization using black phosphorus-tungsten disulfide hybrid structure

A high-performance fiber-optic-based surface plasmon resonance (SPR) sensor is proposed using a hybrid structure of black phosphorus and tungsten disulfide. This study shows the DNA hybridization sensing and the single nucleotide polymorphisms identifying procedure by observing the resonance shift and transmitter power performances for probe deoxyribonucleic acid (DNA), mismatched DNA, and complementary DNA stands. Moreover, the performance parameters, such as sensitivity (S) of 303.43°/RIU, depth-of-figure-of-merit (DFOM) of 760825, quality factor of 121.73 R I U − 1 , and detection accuracy of 3.65 are observed. Finally, this work shows a better SPR performance compared to the state-of-the-art works and includes an additional DFOM parameter, which shows a resonance depth effect.

Ratiometric FRET Encoded Hierarchical ZrMOF @ Au Cluster for Ultrasensitive Quantifying MicroRNA In Vivo.

Here, Zirconium metal-organic frameworks @ gold (ZrMOF @ Au) cluster architectures have been fabricated and then functionalized with two fluorescent dyes (Quasar [QS] and Cyanine5.5 [Cy5.5]) through deoxyribonucleic acid hybridization, to form a fluorescence resonance energy transfer (FRET) encoded ZrMOF @ Au-QS/Cy5.5 complex. In the presence of the target intracellular microRNA (miR)-21, the fluorescence of Cy5.5 at 705nm (F705 ) decreases and the fluorescence of QS at 665nm (F665 ) increases when Cy5.5 is released from the surface of ZrMOF @ Au-QS/Cy5.5. The change in the fluorescence ratio (F705 /F665 ) shows an outstanding linear range of 0.006-67.9 amol/ngRNA , and the limit of detection is 4.51 zmol/ngRNA in living cells. The high ratio loading of nucleic acid on surface of ZrMOF @ Au cluster and two fluorescence encoded signal enables better sensitivity and reliability. Zeptomolar sensitivity and good linearity against target affords distinct imaging-based monitoring of the cancer marker miR-21 both in living cells and in vivo. At the same time, the architecture displays remarkable photothermal conversion efficiency (53.7%) and gives rise to outstanding therapy ability in vivo. This strategy offers new avenues for the intelligent quantification of miRNAs for simultaneous diagnoses and treatments of early-stage cancers.

Scaling up DNA digital data storage by efficiently predicting DNA hybridisation using deep learning

Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in solution, thus enabling search and pattern-matching capabilities. Being able to control and predict the process of DNA hybridisation is crucial for the ambitious future of Hybrid Molecular-Electronic Computing. Current tools are, however, limited in terms of throughput and applicability to large-scale problems. We present the first comprehensive study of machine learning methods applied to the task of predicting DNA hybridisation. For this purpose, we introduce an in silico-generated hybridisation dataset of over 2.5 million data points, enabling the use of deep learning. Depending on hardware, we achieve a reduction in inference time ranging from one to over two orders of magnitude compared to the state-of-the-art, while retaining high fidelity. We then discuss the integration of our methods in modern, scalable workflows.

Multimodules integrated functional DNA nanomaterials for intelligent drug delivery.

Deoxyribonucleic acid (DNA) has been an emerging building block to construct functional biomaterials. Due to their programmable sequences and rich responsiveness, DNA has attracted rising attention in the construction of intelligent nanomaterials with predicable nanostructure and adjustable functions, which has shown great potential in drug delivery. On the one hand, the DNA sequences with molecule recognition, responsiveness, and therapeutic efficacy can be easily integrated to the framework of DNA nanomaterials by sequence designing; on the other hand, the rich chemical groups on DNA molecules provide binding points for other functional units. In this review, we divided the functionalization modules in the construction of DNA nanomaterials into three types, including targeting modules, responsive modules, and therapeutic modules. Based on these modules, five DNA kinds of representative nanomaterials applied in drug delivery were introduced, including DNA nanogel, DNA origami, DNA framework, DNA nanoflower, and DNA hybrid nanosphere. Finally, we discussed the challenges in the transition of DNA materials to clinical applications. We expect that this review can help readers to obtain a deeper understanding of DNA materials, and further promote the development of these intelligent materials to real world's application. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Measuring Excess Heat Capacities of Deoxyribonucleic Acid (DNA) Folding at the Single-Molecule Level.

Measurements of the thermodynamic properties of biomolecular folding (ΔG°, ΔH°, ΔS°, etc.) provide a wealth of information on the folding process and have long played a central role in biophysical investigation. In particular, the excess heat capacity of folding (ΔCP) is crucial, as typically measured in bulk ensemble studies by differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). Here, we report the first measurements of ΔCP at the single-molecule level using the single-molecule fluorescence resonance energy transfer (smFRET) as well as the very first measurements of the heat capacity change associated with achieving the transition state (ΔC‡P) for nucleic acid folding. The deoxyribonucleic acid (DNA) hairpin used in these studies exhibits an excess heat capacity for hybridization (ΔCP = -340 ± 60 J/mol/K per base pair) consistent with the range of literature expectations (ΔCP = -100 to -420 J/mol/K per base pair). Furthermore, the measured activation heat capacities (ΔC‡P) for such hairpin unfolding are consistent with a folding transition state containing few fully formed base pairs, in agreement with prevailing models of DNA hybridization.