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Langmuir : the ACS Journal of Surfaces... May 2021The adsorption and desorption of nucleic acid to a solid surface is ubiquitous in various research areas like pharmaceutics, nanotechnology, molecular biology, and...
The adsorption and desorption of nucleic acid to a solid surface is ubiquitous in various research areas like pharmaceutics, nanotechnology, molecular biology, and molecular electronics. In spite of this widespread importance, it is still not well understood how the negatively charged deoxyribonucleic acid (DNA) binds to the negatively charged silica surface in an aqueous solution. In this article, we study the adsorption of DNA to the silica surface using both modeling and experiments and shed light on the complicated binding (DNA to silica) process. The binding agent mediated DNA adsorption was elegantly captured by cooperative Langmuir model. Bulk-depletion experiments were performed to conclude the necessity of a positively charged binding agent for efficient DNA binding, which complements the findings from the model. A profound understanding of DNA binding will help to tune various processes for efficient nucleic acid extraction and purification. However, this work goes beyond the DNA binding and can shed light on other binding agent mediated surface-surface, surface-molecule, molecule-molecule interaction.
Topics: Adsorption; DNA; Silicon Dioxide; Surface Properties; Water
PubMed: 33951395
DOI: 10.1021/acs.langmuir.1c00381 -
Mikrochimica Acta Aug 2022Adenine (A) and guanine (G) are mainly found in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and play a crucial role in genetic information transfer and...
Adenine (A) and guanine (G) are mainly found in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and play a crucial role in genetic information transfer and protein synthesis. In this study, NH-MIL-53(Fe)/CS/MXene nanocomposites were prepared for detecting guanine and adenine. With high specific surface area, excellent water dispersion, and numerous active sites, MXene (transition metal carbides, nitrides, and carbonitrides) provides a good platform for loading primitive metal-organic frameworks (MOFs). At the same time, the problem of poor conductivity and dispersion of MOFs is solved. The electrochemical catalytic oxidation of adenine and guanine of NH-MIL-53 (Fe)/CS/MXene nanocomposites was carried out by differential pulse voltammetry (DPV). Operating voltage of DPV: 0.7-0.9 V (vs. Ag/AgCl) for G, 1.0-1.2 V (vs. Ag/AgCl) for A, 0.8 V (vs. Ag/AgCl), and 1.1 V (vs. Ag/AgCl) for G and A. The concentration ranges for detecting A and G were 3-118 μM and 2-120 μM with detection limits of 0.57 μM and 0.17 μM (S/N = 3), respectively. The nanocomposite was used for detecting G and A in herring sperm DNA, and the content of G and A was found to be about 9 and 11 μM; the RSD values were 3.4 and 1.3%, respectively.
Topics: Humans; Male; Adenine; DNA; Electrochemical Techniques; Electrodes; Guanine; Metal-Organic Frameworks; Nanocomposites; Semen
PubMed: 35962293
DOI: 10.1007/s00604-022-05376-5 -
Sensors (Basel, Switzerland) Feb 2021Deoxyribonucleic acid (DNA) electrochemical biosensors are devices that incorporate immobilized DNA as a molecular recognition element on the electrode surface, and... (Review)
Review
Deoxyribonucleic acid (DNA) electrochemical biosensors are devices that incorporate immobilized DNA as a molecular recognition element on the electrode surface, and enable probing in situ the oxidative DNA damage. A wide range of DNA electrochemical biosensor analytical and biotechnological applications in pharmacology are foreseen, due to their ability to determine in situ and in real-time the DNA interaction mechanisms with pharmaceutical drugs, as well as with their degradation products, redox reaction products, and metabolites, and due to their capacity to achieve quantitative electroanalytical evaluation of the drugs, with high sensitivity, short time of analysis, and low cost. This review presents the design and applications of label-free DNA electrochemical biosensors that use DNA direct electrochemical oxidation to detect oxidative DNA damage. The DNA electrochemical biosensor development, from the viewpoint of electrochemical and atomic force microscopy (AFM) characterization, and the bottom-up immobilization of DNA nanostructures at the electrode surface, are described. Applications of DNA electrochemical biosensors that enable the label-free detection of DNA interactions with pharmaceutical compounds, such as acridine derivatives, alkaloids, alkylating agents, alkylphosphocholines, antibiotics, antimetabolites, kinase inhibitors, immunomodulatory agents, metal complexes, nucleoside analogs, and phenolic compounds, which can be used in drug analysis and drug discovery, and may lead to future screening systems, are reviewed.
Topics: Biosensing Techniques; DNA; DNA Damage; Electrochemical Techniques; Oxidation-Reduction; Oxidative Stress; Pharmaceutical Preparations
PubMed: 33562790
DOI: 10.3390/s21041125 -
Biochemistry and Cell Biology =... Jun 2022Fast, accessible, and high-quality deoxyribonucleic acid (DNA) is fundamental to advancement in the life sciences that will drive forward fields such as agriculture,...
Fast, accessible, and high-quality deoxyribonucleic acid (DNA) is fundamental to advancement in the life sciences that will drive forward fields such as agriculture, energy, and medicine. Despite their importance in accelerating global progress, bioscience research and biotechnologies can also be misused, endangering humans, animals, and the environment. The ability to accidentally or deliberately endow or enhance the pathogenicity of biological systems is of particular concern. Access to DNA sequences with a clear potential for dual use should be limited to responsible and identifiable groups with legitimate uses. Yet, none of the 195 countries party to the International Health Regulations have national laws that mandate this type of screening. Many DNA providers voluntarily screen orders and absorb increased costs, but this practice is not universally adopted for a variety of reasons. This article explores the incentives and regulatory structures that can bring the screening coverage of DNA orders toward 100%, which may include expedited orders for approved customers, better tools and technology for more efficient screening, funding requirements that grantees use screened DNA, and early education in biosecurity aimed at researchers and students. Ultimately, an incentive-based multistakeholder approach to DNA screening can benefit researchers, industry, and global health security.
Topics: Biological Science Disciplines; DNA; Humans; Motivation; Research Personnel
PubMed: 35290750
DOI: 10.1139/bcb-2021-0504 -
Electrophoresis Sep 2022The laser print, cut, and laminate (PCL) method for microfluidic device fabrication can be leveraged for rapid and inexpensive prototyping of electrophoretic microchips...
The laser print, cut, and laminate (PCL) method for microfluidic device fabrication can be leveraged for rapid and inexpensive prototyping of electrophoretic microchips useful for optimizing separation conditions. The rapid prototyping capability allows the evaluation of fluidic architecture, applied fields, reagent concentrations, and sieving matrix, all within the context of using fluorescence-compatible substrates. Cyclic olefin copolymer and toner-coated polyethylene terephthalate (tPeT) were utilized with the PCL technique and bonding methods optimized to improve device durability during electrophoresis. A series of separation channel designs and centrifugation conditions that provided successful loading of sieving polymer in less than 3 min was described. Separation of a 400-base DNA sizing ladder provided calculated base resolution between 3 and 4 bases, a greater than 18-fold improvement over separations on similar substrates. Finally, the accuracy and precision capabilities of these devices were demonstrated by separating and sizing DNA fragments of 147 and 167 bases as 148.62 ± 2 and 166.48 ± 3 bases, respectively.
Topics: Centrifugation; DNA; Electrophoresis; Lab-On-A-Chip Devices; Polymers
PubMed: 35656648
DOI: 10.1002/elps.202200090 -
Forensic Science International Dec 2022In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to...
In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to the presence of inhibitors which limit the effective extraction and amplification of the deoxyribonucleic acid (DNA) required to produce a reportable DNA profile. There are some extraction methods that have been applied to blood-stained soil in forensic science, but these have produced sporadic results. This research has taken a number of different extraction methods from the fields of ancient DNA and environmental DNA and broken them down into the individual steps of pre-treatment, incubation, separation and purification. These steps were assessed independently then combined into various extraction methods to determine the best technique that can effectively and reliably profile human DNA from blood-stained soil. Testing involved assessment of three extraction buffers, (cetyltrimethylammonium bromide, guanidine thiocyanate, and proteinase K), four pre-treatment methods, (polyvinylpyrrolidone, ethylenediaminetetraacetic acid, hydrochloric acid, and sodium hydroxide), three separation steps, (centrifugation, phenol chloroform, and chloroform) and four purification steps, (size exclusion chromatography, bind elute columns, isopropanol precipitation and silica magnetic beads). The most effective procedure was found to be a polyvinylpyrrolidone pre-treatment with a proteinase K extraction buffer followed by magnetic silica bead purification with or without centrifugation. However, centrifugation separation was found to be equally effective after the pre-treatment step as after the incubation step. Our results shows that most of the current forensic procedures would benefit from the addition of a pre-treatment step prior to processing through the automated DNA profiling pipeline.
Topics: Humans; Soil; Polymerase Chain Reaction; DNA; Chloroform; Povidone; Endopeptidase K; Blood Stains; Silicon Dioxide
PubMed: 36371979
DOI: 10.1016/j.forsciint.2022.111502 -
Biosensors Mar 2023Even today, most biomarker testing is executed in centralized, dedicated laboratories using bulky instruments, automated analyzers, and increased analysis time and... (Review)
Review
Even today, most biomarker testing is executed in centralized, dedicated laboratories using bulky instruments, automated analyzers, and increased analysis time and expenses. The development of miniaturized, faster, low-cost microdevices is immensely anticipated for substituting for these conventional laboratory-oriented assays and transferring diagnostic results directly onto the patient's smartphone using a cloud server. Pioneering biosensor-based approaches might make it possible to test biomarkers with reliability in a decentralized setting, but there are still a number of issues and restrictions that must be resolved before the development and use of several biosensors for the proper understanding of the measured biomarkers of numerous bioanalytes such as DNA, RNA, urine, and blood. One of the most promising processes to address some of the issues relating to the growing demand for susceptible, quick, and affordable analysis techniques in medical diagnostics is the creation of biosensors. This article critically discusses a short review of biosensors used for detecting nucleic acid biomarkers, and their use in biomedical prognostics will be addressed while considering several essential characteristics.
Topics: Humans; Biomarkers; Biosensing Techniques; DNA; Nucleic Acids; Reproducibility of Results
PubMed: 36979624
DOI: 10.3390/bios13030412 -
ACS Biomaterials Science & Engineering Nov 2022Deoxyribonucleic acid (DNA) evolved as a tool for storing and transmitting genetic information within cells, but outside the cell, DNA can also serve as "construction...
Deoxyribonucleic acid (DNA) evolved as a tool for storing and transmitting genetic information within cells, but outside the cell, DNA can also serve as "construction material" present in microbial biofilms or various body fluids, such as cystic fibrosis, sputum, and pus. In the present work, we investigate the mechanics of biofilms formed from Xen 5, Xen 30, and 1408 using oscillatory shear rheometry at different levels of compression and recreate these mechanics in systems of entangled DNA and cells. The results show that the compression-stiffening and shear-softening effects observed in biofilms can be reproduced in DNA networks with the addition of an appropriate number of microbial cells. Additionally, we observe that these effects are cell-type dependent. We also identify other mechanisms that may significantly impact the viscoelastic behavior of biofilms, such as the compression-stiffening effect of DNA cross-linking by bivalent cations (Mg, Ca, and Cu) and the stiffness-increasing interactions of Xen 5 biofilm with Pf1 bacteriophage produced by . This work extends the knowledge of biofilm mechanobiology and demonstrates the possibility of modifying biopolymers toward obtaining the desired biophysical properties.
Topics: Biofilms; Pseudomonas aeruginosa; Staphylococcus aureus; DNA
PubMed: 36301743
DOI: 10.1021/acsbiomaterials.2c00777 -
Lab on a Chip Mar 2022The digital polymerase chain reaction (dPCR) is an irreplaceable variant of PCR techniques due to its capacity for absolute quantification and detection of rare...
The digital polymerase chain reaction (dPCR) is an irreplaceable variant of PCR techniques due to its capacity for absolute quantification and detection of rare deoxyribonucleic acid (DNA) sequences in clinical samples. Image processing methods, including micro-chamber positioning and fluorescence analysis, determine the reliability of the dPCR results. However, typical methods demand high requirements for the chip structure, chip filling, and light intensity uniformity. This research developed an image-to-answer algorithm with single fluorescence image capture and known image-related error removal. We applied the Hough transform to identify partitions in the images of dPCR chips, the 2D Fourier transform to rotate the image, and the 3D projection transformation to locate and correct the positions of all partitions. We then calculated each partition's average fluorescence amplitudes and generated a 3D fluorescence intensity distribution map of the image. We subsequently corrected the fluorescence non-uniformity between partitions based on the map and achieved statistical results of partition fluorescence intensities. We validated the proposed algorithms using different contents of the target DNA. The proposed algorithm is independent of the dPCR chip structure damage and light intensity non-uniformity. It also provides a reliable alternative to analyze the results of chip-based dPCR systems.
Topics: Algorithms; DNA; Image Processing, Computer-Assisted; Polymerase Chain Reaction; Reproducibility of Results
PubMed: 35258048
DOI: 10.1039/d1lc01175h -
Journal of Biomolecular Structure &... Jun 2022In the present study, 21 cytosine tautomers were investigated so that some tautomers were reported for the first time in the gas phase and aqueous solution. C tautomer...
A theoretical study on the role of stability of cytosine and its tautomers in DNA (deoxyribonucleic acid), and investigation of interactions of Na, K, Mg, Ca, Zn metal ions and OH radical with cytosine tautomers.
In the present study, 21 cytosine tautomers were investigated so that some tautomers were reported for the first time in the gas phase and aqueous solution. C tautomer was the most stable tautomer in gas phase but C was the most stable structure in aqueous solution. The potential energy surface of all trajectories was determined for 21 tautomers and 22 transition states. Also, interactions of cytosine tautomers with Na, K, Mg, Ca and Zn metal ions were studied in gas phase and aqueous solution. Three types of interactions among metal ions and (N1 and O10), (N3 and O10) and (N3 and N9) of cytosine tautomers were investigated. The study of interaction energies of all complexes showed the stability of complexes in which interactions among Mg and Zn with tautomers were stronger than interactions among Ca, Na and K with tautomers, respectively. Some interactions of metal ions with cytosine tautomers made the most stable tautomers. So, the stability of rare tutomeric forms had a significant effect on stabilization of anomalous DNA (deoxyribonucleic acid) double helix and spontaneous mutations. Also, one of the most important causes of mutations in DNA (deoxyribonucleic acid) was the reaction of OH radical with nucleotide bases. So, interactions of OH radical with cytosine and its tautomers were investigated in gas phase and aqueous solution.Communicated by Ramaswamy H. Sarma.
Topics: Cytosine; DNA; Ions; Isomerism; Metals; Models, Theoretical; Sodium; Water; Zinc
PubMed: 33252005
DOI: 10.1080/07391102.2020.1850526