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Critical Reviews in Analytical Chemistry 2023Graphene, emerging as a true two-dimensional (2D) material, has attracted increasing attention due to its unique physical and electrochemical properties such as high... (Review)
Review
Graphene, emerging as a true two-dimensional (2D) material, has attracted increasing attention due to its unique physical and electrochemical properties such as high surface area, excellent conductivity, high mechanical strength, and ease of functionalization and mass production. The entire scientific community recognizes the significance and potential impact of graphene. Electrochemical detection strategies have advantages such as being simple, fast, and low-cost. The use of graphene as an excellent interface for electrode modification provides a promising way to construct more sensitive and stable electrochemical (bio)sensors. The review presents sensors based on graphene and its derivatives for electrochemical drug assays from pharmaceutical dosage forms and biological samples. Future perspectives in this rapidly developing field are also discussed. In addition, the interaction of several important anticancer drug molecules with deoxyribonucleic acid (DNA) that was immobilized onto graphene-modified electrodes has been detailed in terms of dosage regulation and utility purposes.
Topics: Graphite; Biosensing Techniques; Electrodes; DNA; Electrochemical Techniques
PubMed: 34941476
DOI: 10.1080/10408347.2021.2018568 -
Current Topics in Medicinal Chemistry 2022Inspired by molecular machines in nature, artificial nanodevices have been designed to realize various biomedical functions. Self-assembled deoxyribonucleic acid (DNA)...
Inspired by molecular machines in nature, artificial nanodevices have been designed to realize various biomedical functions. Self-assembled deoxyribonucleic acid (DNA) nanostructures that feature designed geometries, excellent spatial accuracy, nanoscale addressability, and marked biocompatibility provide an attractive candidate for constructing dynamic nanodevices with biomarker- targeting and stimuli-responsiveness for biomedical applications. Here, a summary of typical construction strategies of DNA nanodevices and their operating mechanisms are presented. We also introduced recent advances in employing DNA nanodevices as platforms for biosensing and intelligent drug delivery. Finally, the broad prospects and main challenges of the DNA nanodevices in biomedical applications are also discussed.
Topics: DNA; Drug Delivery Systems; Nanostructures; Nanotechnology
PubMed: 34749612
DOI: 10.2174/1568026621666211105100240 -
Briefings in Bioinformatics Sep 2023Genome assembly is a computational technique that involves piecing together deoxyribonucleic acid (DNA) fragments generated by sequencing technologies to create a...
Genome assembly is a computational technique that involves piecing together deoxyribonucleic acid (DNA) fragments generated by sequencing technologies to create a comprehensive and precise representation of the entire genome. Generating a high-quality human reference genome is a crucial prerequisite for comprehending human biology, and it is also vital for downstream genomic variation analysis. Many efforts have been made over the past few decades to create a complete and gapless reference genome for humans by using a diverse range of advanced sequencing technologies. Several available tools are aimed at enhancing the quality of haploid and diploid human genome assemblies, which include contig assembly, polishing of contig errors, scaffolding and variant phasing. Selecting the appropriate tools and technologies remains a daunting task despite several studies have investigated the pros and cons of different assembly strategies. The goal of this paper was to benchmark various strategies for human genome assembly by combining sequencing technologies and tools on two publicly available samples (NA12878 and NA24385) from Genome in a Bottle. We then compared their performances in terms of continuity, accuracy, completeness, variant calling and phasing. We observed that PacBio HiFi long-reads are the optimal choice for generating an assembly with low base errors. On the other hand, we were able to produce the most continuous contigs with Oxford Nanopore long-reads, but they may require further polishing to improve on quality. We recommend using short-reads rather than long-reads themselves to improve the base accuracy of contigs from Oxford Nanopore long-reads. Hi-C is the best choice for chromosome-level scaffolding because it can capture the longest-range DNA connectedness compared to 10× linked-reads and Bionano optical maps. However, a combination of multiple technologies can be used to further improve the quality and completeness of genome assembly. For diploid assembly, hifiasm is the best tool for human diploid genome assembly using PacBio HiFi and Hi-C data. Looking to the future, we expect that further advancements in human diploid assemblers will leverage the power of PacBio HiFi reads and other technologies with long-range DNA connectedness to enable the generation of high-quality, chromosome-level and haplotype-resolved human genome assemblies.
Topics: Humans; Sequence Analysis, DNA; Genome, Human; Benchmarking; High-Throughput Nucleotide Sequencing; DNA
PubMed: 37594299
DOI: 10.1093/bib/bbad300 -
Medicine Mar 2022To evaluate the performance of polymerase chain reaction (PCR)-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental...
To evaluate the performance of polymerase chain reaction (PCR)-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection.Five NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing deoxyribonucleic acid (DNA) input and library preparation protocol (PCR-based vs PCR-free protocols for library preparation). The depth of coverage and genotype quality of each sample were compared. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes, and copy number variants. We also developed a systematic WGS pipeline (PCR-free) for the analysis of 11 clinical cases.In general, NA12878-2 (PCR-free WGS) showed better depth of coverage and genotype quality distribution than NA12878-1 (PCR-based WGS). With a mean depth of ∼40×, the sensitivity of homozygous and heterozygous single nucleotide polymorphisms (SNPs) of NA12878-2 showed higher sensitivity (>99.77% and >99.82%) than NA12878-1, and positive predictive value exceeded 99.98% and 99.07%. The sensitivity and positive predictive value of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and copy number variants are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. All the 19 previously confirmed variants in 11 clinical cases were successfully detected by our WGS pipeline (PCR free).Different experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.
Topics: DNA; DNA Copy Number Variations; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Whole Genome Sequencing
PubMed: 35451387
DOI: 10.1097/MD.0000000000028972 -
Bioengineered Mar 2022The research aimed to explore the biological role of p53 protein and long non-coding RNA (lncRNA) taurine upregulated gene 1 (TUG1) in bupivacaine (bup)-induced...
The research aimed to explore the biological role of p53 protein and long non-coding RNA (lncRNA) taurine upregulated gene 1 (TUG1) in bupivacaine (bup)-induced neurotoxicity. Our work treated dorsal root ganglion (DRG) cells with bup, detected cell viability through CCK-8, apoptosis through TUNEL assays, DeoxyriboNucleic Acid (DNA) damage through γ-H2AX protein and comet assay, including p53 mRNA, protein and TUG1 expression through q-PCR and western blot, furthermore, cell viability and DNA damage were determined after the silencing of p53 and TUG1, biological information and TUG1 FISH combined with p53 protein immunofluorescence (IF) was performed to determine the cellular localization of these molecule. experiments, we explored the impact of intrathecal injection of bup on p53 mRNA and protein, TUG1, γ-H2AX protein expression. The results showed that bup was available to signally decreased cell viability, promoted apoptosis rate and DNA damage, additionally, bup increased p53 mRNA and protein and TUG1 expression. P53 siRNA and TUG1 siRNA significantly increased DNA damage. Furthermore, bioinformatics analysis and colocalization experiments revealed that the p53 protein is a transcription factor of TUG1, in vivo experiment, intrathecal injection of bup increased the p53 mRNA, p53 protein, TUG1 and γ-H2AX protein in the murine DRG. In this study, it was found p53 and TUG1 promote the repair of the DNA damage induced by bup in murine dorsal root ganglion cells, suggesting a new strategy for the amelioration of bup-induced neurotoxicity.
Topics: Animals; Apoptosis; Bupivacaine; Cell Proliferation; DNA; Mice; MicroRNAs; RNA, Messenger; RNA, Small Interfering; Sensory Receptor Cells; Taurine; Tumor Suppressor Protein p53
PubMed: 35271399
DOI: 10.1080/21655979.2022.2048985 -
Small Methods May 2021An ultrastable, highly dense single-molecule assay ideal for observing protein-DNA interactions is demonstrated. Stable click tethered particle motion leverages next...
An ultrastable, highly dense single-molecule assay ideal for observing protein-DNA interactions is demonstrated. Stable click tethered particle motion leverages next generation click-chemistry to achieve an ultrahigh density of surface tethered reporter particles, and has low non-specific interactions, is stable at elevated temperatures to at least 45 °C, and is compatible with Mg , an important ionic component of many regulatory protein-DNA interactions. Prepared samples remain stable, with little degradation, for >6 months in physiological buffers. These improvements enable the authors to study previously inaccessible sequence and temperature-dependent effects on DNA binding by the bacterial protein, histone-like nucleoid-structuring protein, a global transcriptional regulator found in Escherichia coli. This greatly improved assay can directly be translated to accelerate existing tethered particle-based, single-molecule biosensing applications.
Topics: Bacterial Proteins; DNA; Escherichia coli; Escherichia coli Proteins; Histones; Protein Binding; Temperature
PubMed: 34928085
DOI: 10.1002/smtd.202001180 -
ACS Applied Materials & Interfaces Jan 2023An early and accurate cancer diagnosis holds the potential to improve treatment and prognosis. Nevertheless, the complexity of the biological system limits the...
An early and accurate cancer diagnosis holds the potential to improve treatment and prognosis. Nevertheless, the complexity of the biological system limits the selectivity of existing approaches and makes tumor imaging particularly challenging. In this study, tumor-specific fluorescence imaging was achieved by building intelligent dual-lock deoxyribonucleic acid automatons (IDEAs) that employed a DNA walking system standing on ZrMOF@MnO multifunctional nanocomposites for controllable molecular recognition. The IDEAs exhibited significantly enhanced fluorescence signals only in the coexistence of both miRNA and GSH of tumor cells, enabling accurate distinguishing of tumor cells from healthy ones. Furthermore, the feasibility and specificity of IDEAs were also validated with tumor bearing mice successfully. This work highlights the potential of the proposed IDEA strategy for tumor-specific imaging, paving the way for successful precision diagnosis and treatment.
Topics: Animals; Mice; Manganese Compounds; Oxides; Neoplasms; MicroRNAs; Optical Imaging; DNA
PubMed: 36625537
DOI: 10.1021/acsami.2c20024 -
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 -
International Journal of Molecular... Sep 2022Mitochondria are the main sites for oxidative phosphorylation and synthesis of adenosine triphosphate in cells, and are known as cellular power factories. The phrase... (Review)
Review
Mitochondria are the main sites for oxidative phosphorylation and synthesis of adenosine triphosphate in cells, and are known as cellular power factories. The phrase "secondary mitochondrial diseases" essentially refers to any abnormal mitochondrial function other than primary mitochondrial diseases, i.e., the process caused by the genes encoding the electron transport chain (ETC) proteins directly or impacting the production of the machinery needed for ETC. Mitochondrial diseases can cause adenosine triphosphate (ATP) synthesis disorder, an increase in oxygen free radicals, and intracellular redox imbalance. It can also induce apoptosis and, eventually, multi-system damage, which leads to neurodegenerative disease. The catechin compounds rich in tea have attracted much attention due to their effective antioxidant activity. Catechins, especially acetylated catechins such as epicatechin gallate (ECG) and epigallocatechin gallate (EGCG), are able to protect mitochondria from reactive oxygen species. This review focuses on the role of catechins in regulating cell homeostasis, in which catechins act as a free radical scavenger and metal ion chelator, their protective mechanism on mitochondria, and the protective effect of catechins on mitochondrial deoxyribonucleic acid (DNA). This review highlights catechins and their effects on mitochondrial functional metabolic networks: regulating mitochondrial function and biogenesis, improving insulin resistance, regulating intracellular calcium homeostasis, and regulating epigenetic processes. Finally, the indirect beneficial effects of catechins on mitochondrial diseases are also illustrated by the warburg and the apoptosis effect. Some possible mechanisms are shown graphically. In addition, the bioavailability of catechins and peracetylated-catechins, free radical scavenging activity, mitochondrial activation ability of the high-molecular-weight polyphenol, and the mitochondrial activation factor were also discussed.
Topics: Adenosine Triphosphate; Antioxidants; Calcium; Catechin; Chelating Agents; DNA, Mitochondrial; Free Radical Scavengers; Free Radicals; Humans; Mitochondrial Diseases; Neurodegenerative Diseases; Polyphenols; Reactive Oxygen Species; Tea
PubMed: 36232871
DOI: 10.3390/ijms231911569