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BMC Bioinformatics Apr 2023Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both increased the... (Review)
Review
Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both increased the capacity and decreased the cost of storing information in de novo synthesized DNA pools. In this survey, we review methods for translating digital data to and/or from DNA molecules. An emphasis is placed on methods which have been validated by storing and retrieving real-world data via in-vitro experiments.
Topics: DNA; Sequence Analysis, DNA
PubMed: 37085766
DOI: 10.1186/s12859-023-05264-6 -
Bioengineered Dec 2020The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like...
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
Topics: DNA; Humans; Metagenomics; Nucleic Acids
PubMed: 32149573
DOI: 10.1080/21655979.2020.1736238 -
The Turkish Journal of Gastroenterology... Apr 2023This study aimed to analyze the relationship between quantitative hepatitis B surface antigen and hepatitis B virus deoxyribonucleic acid in hepatitis B e...
Correlation Between Quantitative Hepatitis B Surface Antigen and Hepatitis B Virus Deoxyribonucleic Acid Levels in Hepatitis B e Antigen-Positive and Hepatitis B e AntigenNegative Chronic Hepatitis B Patients.
BACKGROUND
This study aimed to analyze the relationship between quantitative hepatitis B surface antigen and hepatitis B virus deoxyribonucleic acid in hepatitis B e antigen-positive and hepatitis B e antigen-negative chronic hepatitis B patients and to determine the best cut-off value for quantitative hepatitis B surface antigen to predict high hepatitis B virus deoxyribonucleic acid levels (≥2000 IU/mL).
METHODS
Ninety-seven sera from chronic hepatitis B patients were collected in this study. Hepatitis B virus deoxyribonucleic acid levels were quantified by real-time polymerase chain reaction. Quantitative hepatitis B surface antigen and hepatitis B e antigen levels were determined by two-site sandwich chemiluminescence immunoassay. Alanine transaminase levels were measured by the International Federation of Clinical Chemistry-approved methods.
RESULTS
A significant correlation between quantitative hepatitis B surface antigen and hepatitis B virus deoxyribonucleic acid levels was observed in hepatitis B e antigen-positive group (r = 0.453, P = .002), but not in hepatitis B e antigen-negative group (r = 0.117, P = .454). No significant correlation between quantitative hepatitis B surface antigen and alanine transaminase was found in the hepatitis B e antigen-positive group (r = 0.521, P = .241). However, a significant correlation was shown between quantitative hepatitis B surface antigen and alanine transaminase levels in the hepatitis B e antigen-negative group (r = 0.455, P = .001). The best cut-off value of quantitative hepatitis B surface antigen for predicting high hepatitis B virus deoxyribonucleic acid levels was 3.422 × 103 IU/mL.
CONCLUSION
Correlation between quantitative hepatitis B surface antigen and hepatitis B virus deoxyribonucleic acid levels is significant in the hepatitis B e antigen-positive group. Quantitative hepatitis B surface antigen can be used to predict high hepatitis B virus deoxyribonucleic acid levels in the hepatitis B e antigen-positive group.
Topics: Humans; Hepatitis B, Chronic; Hepatitis B Surface Antigens; Hepatitis B virus; Hepatitis B e Antigens; Alanine Transaminase; DNA, Viral; Hepatitis A; Hepatitis B
PubMed: 37089049
DOI: 10.5152/tjg.2020.19612 -
Journal of Biomolecular Structure &... Feb 2021Nalidixic acid is a bacterial DNA gyrase inhibitor and the first member of the synthetic quinolone antibiotics. It is used in the treatment of various infectious...
Nalidixic acid is a bacterial DNA gyrase inhibitor and the first member of the synthetic quinolone antibiotics. It is used in the treatment of various infectious diseases like urinary tract infections, respiratory infections, sexually transmitted diseases, acute bronchitis, and sinusitis. Interactions studies are of great significance as it will be beneficial for designing new therapeutic molecules with preferable plasma solubility and its efficacy. In this paper, we have aim to ascertain the binding mode of nalidixic acid with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) through various biophysical and method. UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with ct-DNA. The binding constant is in the range of 10 , indicating the groove binding mode between ct-DNA and nalidixic acid. Groove binding mode was also validated by competitive displacement assay, potassium iodide quenching experiment, circular dichroism, DNA melting studies. In the case of BSA, UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with BSA. The value of a binding constant in the case of BSA was found to be 1.517 × 10 . The site marker displacement experiment revealed the binding location of nalidixic acid to a site I in BSA. Secondary structural and microenvironmental changes also studied through circular dichroism and three-dimensional fluorescence. Furthermore, the synchronous fluorescence spectra of BSA with nalidixic acid showed that there were changes in the microenvironment around tryptophan residues. molecular docking further confirmed the binding of nalidixic acid to site I in BSA and the minor groove of DNA.Communicated by Ramaswamy H. Sarma.
Topics: Binding Sites; Circular Dichroism; DNA; Molecular Docking Simulation; Nalidixic Acid; Protein Binding; Serum Albumin; Serum Albumin, Bovine; Spectrometry, Fluorescence; Thermodynamics
PubMed: 31910794
DOI: 10.1080/07391102.2020.1711808 -
Biopreservation and Biobanking Dec 2023The measurement of nucleic acid quality, especially the analysis of integrity, is a key step for many downstream experiments in biomedical research and quality control...
The measurement of nucleic acid quality, especially the analysis of integrity, is a key step for many downstream experiments in biomedical research and quality control of biomaterials. General gel electrophoresis is a traditional method for nucleic acid integrity analysis. Currently, more electrophoresis techniques are becoming standardized and automated operations with higher precision. In this study, we have evaluated the comparability and bias of the outcomes from three commercial assay systems. Seventy-two deoxyribonucleic acid (DNA) and 67 ribonucleic acid (RNA) samples were selected for methodological comparison among different systems. The DNA Quality Number (DQN) and RNA Quality Number (RQN) of BIOptic Qsep400, DNA Quality Score (DQS) and RNA Quality Score (RQS) of PerkinElmer Labchip GX Touch HT were separately compared with the DNA Integrity Number (DIN) and RNA Integrity Number (RIN) of the Agilent 4200 TapeStation according to Clinical and Laboratory Standards Institute (CLSI) guideline (EP09-A3). The biases of the mean estimated between DQN and DIN, DQS and DIN both exceeded the acceptance criteria. The Passing-Bablok regression analysis between DQN and DIN, and the Deming regression analysis between DQS and DIN, showed the biases were both within the acceptance criteria, and the bias between DQN and DIN was smaller. For the comparisons of RQN and RIN, RQS and RIN, the regression analyses revealed the biases were both within the acceptance criteria. The bias of the mean estimated between RQS and RIN was outside of the acceptance criteria. There was a good comparability in nucleic acid integrity detection between BIOptic Qsep400 and PerkinElmer Labchip GX Touch HT with the Agilent 4200 TapeStation. However, the bias and linear correlations require more attention between systems.
Topics: RNA; Nucleic Acids; Quality Control; Reference Standards; DNA
PubMed: 36735544
DOI: 10.1089/bio.2022.0171 -
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 -
Journal of AOAC International Mar 2019Appropriate use of genetic methods for botanical identification is based on the type of sequencing used as well as testing region selection. Although Sanger sequencing... (Review)
Review
Appropriate use of genetic methods for botanical identification is based on the type of sequencing used as well as testing region selection. Although Sanger sequencing is useful for single-target species identification, targeted next generation sequencing is ideal for testing blended products or those that contain unexpected species. Unknown, fresh, or lightly processed materials are best tested through the use of long, universal deoxyribonucleic acid (DNA) regions (e.g., DNA barcodes). For highly processed products, using shorter and more specific regions helps to prevent false negatives and positives. All approaches must use DNA extraction techniques that address the presence of inhibitory compounds, which often occur in abundance within herbs and spices. The accuracy of identifications is improved when comparing genetic data of any type with a reference database that contains expertly determined vouchered materials, a variety of closely related species, and multiple specimens of the same species.
Topics: DNA Barcoding, Taxonomic; DNA, Plant; Databases, Genetic; Plants, Medicinal; Polymerase Chain Reaction; Spices
PubMed: 30563583
DOI: 10.5740/jaoacint.18-0388 -
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 -
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