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Molecules (Basel, Switzerland) Feb 2020Deoxyribonucleic acid (DNA) serves not only as a genetic information carrier but also as an excellent material for programmable nanoscale assembly [...].
Deoxyribonucleic acid (DNA) serves not only as a genetic information carrier but also as an excellent material for programmable nanoscale assembly [...].
Topics: DNA; Nanostructures; Nanotechnology
PubMed: 32028556
DOI: 10.3390/molecules25030639 -
Frontiers in Bioscience (Landmark... Apr 2021Being polymorphic, deoxyribonucleic acid is worthy of raise a variety of structure like right-handed B to left-handed Z conformation. In left-handed contour of DNA... (Comparative Study)
Comparative Study Review
Being polymorphic, deoxyribonucleic acid is worthy of raise a variety of structure like right-handed B to left-handed Z conformation. In left-handed contour of DNA consecutive nucleotides substitute between syn-arrangement and anti-arrangement, through the chain. 2D gel electrophoresis comprising d(PCpG)n of topo isomers of a plasmid inserts d(pCpG)n, in this 'n' ranges among 8 to 21, indicate the change of B-Z DNA. The high denseness of salt is required for conversion of B configuration d(CG)n toward Z configuration. The rate of B to Z transition is measured by "Cytosine Analogues" and "Fluorescence Spectroscopy". h-ZαADAR1 that a Z-DNA's binding domain, binds and stabilizes one part in Z configuration and therefore the remaining half in B deoxyribonucleic acid configuration. At halfway point, it creates B-Z junction. "Stacking" is the main reason for the B-Z DNA junction construction. Upregulation of ADAM-12, related with Z-DNA is said to a cause for cancer, arthritis, and hypertrophy. Z-DNA forming sequence (ZFS) conjointly generates massive - scale deletion in cells from mammals.
Topics: Alzheimer Disease; Autoimmune Diseases; Biophysics; Cytosine; DNA; DNA, Z-Form; Genome, Human; Humans; Nucleic Acid Conformation; Protein Binding; Protein Domains
PubMed: 34027648
DOI: 10.52586/4922 -
Nucleic Acids Research Jun 2021Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases... (Review)
Review
Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.
Topics: DNA; Genes, Synthetic; Information Storage and Retrieval
PubMed: 33836076
DOI: 10.1093/nar/gkab230 -
British Medical Journal Apr 1956
Topics: DNA; Nucleic Acids
PubMed: 13304356
DOI: No ID Found -
Journal of Cancer Research and... 2019Epigenomics is the study of the gene expression changes due to epigenetic processes and not due to the deoxyribonucleic acid (DNA) base sequence alterations. The key... (Review)
Review
Epigenomics is the study of the gene expression changes due to epigenetic processes and not due to the deoxyribonucleic acid (DNA) base sequence alterations. The key mechanisms of epigenetic regulation include DNA methylation, histone modifications, and noncoding RNAs. Epigenetic alterations in cancer are predominantly linked with hypermethylation of promoters of the tumor suppressor genes, global DNA hypomethylation, and increased expression of histone deacetylases (HDAC). There is a growing need to investigate epigenetic patterns and to provide safe and effective, innovative therapeutic strategies for oncology patients, who did not improve on traditional anticancer regimens. The epi-drugs (e.g., DNA methyltransferase inhibitors, e.g., azacitidine and decitabine and HDAC inhibitors, e.g., vorinostat and romidepsin) have been approved for the clinical use. In this paper, we provide a brief overview of the mechanisms of action and targets for novel epi-drugs, focusing on their potential clinical applications in patients with solid tumors, resistant to standard oncology treatments.
Topics: DNA; DNA Methylation; Epigenesis, Genetic; Histone Deacetylase Inhibitors; Humans; Methyltransferases; Neoplasms
PubMed: 31603095
DOI: 10.4103/jcrt.JCRT_403_17 -
Journal of Dairy Science Jul 1983Over the last decade, developments in recombinant deoxyribonucleic acid techniques and molecular biology have revolutionized bacterial genetics, creating vast, new... (Review)
Review
Over the last decade, developments in recombinant deoxyribonucleic acid techniques and molecular biology have revolutionized bacterial genetics, creating vast, new potential uses of bacteria (as well as animal and plant cells) that were not even considered previously. Bacterial production of hormones is but one example. With bacterial species with well developed genetic systems, such as Escherichia coli, it is now possible genetically to "design" or "engineer" bacterial strains having specific characteristics. One reasonable future approach toward improvement of animal agriculture would be manipulation of the rumen ecosystem via the use of genetically modified ruminal bacteria, but significant obstacles exist with this approach. Genetic systems of ruminal and of anaerobic bacteria of the mammalian gastrointestinal tract, in general, have not been studied and are largely unknown. In this paper, the various criteria for possible establishment of recombinant deoxyribonucleic acid systems in ruminal bacteria are outlined. Secondly, applications for utilizing genetically engineered ruminal bacteria to control digestion of specific feedstuffs, to regulate specific fermentation products, and to control growth of specific bacterial species are discussed.
Topics: Anaerobiosis; Animals; Bacteria; Cattle; Cellulose; DNA, Bacterial; DNA, Recombinant; Digestion; Fermentation; Genetic Engineering; Plasmids; Rumen
PubMed: 6350393
DOI: 10.3168/jds.S0022-0302(83)81970-5 -
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 -
Chimia Nov 2018The exponential improvements made in DNA sequencing technologies, together with the rapidly declining associated costs, has increasingly led to the expansion of the... (Review)
Review
The exponential improvements made in DNA sequencing technologies, together with the rapidly declining associated costs, has increasingly led to the expansion of the field of personalised genomic medicine. Changes in the sequence or copy number of specific deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules represent key signatures for the diagnosis, prognosis, classification and monitoring of a broad range of pathologies, most notably cancer. Technologies that can detect these changes require analytical tools that can detect DNA or RNA with high sensitivity and high specificity. Sensing based on bioorthogonal oligonucleotide-templated reactions (OTRs) has been recognised as an elegant strategy that satisfies these criteria and was successfully used for the quantitative detection of nucleic acids both and . Herein, we will focus on recent efforts to implement bioorthogonal OTRs into clinically useful biosensors using probes immobilised on or embedded in customised materials and platforms.
Topics: Biosensing Techniques; DNA; Microfluidic Analytical Techniques; Nucleic Acid Amplification Techniques; Oligonucleotides
PubMed: 30514424
DOI: 10.2533/chimia.2018.809 -
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 -
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