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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 -
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 -
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 -
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 -
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 -
British Medical Journal Apr 1956
Topics: DNA; Nucleic Acids
PubMed: 13304356
DOI: No ID Found -
The Journal of Physical Chemistry. B Sep 2022The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three...
The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3' and 5' ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3' and 5' ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure.
Topics: Amines; DNA; Graphite; Humans; Molecular Dynamics Simulation; Telomere
PubMed: 36036695
DOI: 10.1021/acs.jpcb.2c04327 -
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 -
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