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Bioscience Reports Dec 2018Polymerase chain reaction (PCR) is a molecular biology technique used to multiply certain deoxyribonucleic acid (DNA) fragments. It is a common and indispensable... (Review)
Review
Polymerase chain reaction (PCR) is a molecular biology technique used to multiply certain deoxyribonucleic acid (DNA) fragments. It is a common and indispensable technique that has been applied in many areas, especially in clinical laboratories. The third generation of polymerase chain reaction, droplet digital polymerase chain reaction (ddPCR), is a biotechnological refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify DNA. Droplet digital polymerase chain reaction is now widely used in low-abundance nucleic acid detection and is useful in diagnosis of infectious diseases. Here, we summarized the potential advantages of droplet digital polymerase chain reaction in clinical diagnosis of infectious diseases, including viral diseases, bacterial diseases and parasite infections, concluded that ddPCR provides a more sensitive, accurate, and reproducible detection of low-abundance pathogens and may be a better choice than quantitative polymerase chain reaction for clinical applications in the future.
Topics: Communicable Diseases; DNA; Humans; Molecular Diagnostic Techniques; Polymerase Chain Reaction
PubMed: 30341241
DOI: 10.1042/BSR20181170 -
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 -
Chemical Reviews Sep 2021Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express... (Review)
Review
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
Topics: Animals; Communicable Diseases; DNA; Humans; Nucleic Acid Amplification Techniques; Nucleic Acid Probes; RNA
PubMed: 34254782
DOI: 10.1021/acs.chemrev.1c00241 -
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 -
Methods in Molecular Biology (Clifton,... 2023High-resolution melting (HRM) analysis is a simple, fast, and inexpensive real-time polymerase chain reaction (PCR)-based method used to identify genetic variation...
High-resolution melting (HRM) analysis is a simple, fast, and inexpensive real-time polymerase chain reaction (PCR)-based method used to identify genetic variation between populations and detect single-nucleotide polymorphisms (SNPs) in nucleic acid sequences. HRM is a powerful technique that detects the differences between SNP allele melting temperatures by using a fluorescent dye inserted into the duplex deoxyribonucleic acid (DNA) structure. Prior to performing HRM analysis, optimizing the primer design, PCR mixture, and software settings is essential to obtain accurate and reliable results. In this chapter, we describe a detailed SNP genotyping method that includes primer design and the analysis of the shapes and positions of the melt curve of the luminescence intensity of the fluorescent dye attached to amplified DNA using software of qPCR instruments. This protocol is applicable for genotyping germplasm, genetic mapping, and marker-assisted breeding in plants.
Topics: Genotype; Fluorescent Dyes; Plant Breeding; Genotyping Techniques; Polymorphism, Single Nucleotide; Real-Time Polymerase Chain Reaction; DNA; Nucleic Acid Denaturation
PubMed: 36781654
DOI: 10.1007/978-1-0716-3024-2_24 -
Theranostics 2019The elegant properties of deoxyribonucleic acid (DNA), such as accurate recognition, programmability and addressability, make it a well-defined and promising material to... (Review)
Review
The elegant properties of deoxyribonucleic acid (DNA), such as accurate recognition, programmability and addressability, make it a well-defined and promising material to develop various molecular probes, drug delivery carriers and theranostic systems for cancer diagnosis and therapy. In addition, supramolecular chemistry, also termed "chemistry beyond the molecule", is a promising research field that aims to develop functional chemical systems by bringing discrete molecular components together in a manner that invokes noncovalent intermolecular forces, such as hydrophobic interaction, hydrogen bonding, metal coordination, and shape or size matching. Thus, DNA-supramolecule conjugates (DSCs) combine accurate recognition, programmability and addressability of DNA with the greater toolbox of supramolecular chemistry. This review discusses the applications of DSCs in sensing, protein activity regulation, cell behavior manipulation, and biomedicine.
Topics: DNA; Macromolecular Substances; Multifunctional Nanoparticles; Theranostic Nanomedicine
PubMed: 31244953
DOI: 10.7150/thno.31885 -
The Analyst May 2020Deoxyribonucleic acid (DNA), the carrier of genetic information in living life, is an essential biomacromolecule in almost all living systems. DNA has advantages... (Review)
Review
Deoxyribonucleic acid (DNA), the carrier of genetic information in living life, is an essential biomacromolecule in almost all living systems. DNA has advantages including, programmability, predictability, high rigidity, and stability. Through self-assembly or combination with other nanomaterials (such as gold nanoparticles, graphene oxides, quantum dots, and polymers), DNA can be applied to construct specific, stable, biocompatible, and functional nanodevices. DNA nanodevices have made greater contributions in a plethora of fields. In this review, we discuss the recent progress of DNA nanodevices in molecular detection and analysis. Meanwhile, we prospect the development of various DNA devices in biological analysis, clinical diagnosis and biomedical research.
Topics: Animals; Biosensing Techniques; DNA; Humans; Nanotechnology
PubMed: 32319463
DOI: 10.1039/d0an00159g -
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 -
Essays in Biochemistry Apr 2021Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about... (Review)
Review
Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.
Topics: DNA; Kinetics; Nucleic Acid Hybridization; Optical Imaging; Single Molecule Imaging
PubMed: 33491734
DOI: 10.1042/EBC20200040 -
Journal of Biomedical Materials... Nov 2023The development of useful biomaterials has resulted in significant advances in various fields of science and technology. The demand for new biomaterial designs and...
The development of useful biomaterials has resulted in significant advances in various fields of science and technology. The demand for new biomaterial designs and manufacturing techniques continues to grow, with the goal of building a sustainable society. In this study, two types of DNA-cationic surfactant complexes were synthesized using commercially available deoxyribonucleic acid from herring sperm DNA (hsDNA, <50 bp) and deoxyribonucleic acid from salmon testes DNA (stDNA, ~2000 bp). The DNA-surfactant complexes were blended with a polylactic acid (PLA) biopolymer and electrospun to obtain nanofibers, and then copper nanoparticles were synthesized on nanofibrous webs. Scanning electron microscopic images showed that all nanofibers possessed uniform morphology. Interestingly, different diameters were observed depending on the base pairs in the DNA complex. Transmission electron microscopy showed uniform growth of copper nanoparticles on the nanofibers. Fourier-transform infrared spectroscopy spectra confirmed the uniform blending of both types of DNA complexes in PLA. Both stDNA- and hsDNA-derived nanofibers showed greater biocompatibility than native PLA nanofibers. Furthermore, they exerted significant antibacterial activity in the presence of copper nanoparticles. This study demonstrates that DNA is a potentially useful material to generate electrospun nanofibrous webs for use in biomedical sciences and technologies.
Topics: Male; Humans; Nanofibers; Copper; Semen; Polyesters; Biocompatible Materials; Surface-Active Agents; DNA
PubMed: 37539635
DOI: 10.1002/jbm.a.37592