-
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 -
Journal of Neurological Surgery. Part... Nov 2022Since the new World Health Organization (WHO) classification of nervous system tumors (2016, revised, 4th edition) has been released, gliomas are classified depending... (Review)
Review
BACKGROUND
Since the new World Health Organization (WHO) classification of nervous system tumors (2016, revised, 4th edition) has been released, gliomas are classified depending on molecular and genetic markers in connection with histopathology, instead of histopathology itself as it was in the previous classification. Over the last years, epigenetic analysis has taken on increased importance in the diagnosis and treatment of different cancers. Multiple studies confirmed that deoxyribonucleic acid (DNA) methylation and hydroxymethylation play an important role in the regulation of gene expression during carcinogenesis.
METHODS
In this review, we aim to present the current state of knowledge on DNA hydroxymethylation in human high-grade gliomas (WHO grades III and IV).
RESULTS
The correlation between DNA hydroxymethylation and survival in glioblastoma multiforme (GBM) patients was evaluated by different studies. The majority of them showed that the expression of 5-hydroxymethylcytosine (5-hmC) and ten-eleven translocation (TET) enzymes were significantly reduced, sometimes almost undetectable in high-grade gliomas in comparison with the normal brain. A decreased level of 5-hmC was associated with poor survival in patients, but high expression of the TET3 enzyme was related to a better prognosis for GBM patients. This points to the relevance of DNA hydroxymethylation in molecular diagnostics of human gliomas, including survival estimation or differentiating patients in terms of response to the treatment.
CONCLUSION
Future studies may shed some more light on this epigenetic mechanism involved in the pathogenesis of human high-grade gliomas and help develop new targeted therapies.
Topics: Humans; DNA Methylation; Genetic Markers; Epigenesis, Genetic; Glioma; Glioblastoma; DNA
PubMed: 34872125
DOI: 10.1055/a-1713-7699 -
Current Drug Metabolism 2023Deoxyribonucleic acid (DNA), as a natural polymer material, carries almost all the genetic information and is recognized as one of the most intelligent natural polymers.... (Review)
Review
Deoxyribonucleic acid (DNA), as a natural polymer material, carries almost all the genetic information and is recognized as one of the most intelligent natural polymers. In the past 20 years, there have been many exciting advances in the synthesis of hydrogels using DNA as the main backbone or cross-linking agent. Different methods, such as physical entanglement and chemical cross-linking, have been developed to perform the gelation of DNA hydrogels. The good designability, biocompatibility, designable responsiveness, biodegradability and mechanical strength provided by DNA building blocks facilitate the application of DNA hydrogels in cytoscaffolds, drug delivery systems, immunotherapeutic carriers, biosensors and nanozyme-protected scaffolds. This review provides an overview of the main classification and synthesis methods of DNA hydrogels and highlights the application of DNA hydrogel in biomedical fields. It aims to give readers a better understanding of DNA hydrogels and development trends.
Topics: Humans; Hydrogels; Drug Delivery Systems; Polymers; DNA
PubMed: 37431900
DOI: 10.2174/1389200224666230710124838 -
Medwave Apr 2023Rheumatoid arthritis is an autoimmune and inflammatory disease that predominantly affects the diarthrodial joints. In this pathology, environmental or behavioral factors...
Rheumatoid arthritis is an autoimmune and inflammatory disease that predominantly affects the diarthrodial joints. In this pathology, environmental or behavioral factors can act in synergy with genetic predisposition, accelerating the onset and severity of the disease. This link between the environment and the genome is mediated by epigenetic marks on deoxyribonucleic acid, including its methylation, histone modification, and noncoding ribonucleic acid-mediated regulation. Epigenetics can generate heritable phenotypic changes, which are not determined by modifications in the deoxyribonucleic acid sequence and are therefore reversible. Therefore, diet, medications and other environmental factors would have the ability to modulate them. The identification of a specific epigenetic dysregulation can offer a better understanding of the pathophysiology of the disease and positively influence the prevention, diagnosis and development of new therapeutic targets.
Topics: Humans; DNA Methylation; Histones; Epigenesis, Genetic; Arthritis, Rheumatoid; DNA
PubMed: 37094250
DOI: 10.5867/medwave.2023.03.2619 -
International Journal of Molecular... Aug 2021Gestational diabetes mellitus (GDM) is the most common metabolic complication in pregnancy, which affects the future health of both the mother and the newborn. Its... (Review)
Review
Gestational diabetes mellitus (GDM) is the most common metabolic complication in pregnancy, which affects the future health of both the mother and the newborn. Its pathophysiology involves nutritional, hormonal, immunological, genetic and epigenetic factors. Among the latter, it has been observed that alterations in DNA (deoxyribonucleic acid) methylation patterns and in the levels of certain micro RNAs, whether in placenta or adipose tissue, are related to well-known characteristics of the disease, such as hyperglycemia, insulin resistance, inflammation and excessive placental growth. Furthermore, epigenetic alterations of gestational diabetes mellitus are observable in maternal blood, although their pathophysiological roles are completely unknown. Despite this, it has not been possible to determine the causes of the epigenetic characteristics of GDM, highlighting the need for integral and longitudinal studies. Based on this, this article summarizes the most relevant and recent studies on epigenetic alterations in placenta, adipose tissue and maternal blood associated with GDM in order to provide the reader with a general overview of the subject and indicate future research topics.
Topics: Adipose Tissue; DNA; DNA Methylation; Diabetes, Gestational; Epigenesis, Genetic; Epigenomics; Female; Humans; MicroRNAs; Placenta; Pregnancy; Pregnant Women
PubMed: 34502370
DOI: 10.3390/ijms22179462 -
The Analyst Jul 2023A conventional molecular assay-based point-of-care (POC) diagnostic test involves three major stages: deoxyribonucleic acid (DNA) extraction, amplification, and amplicon... (Review)
Review
A conventional molecular assay-based point-of-care (POC) diagnostic test involves three major stages: deoxyribonucleic acid (DNA) extraction, amplification, and amplicon detection. Among these steps, DNA extraction is costly and time-consuming. Nevertheless, it is a crucial step for the identification of sensitive and specific diseases. This review summarizes the advantages and disadvantages of DNA extraction methods over the past 10 years to effectively implement POC pathogen testing in the future. The first section briefly explains the necessity of DNA extraction and molecular assays for food pathogen detection. The second section extensively discusses DNA extraction based on liquid-liquid extraction, solid-phase extraction, and electrophoretic techniques. Molecular assay-based methods and a few commercially available POC devices for the detection of foodborne pathogens are detailed in the third and fourth sections. Finally, present challenges and future perspectives for the fabrication of integrated POC devices are highlighted.
Topics: Point-of-Care Systems; Point-of-Care Testing; Solid Phase Extraction; DNA; Nucleic Acid Amplification Techniques; Biosensing Techniques
PubMed: 37351846
DOI: 10.1039/d3an00045a -
Biosensors & Bioelectronics Oct 2023Polymerase chain reaction (PCR) in small fluidic systems not only improves speed and sensitivity of deoxyribonucleic acid (DNA) amplification but also achieves...
Polymerase chain reaction (PCR) in small fluidic systems not only improves speed and sensitivity of deoxyribonucleic acid (DNA) amplification but also achieves high-throughput quantitative analyses. However, air bubble trapping and growth during PCR has been considered as a critical problem since it causes the failure of DNA amplification. Here we report bubble-free diatom PCR by exploiting a hierarchically porous silica structure of single-celled algae. We show that femtoliters of PCR solution can be spontaneously loaded into the diatom interior without air bubble trapping due to the surface hydrophilicity and pore structure of the diatom. We discover that a large pressure gradient between air bubbles and nanopores rapidly removes residual air bubbles through the periodically arrayed nanopores during thermal cycling. We demonstrate the DNA amplification by diatom PCR without air bubble trapping and growth. Finally, we successfully detect DNA fragments of SARS-CoV-2 with as low as 10 copies/μl by devising a microfluidic device integrated with diatoms assembly. We believe that our work can be applied to many PCR applications for innovative molecular diagnostics and provides new opportunities for naturally abundant diatoms to create innovative biomaterials in real-world applications.
Topics: Humans; Diatoms; Biosensing Techniques; COVID-19; SARS-CoV-2; Polymerase Chain Reaction; DNA; COVID-19 Testing
PubMed: 37402347
DOI: 10.1016/j.bios.2023.115489 -
Macromolecular Bioscience Dec 2022Deoxyribonucleic acid (DNA) is a biological macromolecule that plays a genetic role in cells. DNA molecules with specific recognition, self-assembly capabilities, and... (Review)
Review
Deoxyribonucleic acid (DNA) is a biological macromolecule that plays a genetic role in cells. DNA molecules with specific recognition, self-assembly capabilities, and sequence programmability have become an excellent construction material for micro- and nanostructures. Based on DNA self-assembly technology, a series of molecular devices and materials are constructed. Among them, DNA hydrogels with the advantages of good biocompatibility, biodegradability, and containing designable stimuli-responsive units have attracted much attention. This review introduces the formation strategy of DNA supramolecular hydrogels, and focuses on its applications in tissue engineering, including cell encapsulation, cell culture, cell capture and release, wound dressings, and tissue growth. The unique properties and application prospects of DNA supramolecular hydrogels in tissue engineering are also discussed.
Topics: Hydrogels; Tissue Engineering; Biocompatible Materials; Nanostructures; DNA
PubMed: 35917391
DOI: 10.1002/mabi.202200152 -
ChemPlusChem Jan 2023Micro ribonucleic acids (miRNAs) in exosomes have been proven as reliable biomarkers to detect disease progression. In recent years, deoxyribonucleic acid (DNA)-based... (Review)
Review
Micro ribonucleic acids (miRNAs) in exosomes have been proven as reliable biomarkers to detect disease progression. In recent years, deoxyribonucleic acid (DNA)-based nanomaterials show great potential in the field of diagnosis due to the programmable sequence, various molecule recognition and predictable assembly/disassembly of DNA. In this review, we focus on the molecular design and detection mechanism of DNA nanomaterials, and the developed DNA nanomaterial-based optical probes for exosomal miRNA detection are summarized and discussed. The rationally-designed DNA sequences endows these probes with low background signal and high sensitivity in exosomal miRNA detection, and the detection mechanisms based on different DNA nanomaterials are detailly introduced. At the end, the challenges and future opportunities of DNA nanomaterial-based optical probes in exosomal miRNA detection are discussed. We envision that DNA nanomaterial-based optical probes will be promising in precise biomedicine.
Topics: MicroRNAs; Nanostructures; Exosomes; DNA
PubMed: 36650721
DOI: 10.1002/cplu.202200345