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Biomaterials Science Oct 2021Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic... (Review)
Review
Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.
Topics: Cell Membrane; DNA; Engineering; Ions
PubMed: 34494042
DOI: 10.1039/d1bm01057c -
Expert Review of Anticancer Therapy 2023Liquid biopsies are used for the detection of tumor-specific elements in body fluid. Their application in prognosis and diagnosis of muscle/non-muscle invasive bladder... (Review)
Review
INTRODUCTION
Liquid biopsies are used for the detection of tumor-specific elements in body fluid. Their application in prognosis and diagnosis of muscle/non-muscle invasive bladder cancer (MIBC/NMIBC) or upper tract urothelial cancer (UTUC) remains poorly known and rarely mentioned in clinical guidelines.
AREAS COVERED
Herein, we provide an overview of current data regarding the use of liquid biopsies in urothelial tumors.
EXPERT OPINION
Studies that were included analyzed liquid biopsies using the detection of circulating tumor cells (CTCs), deoxyribonucleic acid (DNA), ribonucleic acid (RNA), exosomes, or metabolomics. The sensitivity of blood CTC detection in patients with localized cancer was 35% and raised to 50% in patients with metastatic cancer. In NMIBC patients, blood CTC was associated with poor prognosis, whereas discrepancies were seen in MIBC patients. Circulating plasma DNA presented a superior sensitivity to urine and was a good indicator for diagnosis, follow-up, and oncological outcome. In urine, specific bladder cancer (BC) microRNA had an overall sensitivity of 85% and a specificity of 86% in the diagnosis of urothelial cancer. These results are in favor of the use of liquid biopsies as biomarkers for in urothelial cancer management.
Topics: Humans; Urinary Bladder Neoplasms; Carcinoma, Transitional Cell; Prognosis; Liquid Biopsy; DNA
PubMed: 37542214
DOI: 10.1080/14737140.2023.2245144 -
Chemical Society Reviews May 2024With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 10 GB) in 2025. Storing such huge global data would... (Review)
Review
With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 10 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.
Topics: DNA; Information Storage and Retrieval; Oligonucleotide Array Sequence Analysis
PubMed: 38498347
DOI: 10.1039/d3cs00469d -
Briefings in Bioinformatics Jan 2023Deoxyribonucleic acid(DNA) N6-methyladenine plays a vital role in various biological processes, and the accurate identification of its site can provide a more... (Review)
Review
Deoxyribonucleic acid(DNA) N6-methyladenine plays a vital role in various biological processes, and the accurate identification of its site can provide a more comprehensive understanding of its biological effects. There are several methods for 6mA site prediction. With the continuous development of technology, traditional techniques with the high costs and low efficiencies are gradually being replaced by computer methods. Computer methods that are widely used can be divided into two categories: traditional machine learning and deep learning methods. We first list some existing experimental methods for predicting the 6mA site, then analyze the general process from sequence input to results in computer methods and review existing model architectures. Finally, the results were summarized and compared to facilitate subsequent researchers in choosing the most suitable method for their work.
Topics: DNA Methylation; Machine Learning; Research Design; DNA
PubMed: 36502371
DOI: 10.1093/bib/bbac514 -
Biosensors & Bioelectronics Jul 2019During the last decades, by virtue of their unique physicochemical properties and potential application in microelectronics, biosensing and biomedicine, metal... (Review)
Review
During the last decades, by virtue of their unique physicochemical properties and potential application in microelectronics, biosensing and biomedicine, metal nanomaterials (MNs) have attracted great research interest and been highly developed. Deoxyribonucleic acid (DNA) is a particularly interesting ligand for templating bottom-up nanopreparation, by virtue of its excellent properties including nanosized geometry structure, programmable and artificial synthesis, DNA-metal ion interaction and powerful molecular recognition. DNA-templated copper nanoparticles (DNA-CuNPs) has been developed in recent years. Because of its advantages including simple and rapid preparation, high efficiency, MegaStokes shifting and low biological toxicity, DNA-CuNPs has been highly exploited for biochemical sensing from 2010, especially as a label-free detection manner, holding advantages in multiple analytical technologies including fluorescence, electrochemistry, surface plasmon resonance, inductively coupled plasma mass spectrometry and surface enhanced Raman spectroscopy. This review comprehensively tracks the preparation of DNA-CuNPs and its application in biosensing, and highlights the potential development and challenges regarding this field, aiming to promote the advance of this fertile research area.
Topics: Biosensing Techniques; Copper; DNA; Fluorescence; Fluorescent Dyes; Metal Nanoparticles; Spectrometry, Fluorescence; Surface Plasmon Resonance
PubMed: 31085403
DOI: 10.1016/j.bios.2019.05.014 -
Radiation Protection Dosimetry Oct 2023We hypothesised that single-cell whole-genome sequencing has the potential to detect mutational differences in the genomes of the cells that are irradiated with...
We hypothesised that single-cell whole-genome sequencing has the potential to detect mutational differences in the genomes of the cells that are irradiated with different doses of radiation and we set out to test our hypothesis using in silico and in vitro experiments. In this manuscript, we present our findings from a Monte Carlo single-cell irradiation simulation performed in TOPAS-nBio using a custom-built geometric nuclear deoxyribonucleic acid (DNA) model, which predicts a significant dose dependence of the number of cluster damages per cell as a function of radiation dose. We also present preliminary experimental results, obtained from single-cell whole-genome DNA sequencing analysis performed on cells irradiated with different doses of radiation, showing promising agreement with the simulation results.
Topics: Radiometry; Computer Simulation; DNA; Monte Carlo Method; Sequence Analysis, DNA; DNA Damage
PubMed: 37819315
DOI: 10.1093/rpd/ncad055 -
Cellular and Molecular Life Sciences :... Dec 2019The review includes information on the current state of knowledge of immunometric methods with emphasis on the possibility of deoxyribonucleic acid (DNA) damage... (Review)
Review
The review includes information on the current state of knowledge of immunometric methods with emphasis on the possibility of deoxyribonucleic acid (DNA) damage detection. Beginning with basic immunoassay enzyme-linked immunosorbent assay (ELISA), this review describes methods such as tyramide signal amplification (TSA), enhanced polymer one-step staining (EPOS), and time resolved amplified cryptate emission (TRACE) as improvements of ELISA's developed over time to obtain more accurate results. In the second part of the review, surface plasmon resonance (SPR) and quantum dots (QDs) are presented as the newest outlooks in the context of immunoanalysis of biological material and molecular studies. The aim of this review is to briefly present immunoassays with emphasis on DNA damage detection; therefore, the types of methods are listed and described, types of signal indicators, basic definitions such as antigen and antibody are given. Every method is considered with an exemplary application focusing on DNA studies, DNA damage and instability detection.
Topics: DNA; DNA Damage; Enzyme-Linked Immunosorbent Assay; Immunoassay; Organometallic Compounds; Quantum Dots; Surface Plasmon Resonance; Tyramine
PubMed: 31342119
DOI: 10.1007/s00018-019-03239-6 -
Wiley Interdisciplinary Reviews.... Jan 2022Deoxyribonucleic acid (DNA) has been an emerging building block to construct functional biomaterials. Due to their programmable sequences and rich responsiveness, DNA... (Review)
Review
Deoxyribonucleic acid (DNA) has been an emerging building block to construct functional biomaterials. Due to their programmable sequences and rich responsiveness, DNA has attracted rising attention in the construction of intelligent nanomaterials with predicable nanostructure and adjustable functions, which has shown great potential in drug delivery. On the one hand, the DNA sequences with molecule recognition, responsiveness, and therapeutic efficacy can be easily integrated to the framework of DNA nanomaterials by sequence designing; on the other hand, the rich chemical groups on DNA molecules provide binding points for other functional units. In this review, we divided the functionalization modules in the construction of DNA nanomaterials into three types, including targeting modules, responsive modules, and therapeutic modules. Based on these modules, five DNA kinds of representative nanomaterials applied in drug delivery were introduced, including DNA nanogel, DNA origami, DNA framework, DNA nanoflower, and DNA hybrid nanosphere. Finally, we discussed the challenges in the transition of DNA materials to clinical applications. We expect that this review can help readers to obtain a deeper understanding of DNA materials, and further promote the development of these intelligent materials to real world's application. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
Topics: Biocompatible Materials; DNA; Nanostructures; Nanotechnology; Pharmaceutical Preparations
PubMed: 34463046
DOI: 10.1002/wnan.1753 -
International Journal of Clinical... 2023Endometriosis, which is a common disease affecting approximately 10% of women of reproductive age, usually causes dysmenorrhea and infertility, thus seriously harming...
OBJECTIVE
Endometriosis, which is a common disease affecting approximately 10% of women of reproductive age, usually causes dysmenorrhea and infertility, thus seriously harming the patients' physical and mental health. However, there is a mean delay of 6.7 years between the onset of the symptoms and the surgical diagnosis of endometriosis. There is an increasing amount of evidence that suggests that epigenetic aberrations, including deoxyribonucleic acid (DNA) methylation, play a definite role in the pathogenesis of endometriosis. This study aimed to explore the noninvasive or minimally invasive biomarkers of this disease.
MATERIALS AND METHODS
Six patients with surgically confirmed ovarian endometriosis and six patients who received IUD implantation for contraception without endometriosis were recruited in the East Hospital of Tongji University in 2018. The genome methylation profiling of the eutopic and ectopic endometrium of ovarian endometriosis patients and normal endometrial specimens from healthy women was determined using a methylation microarray test. The test screened methylation-differentiated 5'-C-phosphate-G-3' (CpG) sites and then located the target genes affected by these sites following sequence alignment. Then, an additional 22 patients and 26 healthy controls were enrolled to further verify the difference in the selected genes between endometriosis patients and healthy women. The differential DNA methylation of the selected genes was validated via direct bisulfite sequencing and analysis of their messenger ribonucleic acid (mRNA) levels using quantitative reverse transcription polymerase chain reaction (qRT-PCR).
RESULTS
Fifteen differentially methylated CpG sites were found among the patients and healthy women, and five CpG sites were mapped to the introns of the human leukocyte antigen-C (HLA-C) gene; these were highly polymorphic between different HLA-C alleles and were HLA-C07 specific. The results indicated that the HLA-C07 carrier patients exhibited significantly higher DNA methylation levels at the intron VII of HLA-C compared to the HLA-C07 carrier healthy controls. High HLA-C07 mRNA levels were also observed using qRT-PCR with HLA-C07-specific primers, which indicated that the hypermethylation of CpG in intron VII might suppress a silencer that regulates HLA-C07 expressions.
CONCLUSION
Deoxyribonucleic acid hypermethylation in the intron VII of the HLA-C07 gene appears to regulate the expression of HLA-C07. The aberrant DNA methylation in this region was positively correlated with the occurrence of endometriosis.
Topics: Humans; Female; DNA Methylation; Endometriosis; Introns; HLA-C Antigens; RNA, Messenger; DNA
PubMed: 36974156
DOI: 10.1155/2023/2291156 -
Journal of Visualized Experiments : JoVE Jun 2022The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) probes deoxyribonucleic acid (DNA) accessibility using the hyperactive Tn5...
The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) probes deoxyribonucleic acid (DNA) accessibility using the hyperactive Tn5 transposase. Tn5 cuts and ligates adapters for high-throughput sequencing within accessible chromatin regions. In eukaryotic cells, genomic DNA is packaged into chromatin, a complex of DNA, histones, and other proteins, which acts as a physical barrier to the transcriptional machinery. In response to extrinsic signals, transcription factors recruit chromatin remodeling complexes to enable access to the transcriptional machinery for gene activation. Therefore, identifying open chromatin regions is useful when monitoring enhancer and gene promoter activities during biological events such as cancer progression. Since this protocol is easy to use and has a low cell input requirement, ATAC-seq has been widely adopted to define open chromatin regions in various cell types, including cancer cells. For successful data acquisition, several parameters need to be considered when preparing ATAC-seq libraries. Among them, the choice of cell lysis buffer, the titration of the Tn5 enzyme, and the starting volume of cells are crucial for ATAC-seq library preparation in cancer cells. Optimization is essential for generating high-quality data. Here, we provide a detailed description of the ATAC-seq optimization methods for epithelial cell types.
Topics: Chromatin; Chromatin Immunoprecipitation Sequencing; DNA; Epigenesis, Genetic; High-Throughput Nucleotide Sequencing; Neoplasms; Sequence Analysis, DNA; Transcription Factors
PubMed: 35848835
DOI: 10.3791/64242