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Accounts of Chemical Research Aug 2022Facing increasing demand for precision medicine, materials chemistry systems for bioanalysis with accurate molecular design, controllable structure, and adjustable...
Facing increasing demand for precision medicine, materials chemistry systems for bioanalysis with accurate molecular design, controllable structure, and adjustable biological activity are required. As a genetic biomacromolecule, deoxyribonucleic acid (DNA) is created via precise, efficient, and mild processes in life systems and can in turn precisely regulate life activities. From the perspective of materials chemistry, DNA possesses the characteristics of sequence programmability and can be endowed with customized functions by the rational design of sequences. In recent years, DNA has been considered to be a potential biomaterial for analysis and has been applied in the fields of bioseparation, biosensing, and detection imaging. To further improve the precision of bioanalysis, the supramolecular assembly of DNA on micro/nanointerfaces is an effective strategy to concentrate functional DNA modules, and thus the functions of DNA molecules for bioanalysis can be enriched and enhanced. Moreover, the new modes of DNA supramolecular assembly on micro/nanointerfaces enable the integration of DNA with the introduced components, breaking the restriction of limited functions of DNA materials and achieving more precise regulation and manipulation in bioanalysis. In this Account, we summarize our recent work on DNA supramolecular assembly on micro/nanointerfaces for bioanalysis from two main aspects. In the first part, we describe DNA supramolecular assembly on the interfaces of microscale living cells. The synthesis strategy of DNA is based on rolling-circle amplification (RCA), which generates ultralong DNA strands according to circular DNA templates. The templates can be designed with complementary sequences of functional modules such as aptamers, which allow DNA to specifically bind with cellular interfaces and achieve efficient cell separation. In the second part, we describe DNA supramolecular assembly on the interfaces of nanoscale particles. DNA sequences are designed with functional modules such as targeting, drug loading, and gene expression and then are assembled on interfaces of particles including upconversion nanoparticles (UCNPs), gold nanoparticles (AuNPs), and magnetic nanoparticle (MNPs). The integration of DNA with these functional particles achieves cell manipulation, targeted tumor imaging, and cellular regulation. The processes of interfacial assembly are well controlled, and the functions of the obtained bioanalytical materials can be flexibly regulated. We envision that the work on DNA supramolecular assembly on micro/nanointerfaces will be a typical paradigm for the construction of more bioanalytical materials, which we hope will facilitate the development of precision medicine.
Topics: Biocompatible Materials; DNA; Gold; Metal Nanoparticles
PubMed: 35839123
DOI: 10.1021/acs.accounts.2c00170 -
Forensic Science International Apr 2020Plastination allows anatomical samples to be preserved in excellent condition for an indefinite period, free of formalin, and in a format that allows biosafe...
INTRODUCTION
Plastination allows anatomical samples to be preserved in excellent condition for an indefinite period, free of formalin, and in a format that allows biosafe manipulation by students, academics, and researchers. As with other tissue preservation techniques, it is important to establish the level of conservation of deoxyribonucleic acid (DNA) for use in future applications. The object of the present work was to extract and evaluate DNA from plastinated tissues.
METHODS
We used samples of liver from Canis lupus familiaris and skeletal muscle from Rattus norvegicus, Sprague-Dawley strain, extracted from specimens plastinated with silicone at room temperature. The tissue samples were deplastinated by incubation in 5% sodium methoxide dissolved in methanol for 24 or 48 h. The samples were divided into two equal parts and DNA was extracted using two different protocols. After extraction, the DNA was quantified by fluorometry and its integrity was assessed by electrophoresis in a 1% agarose gel.
RESULTS AND DISCUSSION
A high yield of DNA was obtained from the deplastinated samples and the DNA was intact. Plastinated tissues have proven to be stable and easily managed. They can also be used for examination under light and electron microscopes. The DNA extraction technique used here allowed us to obtain intact DNA from samples plastinated with silicone at room temperature, without previous fixing. This technique may allow tissue specimens to be preserved for retrospective studies of archived samples of normal and pathological anatomy in the fields of basic, clinical, forensic, and epidemiological sciences.
CONCLUSIONS
The extracted DNA was intact and suitable for use in subsequent applications. Obtaining whole DNA from plastinated samples using tissue preservation protocols that preserve the tissue for use in subsequent applications, like real-time PCR, opens up many possibilities, with applications in the basic and clinical sciences, epidemiology, and forensic science.
Topics: Animals; DNA; Forensic Sciences; Liver; Muscle, Skeletal; Plastination; Rats; Rats, Sprague-Dawley; Silicones; Tissue Preservation; Wolves
PubMed: 32142992
DOI: 10.1016/j.forsciint.2020.110199 -
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 -
Biomolecules Oct 2022Neutrophil extracellular traps (NETs) are net-like complexes expelled from neutrophils, composing cell-free deoxyribonucleic acid (DNA), histones, and neutrophil granule... (Review)
Review
Neutrophil extracellular traps (NETs) are net-like complexes expelled from neutrophils, composing cell-free deoxyribonucleic acid (DNA), histones, and neutrophil granule proteins. Besides capturing and eliminating pathogens, NETs also exacerbate the inflammatory response associated with various diseases, including systemic lupus erythematosus, rheumatoid arthritis, and psoriasis. Currently, there are growing reports about NETs involved in the pathogenesis of ocular diseases. This review primarily focuses on the pathogenesis of NETs in the ophthalmology field, highlighting their importance in serving as potential targets for the therapy of ocular diseases.
Topics: Extracellular Traps; Histones; Neutrophils; DNA; Cell-Free Nucleic Acids
PubMed: 36291649
DOI: 10.3390/biom12101440 -
Advanced Materials (Deerfield Beach,... Sep 2023Controversy over artwork's authenticity is ongoing despite numerous technologies for copyright protection. Artists should build their own ways to protect the authority,...
Controversy over artwork's authenticity is ongoing despite numerous technologies for copyright protection. Artists should build their own ways to protect the authority, but these are still open to piracy. Here, a platform is proposed for developing anticounterfeiting labels based on physical unclonable functions (PUFs), in an artist-friendly manner, brushstrokes. Deoxyribonucleic acid (DNA), which is natural, biocompatible, and eco-friendly, can be applied as a paint that shows entropy-driven buckling instability of the liquid crystal phase. Brushed and wholly dried DNA exhibits line-shaped zig-zag textures with inherent randomness as a source of the PUF, and its primary performance and reliability are systematically examined. This breakthrough enables the utilization of these drawings in a wider range of applications.
Topics: Reproducibility of Results; Entropy; Liquid Crystals; DNA
PubMed: 37145961
DOI: 10.1002/adma.202302135 -
Fertility and Sterility Jun 2021
Topics: Aneuploidy; DNA; Genetic Testing; Humans; Mitochondrial Diseases; Preimplantation Diagnosis
PubMed: 33795137
DOI: 10.1016/j.fertnstert.2021.03.006 -
Analytical Chemistry Dec 2020Specificity of DNA polymerization plays a critical role in DNA replication and storage of genetic information. Likewise, biotechnological applications, such as nucleic...
Specificity of DNA polymerization plays a critical role in DNA replication and storage of genetic information. Likewise, biotechnological applications, such as nucleic acid detection, DNA amplification, and gene cloning, require high specificity in DNA synthesis catalyzed by DNA polymerases. However, errors in DNA polymerization (such as mis-incorporation and mis-priming) can significantly jeopardize the specificity. Herein, we report our discovery that the specificity of DNA enzymatic synthesis can be substantially enhanced (up to 100-fold higher) by attenuating DNA polymerase kinetics via the phosphorothioate dNTPs. This specificity enhancement allows convenient and sensitive nucleic acid detection, polymerization, PCR, and gene cloning with complex systems (such as human cDNA and genomic DNA). Further, we found that the specificity enhancement offered higher sensitivity (up to 50-fold better) for detecting nucleic acids, such as COVID-19 viral RNAs. Our findings have revealed a simple and convenient strategy for facilitating specificity and sensitivity of nucleic acid detection, amplification, and gene cloning.
Topics: DNA; DNA Nucleotidyltransferases; Humans; Polymerase Chain Reaction; Polymerization; RNA, Viral; SARS-CoV-2
PubMed: 33236629
DOI: 10.1021/acs.analchem.0c03223 -
Journal of Obstetrics and Gynaecology :... Aug 2022This study aimed to investigate the association between deoxyribonucleic acid (DNA) integrity parameters and advanced maternal age (AMA)-related infertility. The...
This study aimed to investigate the association between deoxyribonucleic acid (DNA) integrity parameters and advanced maternal age (AMA)-related infertility. The granulosa cells and the lymphocytes obtained from 119 infertile women were recruited. Patients were divided into two groups: the AMA group (≥35 years, = 26) and the non-AMA group (<35 years, = 93). The tail length, tail moment and tail DNA percentage were evaluated as the DNA integrity parameters using comet assay. Infertility duration (=.001), luteinising hormone (=.01) and progesterone levels (<.0001) were higher and smoking was more prevalent in the AMA group (=.001). AMA group was stimulated with higher gonadotropin doses (=.04) and had decreased anti-mullerian hormone levels (<.0001). All of DNA integrity parameters were distributed homogenously between the groups; however, the tail length of lymphocytes was higher (=.02) in the AMA group. Fertilisation was lower (=.02), oocyte quality was tended to be poor (=.03) and blastocyst transfer was lower in the AMA group (=.03). Embryo quality was distributed homogenously between the groups. Implantation, clinical pregnancy and live birth rates were similar between the groups. Impact Statement Advanced maternal age (AMA)-related infertility is associated with diminished ovarian reserve and alteration in follicular environment resulting in poor oocyte quality; however, the exact pathophysiologic mechanism is not clear. Tail length, tail deoxyribonucleic acid (DNA) percentage, tail moment of granulosa cells were nonsignificantly higher in the AMA group compared to younger patients. All of the DNA integrity parameters of lymphocytes were nonsignificantly higher; however, only tail length of lymphocytes was statistically higher in the AMA group than the non-AMA group. A positive correlation was observed between DNA integrity parameters of lymphocytes and body mass index. There were no correlations between DNA integrity parameters of granulosa cells and lymphocyte and infertility duration, gonadotropin dose, duration of ovarian stimulation, oocyte score, embryo score, basal hormone levels and anti-mullerian hormone levels. Our findings offer new insight for further understanding the role of granulosa cells in mediating the poor reproductive outcome of ageing patients. Understanding the mechanisms of ovarian ageing and poor oocyte quality in women with AMA may help to identify specific targets for improving oocyte quality with ageing.
Topics: Anti-Mullerian Hormone; DNA; Female; Fertilization in Vitro; Gonadotropins; Granulosa Cells; Humans; Infertility, Female; Luteinizing Hormone; Lymphocytes; Ovulation Induction; Pregnancy; Pregnancy Rate; Progesterone
PubMed: 35611871
DOI: 10.1080/01443615.2022.2054689 -
Sub-cellular Biochemistry 2022Nucleic acid methylation is a fundamental epigenetic mechanism that impinges upon several cellular attributes, including metabolism and energy production. The... (Review)
Review
Nucleic acid methylation is a fundamental epigenetic mechanism that impinges upon several cellular attributes, including metabolism and energy production. The dysregulation of deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) methylation can lead to metabolic rewiring in the cell, which in turn facilitates tumor development. Here, we review the current knowledge on the interplay between DNA/RNA methylation and metabolic programs in cancer cells. We also discuss the mechanistic role of these pathways in tumor development and progression.
Topics: Humans; RNA; DNA Methylation; Neoplasms; DNA; Homeostasis
PubMed: 36301496
DOI: 10.1007/978-3-031-07634-3_7 -
Biosensors & Bioelectronics Oct 2023Deoxyribonucleic acid (DNA) is a carrier of genetic information. DNA hybridization is characterized by predictability, diversity, and specificity owing to the strict... (Review)
Review
Deoxyribonucleic acid (DNA) is a carrier of genetic information. DNA hybridization is characterized by predictability, diversity, and specificity owing to the strict complementary base-pairing assembly mode, which stimulates the use of DNA to build a variety of nanomachines, including DNA tweezers, motors, walkers, and robots. DNA nanomachines have become prevalent for signal amplification and transformation in the field of biosensing, providing a new method for constructing highly sensitive sensing analysis strategies. DNA tweezers have exhibited unique advantages in biosensing applications owing to their simple structures and fast responses. The two-state conformation of DNA tweezers, the open and closed states, enable them to open and close autonomously after stimulation, thus facilitating the quick detection of corresponding signal changes of different targets. This review discusses the recent progress in the application of DNA nanotweezers in the field of biosensing, and the trends in their development for application in the field of biosensing are summarized.
Topics: DNA; Biosensing Techniques; Nucleic Acid Hybridization; Nucleic Acid Conformation
PubMed: 37421799
DOI: 10.1016/j.bios.2023.115445