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American Journal of Human Genetics Sep 2023Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires... (Review)
Review
Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices.
Topics: Humans; DNA, Ancient; Reproducibility of Results; Communication; DNA; Databases, Genetic
PubMed: 37541241
DOI: 10.1016/j.ajhg.2023.06.011 -
The Journal of Biological Chemistry Apr 2024DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the... (Review)
Review
DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications.
Topics: Epigenesis, Genetic; Humans; Eukaryota; DNA Methylation; Animals; DNA
PubMed: 38403247
DOI: 10.1016/j.jbc.2024.106791 -
ACS Applied Bio Materials Aug 2023Various diseases, including cancers and inflammatory diseases, are characterized by a disruption of redox homeostasis, suggesting the need for synergistic treatments...
Various diseases, including cancers and inflammatory diseases, are characterized by a disruption of redox homeostasis, suggesting the need for synergistic treatments involving co-delivery of gene therapies and free radical scavengers. In this report, polyethylenimine (PEI), nanoceria (NC), and DNA were complexed to form nanoparticles providing simultaneous delivery of a gene and an antioxidant. NC was coated in citric acid to provide stable, 4 nm particles that electrostatically bound PEI/DNA polyplexes. The resulting ternary particles transfected HeLa cells with similar efficiency to that of ternary polyplexes comprising 15 kDa poly-l-α-glutamic acid/PEI/DNA while providing smaller particle sizes by more than 100 nm. NC/PEI/DNA polyplexes exhibited enhanced radical-scavenging activity compared to free NC, and oxidative stress from the superoxide-generating agent, menadione, could be completely reversed by the delivery of NC/PEI/DNA polyplexes. Transfection by NC/PEI/DNA polyplexes was demonstrated to occur efficiently through caveolin-mediated endocytosis and macropinocytosis. Co-delivery of genes encoding reactive oxygen species-scavenging proteins, transcription factors, growth factors, tumor suppressors, or anti-inflammatory genes with NC, therefore, may be a promising strategy in synergistic therapeutics.
Topics: Humans; Polymers; Antioxidants; HeLa Cells; DNA
PubMed: 37493016
DOI: 10.1021/acsabm.3c00295 -
ACS Applied Materials & Interfaces Dec 2023Functional interfaces and devices for rapid adsorption and immobilization of nucleic acids (NAs) are significant for relevant bioengineering applications. Herein, a...
Functional interfaces and devices for rapid adsorption and immobilization of nucleic acids (NAs) are significant for relevant bioengineering applications. Herein, a microdevice with poly(acrylic acid) (PAA) photosensitive resin was integrated by three-dimensional (3D) printing, named D for short. Precise microscale structures and abundant surface carboxyl functional groups were fabricated for fast and high-throughput deoxyribonucleic acid (DNA) separation. Surface modification was then done using polydopamine (PDA) and poly(ethylene glycol) (PEG) to obtain modified poly(acrylic acid) (PAA)-based devices D and D rich in amino and hydroxyl groups, respectively. The fabricated device D possessed superior printing accuracy (40-50 μm). Functionalization of amino and hydroxyl was successful, and the modified devices D and D maintained a high thermal stability like D. Surface potential analysis and molecular dynamics simulation indicated that the affinity for DNA was in the order of D > D > D. Further DNA separation experiments confirmed the high throughput and high selectivity of DNA separation performance, consistent with the predicted affinity results. D showed relatively the highest DNA extraction yield, while D was the worst. An acidic binding system is more favorable for DNA separation and recovery. D showed significantly better DNA extraction performance than D in a weakly acidic environment (pH 5.0-7.0), and the average DNA yield of the first elution was 2.16 times that of D. This work validates the possibility of modification on integrated 3D microdevices to improve their DNA separation efficiency effectively. It also provides a new direction for the rational design and functionalization of bioengineering separators based on nonmagnetic methods. It may pave a new path for the highly efficient polymerase chain reaction diagnosis.
Topics: Polyethylene Glycols; Nucleic Acids; DNA
PubMed: 38058108
DOI: 10.1021/acsami.3c11681 -
Journal of the American Chemical Society Aug 2023Dynamic molecular interactions in chemical reaction networks lead to complex behaviors in living systems. Whereas recent advances in programming DNA molecular reactions...
Dynamic molecular interactions in chemical reaction networks lead to complex behaviors in living systems. Whereas recent advances in programming DNA molecular reactions have reached a high level of complexity at molecular and nanometer scales, achieving programmable autonomous behavior at submicron or even larger scales remains challenging. Here, we present a mechanism of meta-DNA strand displacement reactions (M-SDRs) that is mediated solely by meta-toehold (M-toehold) using versatile submicron building blocks of meta-DNA (M-DNA). M-SDR emulates the toehold binding and branch migration processes of conventional strand displacement. Importantly, the kinetics of M-SDR can be modulated over a range of five orders of magnitude reaching a maximum rate of about 1.62 × 10 M s. Further, we demonstrate the use of M-SDR to program autonomous reconfiguration in information transmission and logical computation systems. We envision that M-SDR serves as a versatile mechanism for emulating autonomous behavior approaching the cellular level.
Topics: DNA; Kinetics; Logic
PubMed: 37489598
DOI: 10.1021/jacs.3c04884 -
Environmental Monitoring and Assessment Dec 2023In order to detect Ag and Hg in seawater, we explored a multifunctional fluorescence sensor. A multifunctional Ag and Hg sensor was designed by using gold nanoparticles...
In order to detect Ag and Hg in seawater, we explored a multifunctional fluorescence sensor. A multifunctional Ag and Hg sensor was designed by using gold nanoparticles (AuNPs) as quenching agent, PicoGreen dye as fluorescent probe of base pairing double-stranded deoxyribonucleic acid (DNA), and combining the characteristics of Ag making C base mismatch and Hg making T base mismatch. Meanwhile, the DNA logic gate was constructed by establishing logic circuit, truth table, and logic formula. The relevant performances of the sensor were investigated. The results revealed that the sensor can detect Ag in the range of 100 to 700 nM with R = 0.98129, and its detection limit is 16.88 nM (3σ/slope). The detection range of Hgis 100-900 nM with R = 0.99725, and the detection limit is 5.59 nM (3σ/slope). An AND-AND-NOR-AND molecular logic gate has been successfully designed. With the characteristics of high sensitivity, multifunction, and low cost, the recommended detection method has the potential to be applied to the detection of Ag and Hg in seawater.
Topics: Gold; Metal Nanoparticles; Environmental Monitoring; DNA; Mercury; Spectrometry, Fluorescence; Seawater; Limit of Detection
PubMed: 38060083
DOI: 10.1007/s10661-023-12217-2 -
PloS One 2024The HIV/AIDS continues being a significant global public health priority in the 21st century with social and economic consequences Mother-to-child transmission (MTCT)...
INTRODUCTION
The HIV/AIDS continues being a significant global public health priority in the 21st century with social and economic consequences Mother-to-child transmission (MTCT) occurs when an HIV-infected woman passes the virus to her infant and about 90% of these MTCT infections occurs in Africa where children and infants are still dying of HIV. Early definitive diagnosis using Deoxyribonucleic acid reaction of HIV infection in infants is critical to ensuring that HIV-infected infants receive appropriate and timely care and treatment to reduce HIV related morbidity and mortality.
OBJECTIVE
To assess the Infant Deoxyribonucleic acid-Polymerase Chain Reaction (DNA-PCR) Turnaround Time (TAT) of dry blood spots and associated factors in Vihiga, Bungoma, Kakamega and Busia counties, in Kenya.
METHOD
A mixed methods study using a) retrospectively collected data from Ministry of Health Laboratory registers, Early Infant Diagnosis (EID) database from 28 health facilities and b) 9 key informant interviews with laboratory in-charges were conducted. A total of 2,879 HIV exposed babies' data were abstracted from January 2012 to June 2013.
RESULTS
The mean TAT from specimen collection and results received back at the facilities was 46.90 days, Vihiga county having the shortest mean duration at 33.7days and Kakamega county having the longest duration at 51.7days (p = 0.001). In addition, the mean transport time from specimen collection and receipt at Alupe Kenya Medical Research Institute (KEMRI) reference Laboratory was 16.50 days. Vihiga County had the shortest transport time at 13.01 days while Busia had the longest at 18.99 days (p = 0.001). Longer TAT was due to the batching of specimens at the peripheral health facilities and hubbing to the nearest referral hospitals.
CONCLUSION
The TAT for DNA-PCR specimen was 46.90 days with Vihiga County having the shortest TAT due to lack of specimen batching and hubbing.
RECOMMENDATION
Discourage specimen batching/hubbing and support point-of-care early infant diagnosis (EID) tests.
Topics: Humans; Kenya; Infant; HIV Infections; Polymerase Chain Reaction; Female; Infant, Newborn; Infectious Disease Transmission, Vertical; Retrospective Studies; DNA, Viral; Male; Time Factors
PubMed: 38696502
DOI: 10.1371/journal.pone.0302396 -
Analytical Chemistry Dec 2023Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes....
Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.
Topics: Base Pairing; Nucleic Acid Hybridization; DNA; DNA, Single-Stranded; DNA Probes
PubMed: 38055795
DOI: 10.1021/acs.analchem.3c03316 -
Journal of Materials Chemistry. B May 2024DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal... (Review)
Review
DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.
Topics: Biosensing Techniques; Humans; DNA; Nanotechnology; Nanostructures; DNA Methylation; DNA Modification Methylases
PubMed: 38572575
DOI: 10.1039/d3tb02947f -
Proceedings of the National Academy of... Jul 2023ToxR, a transmembrane one-component signal transduction factor, lies within a regulatory cascade that results in the expression of ToxT, toxin coregulated pilus, and...
ToxR, a transmembrane one-component signal transduction factor, lies within a regulatory cascade that results in the expression of ToxT, toxin coregulated pilus, and cholera toxin. While ToxR has been extensively studied for its ability to activate or repress various genes in , here we present the crystal structures of the ToxR cytoplasmic domain bound to DNA at the and promoters. The structures confirm some predicted interactions, yet reveal other unexpected promoter interactions with implications for other potential regulatory roles for ToxR. We show that ToxR is a versatile virulence regulator that recognizes diverse and extensive, eukaryotic-like regulatory DNA sequences, that relies more on DNA structural elements than specific sequences for binding. Using this topological DNA recognition mechanism, ToxR can bind both in tandem and in a twofold inverted-repeat-driven manner. Its regulatory action is based on coordinated multiple binding to promoter regions near the transcription start site, which can remove the repressing H-NS proteins and prepares the DNA for optimal interaction with the RNA polymerase.
Topics: Vibrio cholerae; Transcription Factors; DNA-Binding Proteins; Virulence; Bacterial Proteins; DNA; Gene Expression Regulation, Bacterial
PubMed: 37428913
DOI: 10.1073/pnas.2304378120