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ACS Sensors Jul 2023Antibodies are among the most relevant biomolecular targets for diagnostic and clinical applications. In this Perspective, we provide a critical overview of recent... (Review)
Review
Antibodies are among the most relevant biomolecular targets for diagnostic and clinical applications. In this Perspective, we provide a critical overview of recent research efforts focused on the development and characterization of devices, switches, and reactions based on the use of synthetic antigen-conjugated DNA strands designed to be responsive to specific antibodies. These systems can find applications in sensing, drug-delivery, and antibody-antigen binding characterization. The examples described here demonstrate how the programmability and chemical versatility of synthetic nucleic acids can be used to create innovative analytical tools and target-responsive systems with promising potentials.
Topics: DNA; Biosensing Techniques; Nucleic Acids; Antibodies; Vaccines, Synthetic
PubMed: 37463359
DOI: 10.1021/acssensors.3c00564 -
Nano Letters Aug 2023The bioengineering applications of cells, such as cell printing and multicellular assembly, are directly limited by cell damage and death due to a harsh environment....
The bioengineering applications of cells, such as cell printing and multicellular assembly, are directly limited by cell damage and death due to a harsh environment. Improved cellular robustness thus motivates investigations into cell encapsulation, which provides essential protection. Here we target the cell-surface glycocalyx and cross-link two layers of DNA nanorods on the cellular plasma membrane to form a modular and programmable nanoshell. We show that the DNA origami nanoshell modulates the biophysical properties of cell membranes by enhancing the membrane stiffness and lowering the lipid fluidity. The nanoshell also serves as armor to protect cells and improve their viability against mechanical stress from osmotic imbalance, centrifugal forces, and fluid shear stress. Moreover, it enables mediated cell-cell interactions for effective and robust multicellular assembly. Our results demonstrate the potential of the nanoshell, not only as a cellular protection strategy but also as a platform for cell and cell membrane manipulation.
Topics: Artificial Cells; Cell Membrane; Nanoshells; DNA; Nanostructures
PubMed: 37463308
DOI: 10.1021/acs.nanolett.3c01878 -
Nature Protocols Jul 2023Biological research and diagnostic applications normally require analysis of trace analytes in biofluids. Although considerable advancements have been made in developing... (Review)
Review
Biological research and diagnostic applications normally require analysis of trace analytes in biofluids. Although considerable advancements have been made in developing precise molecular assays, the trade-off between sensitivity and ability to resist non-specific adsorption remains a challenge. Here, we describe the implementation of a testing platform based on a molecular-electromechanical system (MolEMS) immobilized on graphene field-effect transistors. A MolEMS is a self-assembled DNA nanostructure, containing a stiff tetrahedral base and a flexible single-stranded DNA cantilever. Electromechanical actuation of the cantilever modulates sensing events close to the transistor channel, improving signal-transduction efficiency, while the stiff base prevents non-specific adsorption of background molecules present in biofluids. A MolEMS realizes unamplified detection of proteins, ions, small molecules and nucleic acids within minutes and has a limit of detection of several copies in 100 μl of testing solution, offering an assay methodology with wide-ranging applications. In this protocol, we provide step-by-step procedures for MolEMS design and assemblage, sensor manufacture and operation of a MolEMS in several applications. We also describe adaptations to construct a portable detection platform. It takes ~18 h to construct the device and ~4 min to finish the testing from sample addition to result.
Topics: Biosensing Techniques; DNA; Nucleic Acids; DNA, Single-Stranded; Proteins; Graphite
PubMed: 37208410
DOI: 10.1038/s41596-023-00830-x -
Chemical Reviews Dec 2023The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have... (Review)
Review
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
Topics: DNA Replication; DNA; Molecular Conformation
PubMed: 37971892
DOI: 10.1021/acs.chemrev.3c00436 -
Cell Reports Jul 2023The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have...
The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have characterized 22 high-resolution co-crystallographic PU.1/DNA complexes across the addressable affinity range in myeloid gene transactivation. Over a purine-rich core (such as 5'-GGAA-3') flanked by variable sequences, affinity is negotiated by direct readout on the 5' flank via a critical glutamine (Q226) sidechain and by indirect readout on the 3' flank by sequence-dependent helical flexibility. Direct readout by Q226 dynamically specifies PU.1's characteristic preference for purines and explains the pathogenic mutation Q226E in Waldenström macroglobulinemia. The structures also reveal how disruption of Q226 mediates strand-specific inhibition by DNA methylation and the recognition of non-canonical sites, including the authentic binding sequence at the CD11b promoter. A re-synthesis of phylogenetic and structural data on the ETS family, considering the centrality of Q226 in PU.1, unifies the model of DNA selection by ETS proteins.
Topics: Phylogeny; Binding Sites; Trans-Activators; DNA
PubMed: 37352101
DOI: 10.1016/j.celrep.2023.112671 -
European Review For Medical and... Oct 2023Human papillomavirus (HPV), which is known to play a very important role in genital area (vulva, vagina, and cervix) cancers in women, is responsible for almost all...
OBJECTIVE
Human papillomavirus (HPV), which is known to play a very important role in genital area (vulva, vagina, and cervix) cancers in women, is responsible for almost all cervical cancers. However, a significant proportion of cervical carcinomas (approximately 7%) is HPV-negative. Therefore, there are still two important questions to be answered: 1. Why is HPV Deoxyribonucleic acid (DNA) not found in all cervical carcinomas? 2. Are HPV-DNA-negative cervical cancers a specific subgroup of cervical cancers with different biological behavior (worse prognosis)? In this article, we aimed to evaluate the clinicopathological characteristics and survival of patients with confirmed HPV-negative tumors in order to answer these two questions.
PATIENTS AND METHODS
A total of 97 patients who underwent HPV-DNA testing and received a histological diagnosis of cervical cancer were included in the study. 14 HPV-DNA negative and 83 HPV-DNA positive cervical carcinoma patients were detected. Demographic profiles, clinicopathological characteristics, progression-free, and overall survival of all patients were analyzed.
RESULTS
Women with HPV-negative tumors were diagnosed at an older age range (p=0.05), and their demographic data other than age range were similar to HPV-positive tumors. P16 staining pattern was not observed in any of the HPV-negative tumors (p=0.001), and a positive P53 staining pattern was detected in 35.7% of the HPV-negative tumors. Although disease-free survival (PFS) (p=0.224) and overall survival (OS) (p=0.219) were worse in the HPV-negative patient group, this difference was not statistically significant.
CONCLUSIONS
HPV-negative cervical cancers do not have a poor prognosis unlike their counterparts in other anatomical regions where HPV-associated tumors are present.
Topics: Humans; Female; Uterine Cervical Neoplasms; Papillomavirus Infections; Prognosis; Disease-Free Survival; Human Papillomavirus Viruses; DNA, Viral; Papillomaviridae
PubMed: 37843334
DOI: 10.26355/eurrev_202310_33948 -
Briefings in Bioinformatics Mar 2024In this review, we provide a comprehensive overview of the different computational tools that have been published for the deconvolution of bulk DNA methylation (DNAm)... (Review)
Review
In this review, we provide a comprehensive overview of the different computational tools that have been published for the deconvolution of bulk DNA methylation (DNAm) data. Here, deconvolution refers to the estimation of cell-type proportions that constitute a mixed sample. The paper reviews and compares 25 deconvolution methods (supervised, unsupervised or hybrid) developed between 2012 and 2023 and compares the strengths and limitations of each approach. Moreover, in this study, we describe the impact of the platform used for the generation of methylation data (including microarrays and sequencing), the applied data pre-processing steps and the used reference dataset on the deconvolution performance. Next to reference-based methods, we also examine methods that require only partial reference datasets or require no reference set at all. In this review, we provide guidelines for the use of specific methods dependent on the DNA methylation data type and data availability.
Topics: DNA Methylation; Humans; Computational Biology; DNA; Algorithms
PubMed: 38762790
DOI: 10.1093/bib/bbae234 -
Fa Yi Xue Za Zhi Oct 2023Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to... (Review)
Review
Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to retain DNA under natural condition. In many cases, such as historical figure identification, aged skeleton and teeth are usually the only biological samples. However, their DNA is in a state of trace, damage and degradation to different degrees, which requires special experimental treatment to achieve identification. This paper reviews the sample selection, DNA extraction, DNA enrichment and analysis approaches based on relevant research reports in recent years, aiming to promote the further development and improvement of the aged skeleton and teeth identification system.
Topics: Humans; Aged; Body Remains; DNA; Tooth; DNA Fingerprinting; Sequence Analysis, DNA
PubMed: 38006268
DOI: 10.12116/j.issn.1004-5619.2021.511209 -
ACS Nano Aug 2023Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and... (Review)
Review
Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.
Topics: Nucleic Acids; Liposomes; DNA; Membrane Fusion; Cell Membrane
PubMed: 37549398
DOI: 10.1021/acsnano.3c04415 -
Science Advances Sep 2023Lattice-based constructs, often made by additive manufacturing, are attractive for many applications. Typically, such constructs are made from microscale or larger...
Lattice-based constructs, often made by additive manufacturing, are attractive for many applications. Typically, such constructs are made from microscale or larger elements; however, smaller nanoscale components can lead to more unusual properties, including greater strength, lighter weight, and unprecedented resiliencies. Here, solid and hollow nanoparticles (nanoframes and nanocages; frame size: ~15 nanometers) were assembled into colloidal crystals using DNA, and their mechanical strengths were studied. Nanosolid, nanocage, and nanoframe lattices with identical crystal symmetries exhibit markedly different specific stiffnesses and strengths. Unexpectedly, the nanoframe lattice is approximately six times stronger than the nanosolid lattice. Nanomechanical experiments, electron microscopy, and finite element analysis show that this property results from the buckling, densification, and size-dependent strain hardening of nanoframe lattices. Last, these unusual open architectures show that lattices with structural elements as small as 15 nanometers can retain a high degree of strength, and as such, they represent target components for making and exploring a variety of miniaturized devices.
Topics: DNA; Nanoparticles
PubMed: 37774024
DOI: 10.1126/sciadv.adj8103