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Methods in Molecular Biology (Clifton,... 2023DNA nanotechnology provides efficient methods for the sequence-programmable construction of mechanical devices with nanoscale dimensions. The resulting nanomachines...
DNA nanotechnology provides efficient methods for the sequence-programmable construction of mechanical devices with nanoscale dimensions. The resulting nanomachines could serve as tools for the manipulation of macromolecules with similar functionalities as mechanical tools and machinery in the macroscopic world. In order to drive and control these machines and to perform specific tasks, a fast, reliable, and repeatable actuation mechanism is required that can work against external loads. Here we describe a highly effective method for actuating DNA structures using externally applied electric fields. To this end, electric fields are generated with controllable direction and amplitude inside a miniature electrophoresis device integrated with an epifluorescence microscope. With this setup, DNA-based nanoelectromechanical devices can be precisely controlled. As an example, we demonstrate how a DNA-based nanorobotic system can be used to dynamically position molecules on a molecular platform with high speeds and accuracy. The microscopy setup also described here allows simultaneous monitoring of a large number of nanorobotic arms in real time and at the single nanomachine level.
Topics: Nanostructures; Nanotechnology; DNA
PubMed: 37166722
DOI: 10.1007/978-1-0716-3028-0_15 -
Chemical Communications (Cambridge,... Mar 2022The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and... (Review)
Review
The diverse surface interactions and functions of a bacterium play an important role in cell signaling, host infection, and colony formation. To understand and synthetically control the biological functions of individual cells as well as the whole community, there is growing attention on the development of chemical and biological tools that can integrate artificial functional motifs onto the bacterial surface to replace the native interactions, enabling a variety of applications in biosynthesis, environmental protection, and human health. Among all these functional motifs, DNA emerges as a powerful tool that can precisely control bacterial interactions at the bio-interface due to its programmability and biorecognition properties. Compared with conventional chemical and genetic approaches, the sequence-specific Watson-Crick interaction enables almost unlimited programmability in DNA nanostructures, realizing one base-pair spatial control and bio-responsive properties. This highlight aims to provide an overview on this emerging research topic of DNA-engineered bacterial interactions from the aspect of synthetic chemists. We start with the introduction of native bacterial surface ligands and established synthetic approaches to install artificial ligands, including direct modification, metabolic engineering, and genetic engineering. A brief overview of DNA nanotechnology, reported DNA-bacteria conjugation chemistries, and several examples of DNA-engineered bacteria are included in this highlight. The future perspectives and challenges in this field are also discussed, including the development of dynamic bacterial surface chemistry, assembly of programmable multicellular community, and realization of bacteria-based theranostic agents and synthetic microbiota as long-term goals.
Topics: Bacteria; DNA, Bacterial; Genetic Engineering; Ligands; Metabolic Engineering
PubMed: 35077527
DOI: 10.1039/d1cc06138k -
Current Issues in Molecular Biology 2020Modern genomic sequencing and bioinformatics approaches have detected numerous examples of DNA sequences derived from DNA and RNA virus genomes integrated into both... (Review)
Review
Modern genomic sequencing and bioinformatics approaches have detected numerous examples of DNA sequences derived from DNA and RNA virus genomes integrated into both vertebrate and insect genomes. Retroviruses encode RNA-dependent DNA polymerases (reverse transcriptases) and integrases that convert their RNA viral genomes into DNA proviruses and facilitate proviral DNA integration into the host genome. Surprisingly, DNA sequences derived from RNA viruses that do not encode these enzymes also occur in host genomes. Non-retroviral integrated RNA virus sequences (NIRVS) occur at relatively high frequency in the genomes of the arboviral vectors and , are not distributed randomly and possibly contribute to mosquito antiviral immunity, suggesting these mosquitoes could serve as a model system for unravelling the function of NIRVS. Here we address the following questions: What drives DNA synthesis from the genomes of non-retroviral RNA viruses? How does integration of virus cDNA into host DNA occur, and what is its biological function (if any)? We review current knowledge of viral integrations in insect genomes, hypothesize mechanisms of NIRVS formation and their potential impact on insect biology, particularly antiviral immunity, and suggest directions for future research.
Topics: Aedes; Animals; Computational Biology; DNA Viruses; Endogenous Retroviruses; Genome, Insect; Genomics; Host-Pathogen Interactions; Insecta; Mosquito Vectors; RNA Viruses; RNA, Small Interfering; Retroelements; Virus Integration
PubMed: 31167954
DOI: 10.21775/cimb.034.013 -
Scientific Reports May 2023The tetrameric tumor suppressor p53 represents a great challenge for 3D-structural analysis due to its high degree of intrinsic disorder (ca. 40%). We aim to shed light...
The tetrameric tumor suppressor p53 represents a great challenge for 3D-structural analysis due to its high degree of intrinsic disorder (ca. 40%). We aim to shed light on the structural and functional roles of p53's C-terminal region in full-length, wild-type human p53 tetramer and their importance for DNA binding. For this, we employed complementary techniques of structural mass spectrometry (MS) in an integrated approach with computational modeling. Our results show no major conformational differences in p53 between DNA-bound and DNA-free states, but reveal a substantial compaction of p53's C-terminal region. This supports the proposed mechanism of unspecific DNA binding to the C-terminal region of p53 prior to transcription initiation by specific DNA binding to the core domain of p53. The synergies between complementary structural MS techniques and computational modeling as pursued in our integrative approach is envisioned to serve as general strategy for studying intrinsically disordered proteins (IDPs) and intrinsically disordered region (IDRs).
Topics: Humans; Tumor Suppressor Protein p53; Computer Simulation; Intrinsically Disordered Proteins; DNA; Mass Spectrometry; Protein Binding
PubMed: 37231156
DOI: 10.1038/s41598-023-35437-5 -
Analytical Biochemistry Jan 2021DNA-binding proteins perform important roles in cellular processes and are involved in many biological activities. These proteins include crucial protein-DNA binding...
BACKGROUND
DNA-binding proteins perform important roles in cellular processes and are involved in many biological activities. These proteins include crucial protein-DNA binding domains and can interact with single-stranded or double-stranded DNA, and accordingly classified as single-stranded DNA-binding proteins (SSBs) or double-stranded DNA-binding proteins (DSBs). Computational prediction of SSBs and DSBs helps in annotating protein functions and understanding of protein-binding domains.
RESULTS
Performance is reported using the DNA-binding protein dataset that was recently introduced by Wang et al., [1]. The proposed method achieved a sensitivity of 0.600, specificity of 0.792, AUC of 0.758, MCC of 0.369, accuracy of 0.744, and F-measure of 0.536, on the independent test set.
CONCLUSION
The proposed method with the hidden Markov model (HMM) profiles for feature extraction, outperformed the benchmark method in the literature and achieved an overall improvement of approximately 3%. The source code and supplementary information of the proposed method is available at https://github.com/roneshsharma/Predict-DNA-binding-proteins/wiki.
Topics: Amino Acid Sequence; Computational Biology; DNA; DNA, Single-Stranded; DNA-Binding Proteins; Databases, Protein; Markov Chains; Models, Statistical; Protein Binding; Protein Domains; Sequence Analysis, Protein; Software; Support Vector Machine
PubMed: 32946833
DOI: 10.1016/j.ab.2020.113954 -
Nature Communications Apr 2023Activating signal co-integrator 1 complex (ASCC) subunit 3 (ASCC3) supports diverse genome maintenance and gene expression processes, and contains tandem Ski2-like...
Activating signal co-integrator 1 complex (ASCC) subunit 3 (ASCC3) supports diverse genome maintenance and gene expression processes, and contains tandem Ski2-like NTPase/helicase cassettes crucial for these functions. Presently, the molecular mechanisms underlying ASCC3 helicase activity and regulation remain unresolved. We present cryogenic electron microscopy, DNA-protein cross-linking/mass spectrometry as well as in vitro and cellular functional analyses of the ASCC3-TRIP4 sub-module of ASCC. Unlike the related spliceosomal SNRNP200 RNA helicase, ASCC3 can thread substrates through both helicase cassettes. TRIP4 docks on ASCC3 via a zinc finger domain and stimulates the helicase by positioning an ASC-1 homology domain next to the C-terminal helicase cassette of ASCC3, likely supporting substrate engagement and assisting the DNA exit. TRIP4 binds ASCC3 mutually exclusively with the DNA/RNA dealkylase, ALKBH3, directing ASCC3 for specific processes. Our findings define ASCC3-TRIP4 as a tunable motor module of ASCC that encompasses two cooperating NTPase/helicase units functionally expanded by TRIP4.
Topics: Nucleoside-Triphosphatase; DNA Helicases; Spliceosomes; RNA Helicases; DNA
PubMed: 37019967
DOI: 10.1038/s41467-023-37528-3 -
The Journal of Physical Chemistry. B Nov 2019DNA integration with silver and gold nanoparticles was carried out by the chemical reduction of silver and gold ions after the formation of their complexes with high...
DNA integration with silver and gold nanoparticles was carried out by the chemical reduction of silver and gold ions after the formation of their complexes with high molecular DNA in solution. It is shown that, for a good association of DNA with nanoparticles, the ions of silver and gold should be linked with DNA bases rather strongly. The proposed model of gold interaction with DNA is the coordination of gold to N7 guanine in a major groove followed by the transformation of the GC pair to Hoogsteen's type pairing, in which the gold atom is located between the bases and is bonded simultaneously to N7 guanine and N3 cytosine. For gold and silver nanoparticles associated with DNA, the peak of plasmon resonance shifts relative to that of free nanoparticles in solution. AFM (atomic force microscopy) images of both free and associated with DNA nanoparticles were obtained. Binding of high molecular DNA to gold and silver nanoparticles leads to a decrease in the size of its molecular coil in solution, but the bending rigidity of DNA helix (persistent length) does not change. The almost 3-fold increase in the optical anisotropy of DNA was observed when DNA was associated with gold nanoparticles. This result was obtained with the flow birefringence method using a light source with a wavelength of 550 nm, which is close to the peak of the plasmon resonance of gold nanoparticles. For DNA associated with silver nanoparticles, a similar result was obtained when using a light source with a wavelength of about 410 nm.
Topics: Anisotropy; Borohydrides; DNA; Gold; Metal Nanoparticles; Nucleic Acid Conformation; Oxidation-Reduction; Silver; Viscosity
PubMed: 31622103
DOI: 10.1021/acs.jpcb.9b07341 -
Acta Biochimica Et Biophysica Sinica May 2022The rapid development of CRISPR-Cas genome editing tools has greatly changed the way to conduct research and holds tremendous promise for clinical applications. During...
The rapid development of CRISPR-Cas genome editing tools has greatly changed the way to conduct research and holds tremendous promise for clinical applications. During genome editing, CRISPR-Cas enzymes induce DNA breaks at the target sites and subsequently the DNA repair pathways are recruited to generate diverse editing outcomes. Besides off-target cleavage, unwanted editing outcomes including chromosomal structural variations and exogenous DNA integrations have recently raised concerns for clinical safety. To eliminate these unwanted editing byproducts, we need to explore the underlying mechanisms for the formation of diverse editing outcomes from the perspective of DNA repair. Here, we describe the involved DNA repair pathways in sealing Cas enzyme-induced DNA double-stranded breaks and discuss the origins and effects of unwanted editing byproducts on genome stability. Furthermore, we propose the potential risk of inhibiting DNA repair pathways to enhance gene editing. The recent combined studies of DNA repair and CRISPR-Cas editing provide a framework for further optimizing genome editing to enhance editing safety.
Topics: CRISPR-Cas Systems; DNA; DNA Breaks, Double-Stranded; DNA Repair; Gene Editing
PubMed: 35643959
DOI: 10.3724/abbs.2022056 -
Proceedings of the National Academy of... Nov 2023is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb);...
is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear integrants of mitochondrial DNA) and NUPTs (nuclear integrants of plastid DNA) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant ME49 nuclear genome-the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not mutant, parasites. Comparisons with , a species that diverged from ~28 mya, revealed that the movement and fixation of five NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb), and reporter assays indicate that some NUMTs have the ability to function as -regulatory elements modulating gene expression. Together, these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.
Topics: Humans; Toxoplasma; Genome; DNA, Mitochondrial; Mitochondria; Evolution, Molecular; Cell Nucleus; Sequence Analysis, DNA
PubMed: 37917792
DOI: 10.1073/pnas.2308569120 -
Talanta Sep 2022Specific and cost-effective methodologies for human papillomavirus (HPV) gene detection are significant for clinical diagnosis and cancer control. Herein, a label-free...
Specific and cost-effective methodologies for human papillomavirus (HPV) gene detection are significant for clinical diagnosis and cancer control. Herein, a label-free and fluorimetric/colorimetric dual-mode sensing strategy was developed for the quantitative determination of HPV DNA based on the integration of fluorescent DNA-silver nanoclusters (DNA/AgNCs) and G-quadruplex/hemin DNAzyme. The fluorimetric sensing strategy was based on the phenomena that the fluorescence enhancement of DNA/AgNCs obtained in proximity of guanine-rich DNA sequences and the photoinduced electron transfer (PET) effect between the electron donor (DNA/AgNCs) and electron receptor (G-quadruplex/hemin). The colorimetric sensing strategy was relied on the peroxidase-like activity of G-quadruplex/hemin DNAzyme. By integrating DNA/AgNCs and DNAzyme, this dual-mode strategy could produce two independent signals to improve the analytical diversity and accuracy. Under optimized conditions, the fluorimetry and colorimetry of the strategy displayed a linear range of 0.01-4 and 0.02-4 nM, with the low detection limit of 2.3 and 5.2 pM, respectively. Additionally, this dual-mode strategy has been successfully applied to HPV DNA analysis in different real samples with excellent results. Moreover, the sensing platform could be developed for different HPVs DNA assay by only adjusting the recognition sequence, which provided a universal strategy for various kinds of virus analysis.
Topics: Biosensing Techniques; Colorimetry; DNA; DNA, Catalytic; G-Quadruplexes; Hemin; Humans; Nanostructures; Papillomavirus Infections; Silver
PubMed: 35653859
DOI: 10.1016/j.talanta.2022.123554