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Bioconjugate Chemistry Jan 2023Over the past 40 years, structural and dynamic DNA nanotechnologies have undoubtedly demonstrated to be effective means for organizing matter at the nanoscale and... (Review)
Review
Over the past 40 years, structural and dynamic DNA nanotechnologies have undoubtedly demonstrated to be effective means for organizing matter at the nanoscale and reconfiguring equilibrium structures, in a predictable fashion and with an accuracy of a few nanometers. Recently, novel concepts and methodologies have been developed to integrate nonequilibrium dynamics into DNA nanostructures, opening the way to the construction of synthetic materials that can adapt to environmental changes and thus acquire new properties. In this Review, we summarize the strategies currently applied for the construction of synthetic DNA filaments and conclude by reporting some recent and most relevant examples of DNA filaments that can emulate typical structural and dynamic features of the cytoskeleton, such as compartmentalization in cell-like vesicles, support for active transport of cargos, sustained or transient growth, and responsiveness to external stimuli.
Topics: Cytoskeleton; Nanotechnology; Nanostructures; Microtubules; DNA
PubMed: 36174970
DOI: 10.1021/acs.bioconjchem.2c00312 -
International Journal of Molecular... Feb 2023The integration of a DNA copy of an HIV-1 RNA genome into the host genome, carried out by the viral enzyme integrase, results in the formation of single-stranded gaps in...
The integration of a DNA copy of an HIV-1 RNA genome into the host genome, carried out by the viral enzyme integrase, results in the formation of single-stranded gaps in cellular DNA that must be repaired. Here, we have analyzed the involvement of the PI3K kinases, ATM, ATR, and DNA-PKcs, which are important players in the DNA damage response (DDR) in HIV-1 post-integrational DNA repair (PIR). The participation of the DNA-PK complex in HIV-1 PIR has been previously shown, and the formation of a complex between the viral integrase and the DNA-PK subunit, Ku70, has been found to be crucial for efficient PIR. Now, we have shown that the inhibition of both DNA-PKcs and ATM, but not ATR, significantly reduces PIR efficiency. The activation of both kinases is a sequential process, where one kinase, being activated, activates the other, and it occurs simultaneously with the integration of viral DNA. This fact suggests that the activation of both kinases triggers PIR. Most interestingly, the activation of not only DNA-PKcs, but also ATM depends on the complex formation between integrase and Ku70. The elucidation of the interactions between viruses and DDR is important both for understanding the modulation of host cell functions by these pathogens and for developing new approaches to combat viral infections.
Topics: HIV-1; Ataxia Telangiectasia Mutated Proteins; DNA-Activated Protein Kinase; DNA Repair; DNA Damage; DNA, Viral; Integrases
PubMed: 36769109
DOI: 10.3390/ijms24032797 -
International Journal of Molecular... Jan 2020The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of... (Review)
Review
The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.
Topics: Cell Nucleus; Cell Proliferation; DNA End-Joining Repair; DNA, Chloroplast; DNA, Mitochondrial; Evolution, Molecular; Genome Size; Genome, Plant; Mitochondria; Mutation; Plants; Plastids; Sex Chromosomes
PubMed: 31973163
DOI: 10.3390/ijms21030707 -
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 -
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... Oct 1996Adeno-associated virus (AAV) has attracted considerable interest as a potential vector for gene delivery. Wild-type virus is notable for the lack of association with any... (Review)
Review
Adeno-associated virus (AAV) has attracted considerable interest as a potential vector for gene delivery. Wild-type virus is notable for the lack of association with any human disease and the ability to stably integrate its genome in a site-specific manner in a locus on human chromosome 19 (AAVS1). Use of a functional model system for AAV DNA integration into AAVS1 has allowed us to conclude that the recombination event is directed by cellular DNA sequences. Recombinant junctions isolated from our integration assay were analyzed and showed characteristics similar to those found in latently infected cell lines. The minimal DNA signals within AAVS1 required for targeted integration were identified and shown to contain functional motifs of the viral origin of replication. A replication mediated model of AAV DNA integration is proposed.
Topics: Base Sequence; Chromosomes, Human, Pair 19; DNA; DNA Replication; DNA, Viral; Dependovirus; Genetic Vectors; Humans; Models, Genetic; Molecular Sequence Data; Nucleic Acid Conformation; Recombination, Genetic; Virus Integration; Virus Replication
PubMed: 8876128
DOI: 10.1073/pnas.93.21.11288 -
Nature Communications Nov 2019Powerful information processing and ubiquitous computing are crucial for all machines and living organisms. The Watson-Crick base-pairing principle endows DNA with...
Powerful information processing and ubiquitous computing are crucial for all machines and living organisms. The Watson-Crick base-pairing principle endows DNA with excellent recognition and assembly abilities, which facilitates the design of DNA computers for achieving intelligent systems. However, current DNA computational systems are always constrained by poor integration efficiency, complicated device structures or limited computational functions. Here, we show a DNA arithmetic logic unit (ALU) consisting of elemental DNA logic gates using polymerase-mediated strand displacement. The use of an enzyme resulted in highly efficient logic gates suitable for multiple and cascaded computation. Based on our basic single-rail DNA configuration, additional combined logic gates (e.g., a full adder and a 4:1 multiplexer) have been constructed. Finally, we integrate the gates and assemble the crucial ALU. Our strategy provides a facile strategy for assembling a large-scale complex DNA computer system, highlighting the great potential for programming the molecular behaviors of complicated biosystems.
Topics: Computers, Molecular; DNA, Single-Stranded; Equipment Design; Logic; Real-Time Polymerase Chain Reaction
PubMed: 31772166
DOI: 10.1038/s41467-019-13310-2 -
Accounts of Chemical Research Sep 2019Nanoparticles (NPs) have enormous potential to improve disease diagnosis and treatment due to their intrinsic electronic, optical, magnetic, mechanical, and... (Review)
Review
Nanoparticles (NPs) have enormous potential to improve disease diagnosis and treatment due to their intrinsic electronic, optical, magnetic, mechanical, and physiological properties. To realize their full potential for nanomedicine, NPs must be biocompatible and targetable toward specific biomolecules to ensure selective sensing, imaging, and drug delivery in complex environments such as living cells, tissues, animals, and human bodies. In this Account, we summarize our efforts to impart specific biocompatibility and biorecognition functionality to NPs by developing strategies to integrate inorganic and organic NPs with functional DNA (fDNA), including aptamers, DNAzymes, and aptazymes to create fDNA-NPs. These hybrid NPs take advantage of fDNA's ability to either bind targets or catalyze reactions in the presence of targets selectively and utilize their unique physicochemical properties including small size, low immunogenicity, and ease of synthesis and chemical modification in comparison with other molecules such as antibodies. By integrating inorganic NPs such as gold NPs, quantum dots, and iron oxide nanoparticles with fDNA, we designed stimuli-responsive fDNA-NPs that exhibit target induced assembly and disassembly of NPs, resulting in a variety of colorimetric, fluorescent, and magnetic resonance imaging (MRI)-based sensors for diagnostic of a broad range of analytes. To impart both biocompatibility and selectivity on inorganic NPs for targeted bioimaging, we have demonstrated DNA-mediated surface functionalization, shape-controlled synthesis, and coordinative assembly of such NPs as specific bioprobes. A highlight is provided on the construction of fDNA-based nanoprobes with light-activatable sensing and imaging functions, which provides precise control of recognition properties of fDNA with high spatiotemporal resolution. To explore the potential of organic NPs for biosensing applications, we have developed an enzyme-responsive fDNA-liposome as a universal sensing platform compatible with diverse biological targets as well as different detection methods including fluorescence, MRI, or temperature, making possible point-of-care diagnostics. To expand the application regime of organic NPs, we collaborated with the Zimmerman group to prepare single-chain block copolymer-based NPs and incorporated it with a variety of functions, including monovalent DNA for assembly, tunable surface chemistry for cellular imaging, and coordinative Cu(II) sites for catalyzing intracellular click reactions, demonstrating the potential of using organic NPs to create promising fDNA-NP systems with programmable functionalities. Furthermore, we survey our recent endeavor in integration of cell-specific aptamers with different NPs for targeted drug delivery, showing that introducing stimuli-responsive properties into NPs that target tumor microenvironments would enable safer and more effective therapy for cancers. Finally, current challenges and future perspectives in fDNA-mediated engineering of NPs for biomedical applications are discussed.
Topics: Animals; Biomedical Research; Biosensing Techniques; Colorimetry; DNA; Humans; Magnetic Resonance Imaging; Microscopy, Fluorescence; Nanoparticles
PubMed: 31411853
DOI: 10.1021/acs.accounts.9b00167 -
The Plant Journal : For Cell and... Jan 2022Agrobacterium tumefaciens-mediated transformation has been for decades the preferred tool to generate transgenic plants. During this process, a T-DNA carrying transgenes...
Agrobacterium tumefaciens-mediated transformation has been for decades the preferred tool to generate transgenic plants. During this process, a T-DNA carrying transgenes is transferred from the bacterium to plant cells, where it randomly integrates into the genome via polymerase theta (Polθ)-mediated end joining (TMEJ). Targeting of the T-DNA to a specific genomic locus via homologous recombination (HR) is also possible, but such gene targeting (GT) events occur at low frequency and are almost invariably accompanied by random integration events. An additional complexity is that the product of recombination between T-DNA and target locus may not only map to the target locus (true GT), but also to random positions in the genome (ectopic GT). In this study, we have investigated how TMEJ functionality affects the biology of GT in plants, by using Arabidopsis thaliana mutated for the TEBICHI gene, which encodes for Polθ. Whereas in TMEJ-proficient plants we predominantly found GT events accompanied by random T-DNA integrations, GT events obtained in the teb mutant background lacked additional T-DNA copies, corroborating the essential role of Polθ in T-DNA integration. Polθ deficiency also prevented ectopic GT events, suggesting that the sequence of events leading up to this outcome requires TMEJ. Our findings provide insights that can be used for the development of strategies to obtain high-quality GT events in crop plants.
Topics: Agrobacterium tumefaciens; Arabidopsis; DNA, Bacterial; DNA, Plant; DNA-Directed DNA Polymerase; Gene Targeting; Homologous Recombination; Plants, Genetically Modified; Transgenes
PubMed: 34713516
DOI: 10.1111/tpj.15557 -
International Journal of Molecular... Oct 2023Hepatitis B virus (HBV) remains a dominant cause of hepatocellular carcinoma (HCC). Recently, it was shown that HBV and woodchuck hepatitis virus (WHV) integrate into... (Review)
Review
Hepatitis B virus (HBV) remains a dominant cause of hepatocellular carcinoma (HCC). Recently, it was shown that HBV and woodchuck hepatitis virus (WHV) integrate into the hepatocyte genome minutes after invasion. Retrotransposons and transposable sequences were frequent sites of the initial insertions, suggesting a mechanism for spontaneous HBV DNA dispersal throughout the hepatocyte genome. Several somatic genes were also identified as early insertional targets in infected hepatocytes and woodchuck livers. Head-to-tail joints (HTJs) dominated amongst fusions, indicating their creation by non-homologous end-joining (NHEJ). Their formation coincided with the robust oxidative damage of hepatocyte DNA. This was associated with the activation of poly(ADP-ribose) polymerase 1 (PARP1)-mediated dsDNA repair, as reflected by the augmented transcription of PARP1 and XRCC1; the PARP1 binding partner OGG1, a responder to oxidative DNA damage; and increased activity of NAD, a marker of PARP1 activation, and HO1, an indicator of cell oxidative stress. The engagement of the PARP1-mediated NHEJ repair pathway explains the HTJ format of the initial merges. The findings show that HBV and WHV are immediate inducers of oxidative DNA damage and hijack dsDNA repair to integrate into the hepatocyte genome, and through this mechanism, they may initiate pro-oncogenic processes. Tracking initial integrations may uncover early markers of HCC and help to explain HBV-associated oncogenesis.
Topics: Humans; Hepatitis B virus; Carcinoma, Hepatocellular; Liver Neoplasms; Hepatocytes; Cell Transformation, Neoplastic; Carcinogenesis; Genomics; DNA, Viral; Hepatitis B; X-ray Repair Cross Complementing Protein 1
PubMed: 37834296
DOI: 10.3390/ijms241914849