241,941 results match your criteria dna synthesis


β-CASP proteins removing RNA polymerase from DNA: when a torpedo is needed to shoot a sitting duck.

Nucleic Acids Res 2021 Sep 22. Epub 2021 Sep 22.

Department of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague CZ-14220, Czech Republic.

During the first step of gene expression, RNA polymerase (RNAP) engages DNA to transcribe RNA, forming highly stable complexes. These complexes need to be dissociated at the end of transcription units or when RNAP stalls during elongation and becomes an obstacle ('sitting duck') to further transcription or replication. In this review, we first outline the mechanisms involved in these processes. Read More

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September 2021

Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

Nucleic Acids Res 2021 Sep 22. Epub 2021 Sep 22.

School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Ribonucleoside triphosphate (rNTP) incorporation in DNA by DNA polymerases is a frequent phenomenon that results in DNA structural change and genome instability. However, it is unclear whether the rNTP incorporation into DNA follows any specific sequence patterns. We analyzed multiple datasets of ribonucleoside monophosphates (rNMPs) embedded in DNA, generated from three rNMP-sequencing techniques. Read More

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September 2021

Replication-dependent cytotoxicity and Spartan-mediated repair of trapped PARP1-DNA complexes.

Nucleic Acids Res 2021 Sep 22. Epub 2021 Sep 22.

Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.

The antitumor activity of poly(ADP-ribose) polymerase inhibitors (PARPis) has been ascribed to PARP trapping, which consists in tight DNA-protein complexes. Here we demonstrate that the cytotoxicity of talazoparib and olaparib results from DNA replication. To elucidate the repair of PARP1-DNA complexes associated with replication in human TK6 and chicken DT40 lymphoblastoid cells, we explored the role of Spartan (SPRTN), a metalloprotease associated with DNA replication, which removes proteins forming DPCs. Read More

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September 2021

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity.

Cell Rep 2021 Sep;36(12):109722

Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia. Electronic address:

DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Read More

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September 2021

Reading ADP-ribosylation signaling using chemical biology and interaction proteomics.

Mol Cell 2021 Sep 15. Epub 2021 Sep 15.

Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands. Electronic address:

ADP-ribose (ADPr) readers are essential components of ADP-ribosylation signaling, which regulates genome maintenance and immunity. The identification and discrimination between monoADPr (MAR) and polyADPr (PAR) readers is difficult because of a lack of suitable affinity-enrichment reagents. We synthesized well-defined ADPr probes and used these for affinity purifications combined with relative and absolute quantitative mass spectrometry to generate proteome-wide MAR and PAR interactomes, including determination of apparent binding affinities. Read More

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September 2021

Low-dose radiation-induced demethylation of 3β-HSD participated in the regulation of testosterone content.

J Appl Toxicol 2021 Sep 22. Epub 2021 Sep 22.

Tianjin University of Traditional Chinese Medicine, Tianjin, China.

The effects of low-dose radiation (LDR, ≤0.1 Gy) on living organisms have been the hot areas of radiation biology but do not reach a definitive conclusion yet. So far, few studies have adequately accounted for the male reproductive system responses to LDR, particularly the regulation of testosterone content. Read More

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September 2021

Taxonomy update for the family Alphasatellitidae: new subfamily, genera, and species.

Arch Virol 2021 Sep 22. Epub 2021 Sep 22.

Im Broich 38, 50128, Bergheim-Fliesteden, Germany.

Alphasatellites (family Alphasatellitidae) are circular, single-stranded DNA molecules (~1-1.4 kb) that encode a replication-associated protein and have commonly been associated with some members of the families Geminiviridae, Nanoviridae, and Metaxyviridae (recently established). Here, we provide a taxonomy update for the family Alphasatellitidae following the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021. Read More

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September 2021

Antifungal activity and mechanism of action of 2-chloro-N -phenylacetamide: a new molecule with activity against strains of Aspergillus flavus.

An Acad Bras Cienc 2021 20;93(suppl 3):e20200997. Epub 2021 Sep 20.

Universidade Federal da Paraíba, Departamento de Cências Farmacêuticas, Campus I, Loteamento Cidade Universitária, s/n, Castelo Branco, 58051-970 João Pessoa, PB, Brazil.

Aspergillus genus causes many diseases, and the species Aspergillus flavus is highly virulent. Treatment of aspergillosis involves azole derivatives such as voriconazole and polyenes such as amphotericin B. Due to an increase in fungal resistance, treatments are now less effective; the search for new compounds with promising antifungal activity has gained importance. Read More

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September 2021

Understanding the molecular mechanisms of transcriptional bursting.

Phys Chem Chem Phys 2021 Sep 22. Epub 2021 Sep 22.

Department of Chemistry, Department of Physics and Astronomy, Department of Chemical and Biomolecular Engineering and Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1892, USA.

In recent years, it has been experimentally established that transcription, a fundamental biological process that involves the synthesis of messenger RNA molecules from DNA templates, does not proceed continuously as was expected. Rather, it exhibits a distinct dynamic behavior of alternating between productive phases when RNA molecules are actively synthesized and inactive phases when there is no RNA production at all. The bimodal transcriptional dynamics is now confirmed to be present in most living systems. Read More

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September 2021

Characteristics of Immediate-Early 2 (IE2) and UL84 Proteins in UL84-Independent Strains of Human Cytomegalovirus (HCMV).

Microbiol Spectr 2021 Sep 22:e0053921. Epub 2021 Sep 22.

Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, Nevada, USA.

Human cytomegalovirus (HCMV) immediate-early 2 (IE2) protein is the major transactivator for viral gene expression and is required for lytic replication. In addition to transcriptional activation, IE2 is known to mediate transcriptional repression of promoters, including the major immediate-early (MIE) promoter and a bidirectional promoter within the lytic origin of replication (Lyt). The activity of IE2 is modulated by another viral protein, UL84. Read More

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September 2021

The Vancomycin Resistance-Associated Regulatory System VraSR Modulates Biofilm Formation of Staphylococcus epidermidis in an -Dependent Manner.

mSphere 2021 Sep 22:e0064121. Epub 2021 Sep 22.

Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan Universitygrid.8547.e, Shanghai, China.

The two-component system VraSR responds to the cell wall-active antibiotic stress in Staphylococcus epidermidis. To study its regulatory function in biofilm formation, a deletion mutant (Δ) was constructed using S. epidermidis strain 1457 (SE1457) as the parent strain. Read More

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September 2021

CRISPR/Cas9 ablation of integrated HIV-1 accumulates proviral DNA circles with reformed LTRs.

J Virol 2021 Sep 22:JVI0135821. Epub 2021 Sep 22.

Retrovirus Center and Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.

Gene editing may be used to excise the human immunodeficiency virus type-1 (HIV-1) provirus from the host cell genome, possibly eradicating the infection. Here, using cells acutely or latently infected by HIV-1 and treated with long terminal repeat-targeting CRISPR/Cas9, we show that the excised HIV-1 provirus persists for a few weeks and may rearrange in circular molecules. Although circular proviral DNA is naturally formed during HIV-1 replication, we observed that gene-editing might increase proviral DNA circles with restored LTRs. Read More

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September 2021

Synthesis, structure and cytotoxicity of N,N and N,O coordinated RuII complexes of 3-aminobenzoate Schiff bases against triple-negative breast cancer.

Chem Asian J 2021 Sep 22. Epub 2021 Sep 22.

Indian Institute of Science Education and Research Kolkata, Department of Chemical Sciences, BCKV campus, 741252, Mohanpur, INDIA.

Half-sandwich Ru II complexes, [(YZ)Ru II (η 6 -arene)(X)]+, (YZ= chelating bidentate ligand, X = halide), with N , N and N , O coordination ( 1-9 ) show significant antiproliferative activity against the metastatic triple negative breast carcinoma (MDA-MB-231). 3-aminobenzoic acid or its methyl ester is used in all the ligands while varying the aldehyde for N , N and N , O coordination. In the N,N coordinated complex the coordinated halide(X) is varied for enhancing stability in solution (X = Cl, I). Read More

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September 2021

Synthesis and DNA interaction studies of Ru(II) cell penetrating peptide (CPP) bioconjugates.

Dalton Trans 2021 Sep 22. Epub 2021 Sep 22.

Inorganic Chemistry I - Bioinorganic Chemistry, Ruhr-University Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany.

The synthesis of the first bioconjugates of a set of ruthenium(II) dipyridophenazine complexes with two different cell penetrating peptides (CPPs) is described. The CPPs, an arginine rich TAT-9 (RKKRRQRRR) sequence and the Xentry peptide (LCLRPVG), were synthesized using standard SPPS protocols, and the bioconjugates were obtained by the microwave-assisted coupling of the HOBt/TBTU preactivated metal complexes with the respective peptides on Wang resin. The racemic metal complexes were obtained by modified literature procedures. Read More

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September 2021

Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity.

Exp Mol Med 2021 Sep 21. Epub 2021 Sep 21.

Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.

Endogenous DNA damage is a major contributor to mutations, which are drivers of cancer development. Bromodomain (BRD) proteins are well-established participants in chromatin-based DNA damage response (DDR) pathways, which maintain genome integrity from cell-intrinsic and extrinsic DNA-damaging sources. BRD proteins are most well-studied as regulators of transcription, but emerging evidence has revealed their importance in other DNA-templated processes, including DNA repair and replication. Read More

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September 2021

Bacteriophage origin of some minimal ATP-dependent DNA ligases: a new structure from Burkholderia pseudomallei with striking similarity to Chlorella virus ligase.

Sci Rep 2021 Sep 21;11(1):18693. Epub 2021 Sep 21.

School of Science, University of Waikato, Hamilton, 3240, New Zealand.

DNA ligases, the enzymes responsible for joining breaks in the phosphodiester backbone of DNA during replication and repair, vary considerably in size and structure. The smallest members of this enzyme class carry out their functions with pared-down protein scaffolds comprising only the core catalytic domains. Here we use sequence similarity network analysis of minimal DNA ligases from all biological super kingdoms, to investigate their evolutionary origins, with a particular focus on bacterial variants. Read More

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September 2021

Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production.

BMC Genomics 2021 Sep 22;22(1):686. Epub 2021 Sep 22.

Food System Integrity team, Hopkirk Research Institute, AgResearch Ltd, Massey University, 4474, Palmerston North, New Zealand.

Background: Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooked in bioactive compound discovery. As Clostridium spp. Read More

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September 2021

Role of GATA3 in tumor diagnosis: A review.

Pathol Res Pract 2021 Sep 13;226:153611. Epub 2021 Sep 13.

Department of Pathology, Dr. Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran; Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran. Electronic address:

GATA binding protein 3 (GATA3) belongs to a family of transcription factors comprising six members. These proteins identify G-A-T-A containing sequences in the target gene and bind to DNA target via two zinc-finger domains. The aim of this study was to evaluate the role of GATA3 in the diagnosis of tumors and its value as a prognostic marker. Read More

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September 2021

COVID-eVax, an electroporated plasmid DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain, elicits protective immune responses in animal models of COVID-19.

Mol Ther 2021 Sep 18. Epub 2021 Sep 18.

Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.

The COVID-19 pandemic caused by SARS-CoV-2 has made the development of safe and effective vaccines a critical priority. To date, four vaccines have been approved by European and American authorities for preventing COVID-19 but the development of additional vaccine platforms with improved supply and logistics profiles remains a pressing need. Here we report the preclinical evaluation of a novel COVID-19 vaccine candidate based on the electroporation of engineered, synthetic cDNA encoding a viral antigen in the skeletal muscle. Read More

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September 2021

Controlling the topology of mammalian mitochondrial DNA.

Open Biol 2021 Sep 22;11(9):210168. Epub 2021 Sep 22.

Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.

The genome of mitochondria, called mtDNA, is a small circular DNA molecule present at thousands of copies per human cell. MtDNA is packaged into nucleoprotein complexes called nucleoids, and the density of mtDNA packaging affects mitochondrial gene expression. Genetic processes such as transcription, DNA replication and DNA packaging alter DNA topology, and these topological problems are solved by a family of enzymes called topoisomerases. Read More

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September 2021

Proteomic landscape of Japanese encephalitis virus-infected fibroblasts.

J Gen Virol 2021 Sep;102(9)

Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.

Advances in proteomics have enabled a comprehensive understanding of host-pathogen interactions. Here we have characterized Japanese encephalitis virus (JEV) infection-driven changes in the mouse embryonic fibroblast (MEF) proteome. Through tandem mass tagging (TMT)-based mass spectrometry, we describe changes in 7. Read More

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September 2021

First Report of Berkeleyomyces basicola Causing Black Root Rot on Lisianthus (Eustoma grandiflorum) in China.

Plant Dis 2021 Sep 21. Epub 2021 Sep 21.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, No. 12, Zhongguancun Nandajie, Beijing, 100081, China, Beijing, China, 100081;

Lisianthus (Eustoma grandiflorum (Raf.) Shinn.) is an important ornamental plant ranking in the top 10 cut flowers worldwide (Xiao et al. Read More

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September 2021

O-GlcNAcylation of High Mobility Group Box 1 (HMGB1) Alters Its DNA Binding and DNA Damage Processing Activities.

J Am Chem Soc 2021 Sep 21. Epub 2021 Sep 21.

Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard, Austin, Texas 78723, United States.

Protein O-GlcNAcylation is an essential and dynamic regulator of myriad cellular processes, including DNA replication and repair. Proteomic studies have identified the multifunctional nuclear protein HMGB1 as O-GlcNAcylated, providing a potential link between this modification and DNA damage responses. Here, we verify the protein's endogenous modification at S100 and S107 and found that the major modification site is S100, a residue that can potentially influence HMGB1-DNA interactions. Read More

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September 2021

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules.

Chem Rev 2021 Sep 21. Epub 2021 Sep 21.

Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. Read More

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September 2021

A New 1,5-Disubstituted Triazole DNA Backbone Mimic with Enhanced Polymerase Compatibility.

J Am Chem Soc 2021 Sep 21. Epub 2021 Sep 21.

Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, U.K.

Triazole linkages (TLs) are mimics of the phosphodiester bond in oligonucleotides with applications in synthetic biology and biotechnology. Here we report the RuAAC-catalyzed synthesis of a novel 1,5-disubstituted triazole (TL) dinucleoside phosphoramidite as well as its incorporation into oligonucleotides and compare its DNA polymerase replication competency with other TL analogues. We demonstrate that TL has superior replication kinetics to these analogues and is accurately replicated by polymerases. Read More

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September 2021

A 2021 taxonomy update for the family Smacoviridae.

Arch Virol 2021 Sep 21. Epub 2021 Sep 21.

The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA.

The family Smacoviridae (order Cremevirales, class Arfiviricetes, phylum Cressdnaviricota) is comprised of viruses with small circular single-stranded DNA genomes of ~2.3-3 kb in length that have primarily been identified in fecal sample of various animals. Smacovirus genomes carry two genes in ambisense orientation encoding a capsid protein and a rolling-circle replication initiation protein, respectively. Read More

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September 2021

Efficiency and equity in origin licensing to ensure complete DNA replication.

Biochem Soc Trans 2021 Sep 21. Epub 2021 Sep 21.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A.

The cell division cycle must be strictly regulated during both development and adult maintenance, and efficient and well-controlled DNA replication is a key event in the cell cycle. DNA replication origins are prepared in G1 phase of the cell cycle in a process known as origin licensing which is essential for DNA replication initiation in the subsequent S phase. Appropriate origin licensing includes: (1) Licensing enough origins at adequate origin licensing speed to complete licensing before G1 phase ends; (2) Licensing origins such that they are well-distributed on all chromosomes. Read More

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September 2021

Assessment of Mitochondrial DNA Copy Number, Stability, and Repair in Arabidopsis.

Methods Mol Biol 2022 ;2363:301-319

Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France.

Mitochondrial functions depend on the proper maintenance and expression of the mitochondrial genome (mtDNA). Therefore, understanding mtDNA replication and repair requires methods to assess its integrity. Mutations or chemical treatments that affect processes involved in the maintenance or stability of the mtDNA can affect its global copy number, but also the relative abundance of different genomic regions or the frequency of illegitimate recombination across repeated sequences. Read More

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January 2022

Biallelic variants in YRDC cause a developmental disorder with progeroid features.

Hum Genet 2021 Sep 20. Epub 2021 Sep 20.

Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany.

The highly conserved YrdC domain-containing protein (YRDC) interacts with the well-described KEOPS complex, regulating specific tRNA modifications to ensure accurate protein synthesis. Previous studies have linked the KEOPS complex to a role in promoting telomere maintenance and controlling genome integrity. Here, we report on a newborn with a severe neonatal progeroid phenotype including generalized loss of subcutaneous fat, microcephaly, growth retardation, wrinkled skin, renal failure, and premature death at the age of 12 days. Read More

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September 2021

Unwinding of a DNA replication fork by a hexameric viral helicase.

Nat Commun 2021 Sep 20;12(1):5535. Epub 2021 Sep 20.

Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, UK.

Hexameric helicases are motor proteins that unwind double-stranded DNA (dsDNA) during DNA replication but how they are optimised for strand separation is unclear. Here we present the cryo-EM structure of the full-length E1 helicase from papillomavirus, revealing all arms of a bound DNA replication fork and their interactions with the helicase. The replication fork junction is located at the entrance to the helicase collar ring, that sits above the AAA + motor assembly. Read More

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September 2021