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1.
PLoS Pathog ; 16(3): e1008459, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32226051

RESUMO

Hepatitis B virus (HBV) delivers a partially double-stranded, relaxed circular (RC) DNA genome in complete virions to the host cell nucleus for conversion to the covalently closed circular (CCC) DNA, which establishes and sustains viral infection. An overlength pregenomic RNA (pgRNA) is then transcribed from CCC DNA and packaged into immature nucleocapsids (NCs) by the viral core (HBc) protein. pgRNA is reverse transcribed to produce RC DNA in mature NCs, which are then enveloped and secreted as complete virions, or delivered to the nucleus to replenish the nuclear CCC DNA pool. RC DNA, whether originating from extracellular virions or intracellular mature NCs, must be released upon NC disassembly (uncoating) for CCC DNA formation. HBc is known to undergo dynamic phosphorylation and dephosphorylation at its C-terminal domain (CTD) to facilitate pgRNA packaging and reverse transcription. Here, two putative phosphorylation sites in the HBc N-terminal domain (NTD), S44 and S49, were targeted for genetic and biochemical analysis to assess their potential roles in viral replication. The NTD mutant that mimics the non-phosphorylated state (N2A) was competent in all steps of viral replication tested from capsid assembly, pgRNA packaging, reverse transcription, to virion secretion, except for a decrease in CCC DNA formation. On the other hand, the phosphor-mimetic mutant N2E showed a defect in the early step of pgRNA packaging but enhanced the late step of mature NC uncoating and consequently, increased CCC DNA formation. N2E also enhanced phosphorylation in CTD and possibly elsewhere in HBc. Furthermore, inhibition of the cyclin-dependent kinase 2 (CDK2), which is packaged into viral capsids, could block CCC DNA formation. These results prompted us to propose a model whereby rephosphorylation of HBc at both NTD and CTD by the packaged CDK2, following CTD dephosphorylation during NC maturation, facilitates uncoating and CCC DNA formation by destabilizing mature NCs.


Assuntos
DNA Circular/metabolismo , DNA Viral/metabolismo , Vírus da Hepatite B/metabolismo , Hepatite B/metabolismo , Modelos Biológicos , Nucleocapsídeo/metabolismo , Desenvelopamento do Vírus , Quinase 2 Dependente de Ciclina/genética , Quinase 2 Dependente de Ciclina/metabolismo , DNA Circular/genética , DNA Viral/genética , Células HEK293 , Células Hep G2 , Hepatite B/genética , Vírus da Hepatite B/genética , Humanos , Nucleocapsídeo/genética , Fosforilação , Proteínas do Core Viral/genética , Proteínas do Core Viral/metabolismo
2.
Arch Virol ; 165(5): 1241-1244, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32219545

RESUMO

This work describes the characterization and genome annotation of a new lytic phage, vB_EtaM_ET-ABTNL-9 (referred to as PETp9), isolated from waste water samples collected in Dalian, China, that can kill bacteria of the species Edwardsiella tarda. The genome of phage PETp9 is a circular double-stranded DNA molecule that is 89,762 bp in length with a G+C content of 37.26%, contains 132 ORFs, and encodes one tRNA. Phylogenetic analysis indicated that phage PETp9 should be considered a novel phage.


Assuntos
Bacteriófagos/classificação , Bacteriófagos/isolamento & purificação , Edwardsiella tarda/virologia , Genoma Viral , Análise de Sequência de DNA , Águas Residuárias/virologia , Bacteriólise , Bacteriófagos/genética , Bacteriófagos/crescimento & desenvolvimento , Composição de Bases , China , DNA Circular/genética , DNA Viral/genética , Anotação de Sequência Molecular , Filogenia , Homologia de Sequência
3.
Viruses ; 12(2)2020 Jan 26.
Artigo em Inglês | MEDLINE | ID: mdl-31991902

RESUMO

The Sonoran Desert tortoise Gopherus morafkai is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity associated with tortoises (family Testudinidae), and to date no DNA virus has been identified associated with these animals. This study aimed to assess the diversity of DNA viruses associated with the Sonoran Desert tortoise by sampling their fecal matter. A viral metagenomics approach was used to identify the DNA viruses in fecal samples from wild Sonoran Desert tortoises in Arizona, USA. In total, 156 novel single-stranded DNA viruses were identified from 40 fecal samples. Those belonged to two known viral families, the Genomoviridae (n = 27) and Microviridae (n = 119). In addition, 10 genomes were recovered that belong to the unclassified group of circular-replication associated protein encoding single-stranded (CRESS) DNA virus and five circular molecules encoding viral-like proteins.


Assuntos
Vírus de DNA/isolamento & purificação , Fezes/virologia , Tartarugas/virologia , Animais , Arizona , Vírus de DNA/classificação , Vírus de DNA/genética , DNA Circular , DNA de Cadeia Simples/genética , Genoma Viral , Microviridae/classificação , Microviridae/genética , Microviridae/isolamento & purificação , Microvirus/classificação , Microvirus/genética , Microvirus/isolamento & purificação , Filogenia , Recombinação Genética , Proteínas Virais/genética
4.
Proc Natl Acad Sci U S A ; 117(3): 1658-1665, 2020 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-31900366

RESUMO

We explored the presence of extrachromosomal circular DNA (eccDNA) in the plasma of pregnant women. Through sequencing following either restriction enzyme or Tn5 transposase treatment, we identified eccDNA molecules in the plasma of pregnant women. These eccDNA molecules showed bimodal size distributions peaking at ∼202 and ∼338 bp with distinct 10-bp periodicity observed throughout the size ranges within both peaks, suggestive of their nucleosomal origin. Also, the predominance of the 338-bp peak of eccDNA indicated that eccDNA had a larger size distribution than linear DNA in human plasma. Moreover, eccDNA of fetal origin were shorter than the maternal eccDNA. Genomic annotation of the overall population of eccDNA molecules revealed a preference of these molecules to be generated from 5'-untranslated regions (5'-UTRs), exonic regions, and CpG island regions. Two sets of trinucleotide repeat motifs flanking the junctional sites of eccDNA supported multiple possible models for eccDNA generation. This work highlights the topologic analysis of plasma DNA, which is an emerging direction for circulating nucleic acid research and applications.


Assuntos
Ácidos Nucleicos Livres/isolamento & purificação , DNA Circular/isolamento & purificação , Plasma/química , Ácidos Nucleicos Livres/química , Ácidos Nucleicos Livres/genética , DNA Circular/química , DNA Circular/genética , Feminino , Genoma Humano , Hong Kong , Humanos , Teste Pré-Natal não Invasivo , Gravidez
5.
Nucleic Acids Res ; 48(5): e25, 2020 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-31943080

RESUMO

Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISPR-hapC) for haplotyping. Based on the generation (with a pair of CRISPRs) of extrachromosomal circular DNA in cells, the CRISPR-hapC can map haplotypes from a few hundred bases to over 200 Mb. To streamline and demonstrate the applicability of the CRISPR-hapC and asPAM CRISPR for allele-specific gene editing, we reanalyzed the 1000 human pan-genome and generated a high frequency asPAM SNP and CRISPR database (www.crispratlas.com/knockout) for four CRISPR systems (SaCas9, SpCas9, xCas9 and Cas12a). Using the huntingtin (HTT) CAG expansion and transthyretin (TTR) exon 2 mutation as examples, we showed that the asPAM CRISPRs can specifically discriminate active and dead PAMs for all 23 loci tested. Combination of the CRISPR-hapC and asPAM CRISPRs further demonstrated the capability for achieving highly accurate and haplotype-specific deletion of the HTT CAG expansion allele and TTR exon 2 mutation in human cells. Taken together, our study provides a new approach and an important resource for genome research and allele-specific (haplotype-specific) gene therapy.


Assuntos
Proteína 9 Associada à CRISPR/genética , Sistemas CRISPR-Cas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , DNA Circular/genética , RNA Guia/genética , Alelos , Sequência de Bases , Proteína 9 Associada à CRISPR/metabolismo , Linhagem Celular Tumoral , DNA Circular/metabolismo , Edição de Genes/métodos , Células HEK293 , Haplótipos , Células Hep G2 , Humanos , Plasmídeos/química , Plasmídeos/metabolismo , RNA Guia/metabolismo
6.
PLoS One ; 15(1): e0227296, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31910237

RESUMO

The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.


Assuntos
DNA Circular/isolamento & purificação , DNA de Cadeia Simples/isolamento & purificação , DNA Ambiental/isolamento & purificação , Solo/química , Itália
7.
Biochimie ; 168: 259-267, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31765671

RESUMO

Over the last two decades, isothermal amplification of nucleic acids has gained more attention due to a number of advantages over the widely used polymerase chain reaction. For isothermal amplification, DNA polymerases with strand-displacement activity are needed, and Bst exo- polymerase is one of the most commonly used. Unfortunately, Bst exo- causes nonspecific DNA amplification (so-called multimerization) under isothermal conditions that results in undesirable products (multimers) consisting of tandem nucleotide repeats. Multimerization occurs only for short ssDNA or primer dimers, and the efficiency of multimerization depends significantly on the reaction conditions, but slightly depends on the sequence of DNA templates. In this study we report the prevention of DNA multimerization using a new type of modified oligonucleotide primers with internucleosidic phosphates containing 1,3-dimethyl-2-imino-imidazolidine moieties (phosphoryl guanidine (PG) groups). Primers with one, two or three PG groups located at the 3'- or 5'-ends or in the middle of the primers were designed. It turned out, such bulky groups interfere with the moving of Bst exo- polymerase along DNA chains. However, one modified phosphate does not notably affect the efficiency of polymerization, and the elongation is completely inhibited only when three contiguous modifications occur. Multimerization of the linear ssDNA templates is blocked by three modifications in the middle of both primers whereas specific amplification of the circular ssDNA by rolling circle amplification is not inhibited. Thus, incorporation of three PG groups is sufficient to prevent multimerization and allows to create improved primers for reliable isothermal amplification with Bst exo- DNA polymerase.


Assuntos
DNA Circular/metabolismo , DNA Polimerase Dirigida por DNA/metabolismo , Técnicas de Amplificação de Ácido Nucleico/métodos , Oligonucleotídeos/metabolismo , Replicação do DNA , Polimerização
8.
J Chromatogr A ; 1609: 460444, 2020 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-31455515

RESUMO

Minicircle DNA (mcDNA) is the new cutting-edge technology which researchers have been exploring for gene therapy and DNA vaccination. Although it presents enormous advantages in comparison to conventional plasmid DNA regarding bioactivity and safety, its challenging isolation from parental plasmid and miniplasmid has been setting back its launching in biomedical sciences. In this work, it is demonstrated the use of a simple size exclusion chromatographic method for the isolation of supercoiled mcDNA. Sephacryl S-1000 SF matrix was explored under different conditions (flow, peak fractionation volume and sample loading) to achieve the best performance and retrieve a mcDNA sample devoid of other bacterial contaminants or plasmid species resultant from the recombination process. This isolation methodology resulted in 66.7% of mcDNA recovery with 98.1% of purity. In addition, to show the robustness of the method, the potential of using this matrix for the isolation of a larger mcDNA was also evaluated. Upon adjusting the flow or the column volume, the larger mcDNA molecule was also successfully isolated. Overall, a simple and effective strategy has been established for the isolation of supercoiled mcDNA, underlining the potential of size exclusion chromatography in mcDNA separation.


Assuntos
Cromatografia em Gel/métodos , DNA Circular/isolamento & purificação , DNA Super-Helicoidal/isolamento & purificação , Escherichia coli/genética , Plasmídeos , Proteína Supressora de Tumor p53/isolamento & purificação
9.
Genome Biol Evol ; 12(1): 3762-3777, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31882998

RESUMO

Extrachromosomal circular DNA (eccDNA) elements of chromosomal origin are known to be common in a number of eukaryotic species. However, it remains to be addressed whether genomic features such as genome size, the load of repetitive elements within a genome, and/or animal physiology affect the number of eccDNAs. Here, we investigate the distribution and numbers of eccDNAs in a condensed and less repeat-rich genome compared with the human genome, using Columba livia domestica (domestic rock pigeon) as a model organism. By sequencing eccDNA in blood and breast muscle from three pigeon breeds at various ages and with different flight behavior, we characterize 30,000 unique eccDNAs. We identify genomic regions that are likely hotspots for DNA circularization in breast muscle, including genes involved in muscle development. We find that although eccDNA counts do not correlate with the biological age in pigeons, the number of unique eccDNAs in a nonflying breed (king pigeons) is significantly higher (9-fold) than homing pigeons. Furthermore, a comparison between eccDNA from skeletal muscle in pigeons and humans reveals ∼9-10 times more unique eccDNAs per human nucleus. The fraction of eccDNA sequences, derived from repetitive elements, exist in proportions to genome content, that is, human 72.4% (expected 52.5%) and pigeon 8.7% (expected 5.5%). Overall, our results support that eccDNAs are common in pigeons, that the amount of unique eccDNA types per nucleus can differ between species as well as subspecies, and suggest that eccDNAs from repeats are found in proportions relative to the content of repetitive elements in a genome.


Assuntos
Cromossomos/química , Columbidae/genética , DNA Circular , Genoma , Sequências Repetitivas de Ácido Nucleico , Animais , Genoma Humano , Humanos , Músculo Esquelético/química
10.
Nat Genet ; 52(1): 29-34, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31844324

RESUMO

Extrachromosomal circularization of DNA is an important genomic feature in cancer. However, the structure, composition and genome-wide frequency of extrachromosomal circular DNA have not yet been profiled extensively. Here, we combine genomic and transcriptomic approaches to describe the landscape of extrachromosomal circular DNA in neuroblastoma, a tumor arising in childhood from primitive cells of the sympathetic nervous system. Our analysis identifies and characterizes a wide catalog of somatically acquired and undescribed extrachromosomal circular DNAs. Moreover, we find that extrachromosomal circular DNAs are an unanticipated major source of somatic rearrangements, contributing to oncogenic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. Cancer-causing lesions can emerge out of circle-derived rearrangements and are associated with adverse clinical outcome. It is highly probable that circle-derived rearrangements represent an ongoing mutagenic process. Thus, extrachromosomal circular DNAs represent a multihit mutagenic process, with important functional and clinical implications for the origins of genomic remodeling in cancer.


Assuntos
Carcinogênese/patologia , DNA Circular/genética , Herança Extracromossômica/genética , Rearranjo Gênico , Genoma Humano , Neuroblastoma/patologia , Oncogenes/genética , Recombinação Genética , Humanos , Neuroblastoma/genética , Células Tumorais Cultivadas
11.
PLoS Biol ; 17(12): e3000471, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31794573

RESUMO

Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper-resistance gene CUP1. Transcription of the tandemly repeated CUP1 gene causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. We have developed a sensitive and quantitative eccDNA sequencing pipeline that reveals CUP1 eccDNA accumulation on copper exposure to be exquisitely site specific, with no other detectable changes across the eccDNA complement. eccDNA forms de novo from the CUP1 locus through processing of DNA double-strand breaks (DSBs) by Sae2, Mre11 and Mus81, and genome-wide analyses show that other protein coding eccDNA species in aged yeast share a similar biogenesis pathway. Although abundant, we find that CUP1 eccDNA does not replicate efficiently, and high-copy numbers in aged cells arise through frequent formation events combined with asymmetric DNA segregation. The transcriptional stimulation of CUP1 eccDNA formation shows that age-linked genetic change varies with transcription pattern, resulting in gene copy number profiles tailored by environment.


Assuntos
Variações do Número de Cópias de DNA/genética , DNA Circular/genética , Transcrição Genética/genética , Fatores Etários , Cobre/metabolismo , Cobre/farmacologia , DNA Circular/metabolismo , Endonucleases , Dosagem de Genes/genética , Metalotioneína/genética , Metalotioneína/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Sequências de Repetição em Tandem/genética
12.
Nanoscale ; 11(48): 23416-23422, 2019 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-31799532

RESUMO

Despite the importance of the interaction between DNA and cells for its biological activity, little is known about exactly how DNA interacts with cells. To elucidate the relationship between the structural properties of DNA and its cellular uptake, a single-stranded circular DNA of 1801 bases was designed and folded into a series of rectangular DNA (RecDNA) nanostructures with different rigidities using DNA origami technology. Interactions between these structures and cells were evaluated using mouse macrophage-like RAW264.7 cells. RecDNA with 50 staple DNAs, including four that were Alexa Fluor 488-labeled, was designed. RecDNA with fewer staples, down to four staples (all Alexa Fluor 488-labeled), was also prepared. Electrophoresis and atomic force microscopy showed that all DNA nanostructures were successfully obtained with a sufficiently high yield. Flow cytometry analysis showed that folding of the single-stranded circular DNA into RecDNA significantly increased its cellular uptake. In addition, there was a positive correlation between uptake and the number of staples. These results indicate that highly folded DNA nanostructures interact more efficiently with RAW264.7 cells than loosely folded structures do. Based on these results, it was concluded that the interaction of DNA with cells can be controlled by folding using DNA origami technology.


Assuntos
DNA Circular/química , DNA Circular/metabolismo , DNA de Cadeia Simples/química , DNA de Cadeia Simples/metabolismo , Nanotecnologia/métodos , Animais , Camundongos , Nanoestruturas/química , Conformação de Ácido Nucleico , Células RAW 264.7
13.
BMC Bioinformatics ; 20(1): 663, 2019 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-31830908

RESUMO

BACKGROUND: Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data. RESULTS: Here, we propose a new method, Circle-Map that guides the realignment of partially aligned reads using information from discordantly mapped reads to map the short unaligned portions using a probabilistic model. We compared Circle-Map to similar up-to-date methods for circular DNA and RNA detection and we demonstrate how the approach implemented in Circle-Map dramatically increases sensitivity for detection of circular DNA on both simulated and real data while retaining high precision. CONCLUSION: Circle-Map is an easy-to-use command line tool that implements the required pipeline to accurately detect circular DNA from circle enriched next generation sequencing experiments. Circle-Map is implemented in python3.6 and it is freely available at https://github.com/iprada/Circle-Map.


Assuntos
DNA Circular/genética , Nucleotídeos/genética , Alinhamento de Sequência/métodos , Bases de Dados Genéticas , Humanos , Software
14.
Emerg Microbes Infect ; 8(1): 1563-1573, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31672101

RESUMO

The episomal structures of all human bocavirus (HBoV) genotypes have been deciphered, including the circular genome of HBoV2 (HBoV2-C1). To discern the role of the circular HBoV2 genome, three distinct linearized HBoV2-C1 genomes were cloned into pBlueScript SKII(+) to obtain pBlueScript HBoV2 5043-5042 (retaining all secondary structures), pBlueScript-HBoV2 5075-5074 (retaining hairpin number 2 and the 5' terminal structure), and pBlueScript-HBoV2 5220-5219 (retaining only the 5' terminal structure at the 5' -genome end). The recombinant plasmids were separately transfected HEK293 cells, revealing that more HBoV2 DNA had accumulated in the pBlueScript HBoV2 5043-5042-transfected HEK293 cells at 72 h post-transfection, as determined by real-time PCR. However, more mRNA was transcribed by pBlueScript-HBoV2 5075-5074 than by the other constructs, as determined by dot-blot hybridization and RNAscope. No significant differences in NS1-70 protein expression were observed among the three HBoV2 genomic clones. However, electron microscopy showed that HBoV2 virus particles were only present in the pBlueScript HBoV2 5043-5042-transfected HEK293 cells. By using three hetero-recombinant HBoV2 genomic clones in HEK293 transfected cells, only the genome with intact secondary structures produced virus particles, suggesting that retaining these structures in a circular genome is important for HBoV2 DNA replication and virus assembly.


Assuntos
DNA Circular/genética , DNA Viral/genética , Bocavirus Humano/genética , Infecções por Parvoviridae/virologia , RNA não Traduzido/genética , Recombinação Genética , Montagem de Vírus , Replicação do DNA , DNA Circular/química , DNA Circular/metabolismo , DNA Viral/química , DNA Viral/metabolismo , Genoma Viral , Genômica , Genótipo , Células HEK293 , Bocavirus Humano/química , Bocavirus Humano/fisiologia , Humanos , Conformação de Ácido Nucleico , Filogenia , RNA não Traduzido/química , RNA não Traduzido/metabolismo
15.
Nature ; 575(7784): 699-703, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31748743

RESUMO

Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.


Assuntos
Cromatina/genética , DNA Circular/metabolismo , Regulação Neoplásica da Expressão Gênica/genética , Neoplasias/genética , Oncogenes/genética , Linhagem Celular Tumoral , Cromatina/química , DNA Circular/genética , Humanos , Microscopia Eletrônica de Varredura , Neoplasias/fisiopatologia
16.
Arch Pharm (Weinheim) ; 352(12): e1900187, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31583763

RESUMO

A series of the morpholine-liganded palladium(II) complexes (1a-e) bearing N-heterocyclic carbene (NHC) functionalized by benzonitrile were synthesized. These complexes were synthesized from (NHC)Pd(II)(pyridine) complexes (PEPPSI) and morpholine. The new complexes were fully characterized by using 1 H NMR, 13 C NMR, Fourier-transform infrared spectroscopy, and elemental analysis techniques. Single-crystal X-ray diffraction was used to determine the structure of a derivative. The DNA-binding studies of the new (NHC)Pd(II)morpholine complexes were examined using the pBR322 plasmid. The 2,4,6-trimethylbenzyl derivative compound has the most DNA binding activity. In addition, for the 3-methylbenzyl derivative compound, oxidation effects were observed at concentrations higher than 100 µg/ml. Also, the molecular and crystal structures of the complex 3-methylbenzyl derivative compound were recorded by using a single-crystal X-ray diffraction method.


Assuntos
Complexos de Coordenação/síntese química , Metano/análogos & derivados , Morfolinas/síntese química , Paládio/química , Sítios de Ligação , Complexos de Coordenação/química , Complexos de Coordenação/farmacologia , Cristalografia por Raios X , DNA Circular/química , Ligantes , Metano/química , Morfolinas/química , Morfolinas/farmacologia , Nitrilos/química , Plasmídeos/química
17.
Klin Lab Diagn ; 64(9): 565-570, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31610110

RESUMO

To analyze the method HBV covalent-closed circular DNA quantitative determination in liver puncture biopsies and evaluate its significance in identifying HBsAg-negative viral hepatitis B. In this work, samples of liver tissue biopsy material were used from 128 patients living in St. Petersburg, in various regions of the Russian Federation, as well as in the Republic of Uzbekistan. For quantitative analysis of HBV covalently closed circular DNA in a biopsy material a method was developed based on real-time PCR using TaqMan probes for the target fragment and for the endogenous reference gene, based on the detecting ccc HBV DNA method of Pollicino T. et al. When quantifying ccc DNA HBV in liver tissue of 18 moderately HBV activity with HBV DNA PCR positive results patients and 16 inactive HBsAg carriers, the ccc DNA HBV content was significantly different between groups (p<0.034) and in terms 1 copy of the ß-globin gene among moderate activity HBV patients amounted to 1.71±1.32 copies/cell, and for inactive HBsAg carriers 0.15±0.14 copies/cell. In the group of patients with severe liver fibrosis and cirrhosis, the amount of ccc DNA HBV in liver tissue in patients with HBV averaged 2.5±0.4 copies/cell, in patients with HBV + D on average 0.7±0.25 copies/cell, in patients with HCV + HBV co-infection 0.45±0.07 copies/cell, in patients with a preliminary diagnosis of chronic hepatitis C hepatitis, on average 0.12±0.04 copies/cell, in patients with cryptogenic hepatitis 0.2± 0.05 copies/cell. A significant difference was shown between the group of patients with chronic hepatitis B with marked fibrosis and cirrhosis of the liver with other patients groups, except for the group of 18 moderate activity chronic hepatitis B patients. The values of Student's t-test when compared with other groups were respectively: for patients with a HCV preliminary diagnosis t=5,92 p<0,05 f = 19, patients with cryptogenic hepatitis t=5,71 p<0,05 f = 18, with «inactive HBsAg carriage¼ t=5,55 p<0,05 f = 29, with HCV + HBV co-infection t=5,05 p<0,05 f = 15 and HBV + D co-infection t=3,82 p<0,05 f = 17. The covalently closed circular DNA HBV quantitative assessment method in liver puncture biopsies allows identifying HBsAgnegative chronic viral hepatitis B forms and also reflects the virus replication activity, which, in turn, makes it possible to assume further disease progression and evaluate the antiviral therapy effectiveness.


Assuntos
DNA Circular/análise , DNA Viral/análise , Hepatite B Crônica/diagnóstico , Biópsia por Agulha , Antígenos de Superfície da Hepatite B , Vírus da Hepatite B , Humanos , Fígado , Federação Russa
18.
Nucleic Acids Res ; 47(18): 9741-9760, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31504770

RESUMO

Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.


Assuntos
DNA Circular/genética , Rearranjo Gênico/genética , Oxytricha/genética , Recombinação Genética , Citoplasma/genética , Elementos de DNA Transponíveis/genética , DNA de Protozoário/genética , Células Eucarióticas , Genoma de Protozoário/genética , Sequenciamento de Nucleotídeos em Larga Escala
19.
BMC Infect Dis ; 19(1): 802, 2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31510934

RESUMO

BACKGROUND: Chronic infection with hepatitis B virus (HBV) is a serious global health problem. Persistence of the virus occurs as a result of stability of the replication intermediate comprising covalently closed circular DNA (cccDNA). Development of drugs that are capable of disabling this cccDNA is vital. METHODS: To investigate an epigenetic approach to inactivating viral DNA, we engineered transcriptional repressors that comprise an HBV DNA-binding domain of transcription activator like effectors (TALEs) and a fused Krüppel Associated Box (KRAB). These repressor TALEs (rTALEs) targeted the viral surface open reading frame and were placed under transcription control of constitutively active or liver-specific promoters. RESULTS: Evaluation in cultured cells and following hydrodynamic injection of mice revealed that the rTALEs significantly inhibited production of markers of HBV replication without evidence of hepatotoxicity. Increased methylation of HBV DNA at CpG island II showed that the rTALEs caused intended epigenetic modification. CONCLUSIONS: Epigenetic modification of HBV DNA is a new and effective means of inactivating the virus in vivo. The approach has therapeutic potential and avoids potentially problematic unintended mutagenesis of gene editing.


Assuntos
DNA Viral/genética , Vírus da Hepatite B/crescimento & desenvolvimento , Vírus da Hepatite B/genética , Hepatite B/terapia , Hepatite B/virologia , Proteínas Repressoras/metabolismo , Replicação Viral/genética , Animais , Linhagem Celular , Ilhas de CpG , Metilação de DNA , DNA Circular/genética , DNA Viral/biossíntese , Epigênese Genética , Feminino , Fígado/metabolismo , Fígado/virologia , Camundongos , Fases de Leitura Aberta/genética , Regiões Promotoras Genéticas/genética , Proteínas Repressoras/genética
20.
Int J Mol Sci ; 20(17)2019 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-31480501

RESUMO

Hepatitis B virus (HBV) infection is a major health problem affecting about 300 million people globally. Although successful administration of a prophylactic vaccine has reduced new infections, a cure for chronic hepatitis B (CHB) is still unavailable. Current anti-HBV therapies slow down disease progression but are not curative as they cannot eliminate or permanently silence HBV covalently closed circular DNA (cccDNA). The cccDNA minichromosome persists in the nuclei of infected hepatocytes where it forms the template for all viral transcription. Interactions between host factors and cccDNA are crucial for its formation, stability, and transcriptional activity. Here, we summarize the reported interactions between HBV cccDNA and various host factors and their implications on HBV replication. While the virus hijacks certain cellular processes to complete its life cycle, there are also host factors that restrict HBV infection. Therefore, we review both positive and negative regulation of HBV cccDNA by host factors and the use of small molecule drugs or sequence-specific nucleases to target these interactions or cccDNA directly. We also discuss several reporter-based surrogate systems that mimic cccDNA biology which can be used for drug library screening of cccDNA-targeting compounds as well as identification of cccDNA-related targets.


Assuntos
DNA Circular/metabolismo , Vírus da Hepatite B/genética , Hepatite B/genética , Hepatócitos/virologia , Replicação Viral , Animais , DNA Viral , Hepatite B/metabolismo , Vírus da Hepatite B/metabolismo , Vírus da Hepatite B/fisiologia , Hepatócitos/metabolismo , Humanos
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