scholarly journals DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3

2016 ◽  
Vol 113 (38) ◽  
pp. E5544-E5551 ◽  
Author(s):  
Grace Ee-Lu Siaw ◽  
I-Fen Liu ◽  
Po-Yen Lin ◽  
Michael D. Been ◽  
Tao-shih Hsieh
Keyword(s):  
Gene Expression ◽  
Nucleic Acids ◽  
Specific Binding ◽  
Dna And Rna ◽  
Biochemical Assays ◽  
Binding Preference ◽  
Mediator Protein ◽  
Tudor Domain ◽  
Strand Annealing ◽  
Cellular Compartments

Topoisomerase 3β (Top3β) can associate with the mediator protein Tudor domain-containing protein 3 (TDRD3) to participate in two gene expression processes of transcription and translation. Despite the apparent importance of TDRD3 in binding with Top3β and directing it to cellular compartments critical for gene expression, the biochemical mechanism of how TDRD3 can affect the functions of Top3β is not known. We report here sensitive biochemical assays for the activities of Top3β on DNA and RNA substrates in resolving topological entanglements and for the analysis of TDRD3 functions. TDRD3 stimulates the relaxation activity of Top3β on hypernegatively supercoiled DNA and changes the reaction from a distributive to a processive mode. Both supercoil retention assays and binding measurement by fluorescence anisotropy reveal a heretofore unknown preference for binding single-stranded nucleic acids over duplex. Whereas TDRD3 has a structure-specific binding preference, it does not discriminate between DNA and RNA. This unique property for binding with nucleic acids can have an important function in serving as a hub to form nucleoprotein complexes on DNA and RNA. To gain insight into the roles of Top3β on RNA metabolism, we designed an assay by annealing two single-stranded RNA circles with complementary sequences. Top3β is capable of converting two such single-stranded RNA circles into a double-stranded RNA circle, and this strand-annealing activity is enhanced by TDRD3. These results demonstrate that TDRD3 can enhance the biochemical activities of Top3β on both DNA and RNA substrates, in addition to its function of targeting Top3β to critical sites in subcellular compartments.

scholarly journals Circulating nucleic acids in blood as biomarkers

2009 ◽  
Vol 16 (1) ◽  
Author(s):  
Reidun Øvstebø ◽  
Peter Kierulf ◽  
Kari Bente Foss Haug
Keyword(s):  
Gene Expression ◽  
Nucleic Acids ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Global Gene Expression ◽  
Short Review ◽  
Drug Susceptibility ◽  
Nucleotide Polymorphisms ◽  
Cytochrom P450 ◽  
Dna And Rna

<p>This short review on a rapidly expanding domain in biomarkers focuses on the value of markers derived from either circulating intracellular DNA and RNA (leukocytes) or from free DNA and RNA in plasma or serum. In circulating intracellular DNA biomarkers, importance has been pointed to reside in the ever increasing number of SNPs directly related to disease such as hemochromatosis or associated with genetic make up that leads to different drug-susceptibility. Quantitative gene expression profiling, increasingly using global expression platforms, is gaining momentum in various disease states such as cancer, inflammation, cardiovascular disease and diabetes. Circulating free nucleic acids in plasma or serum gain in importance as biomarkers particularly in cancer and foeto-maternal understanding. The surprising recent findings of circulating free mRNA carries the potential of examining normal and diseased plasma for global gene expression profiling – opening avenues to new biomarkers. When appropriate, this review gives reference to methodological considerations and refers the readers to important literature in the fields</p><p>I denne korte oversiktsartikkelen redegjøres det for et biomarkørfelt som utvikler seg hurtig. Gjennom en blodprøve kan man få kjennskap til forandringer i sirkulerende leucocytter, intracellulære nukleinsyrer (DNA og RNA) og fritt DNA og RNA fra plasma eller serum. Single Nucleotide Polymorphisms (SNPs) i DNA har allerede bekreftet sine muligheter som biomarkører (f.eks. Hemokromatose, Faktor V Leiden, Cytochrom P450 (CYP’er)). Stadig flere SNP’er vinner innpass i klinisk sammenheng. Siden sirkulerende hvite blodlegemer kan sies kontinuerlig å overvåke kroppens organer og vev, og dette avspeiles i disse blodcellers genekspresjon (RNA), knyttes det i dag forventninger til sykdomsspesifikke genekspresjonsprofiler. Både ved visse kreftformer, betennelsestilstander og hjertekar-sykdom viser hvite blodlegemer mer eller mindre tydelig sykdomsspesifikke genekspresjonsprofiler. Denne type sykdomsspesifikke genekspresjonsmarkører vil bli økende viktig fremover. Ved slike markører vil man kunne ha nytte av kvantitativ måling av enkeltmarkører, og også globale genekspresjonsprofiler på mikroarray-plattformer. Sirkulerende fritt DNA og kanskje særlig RNA i plasma åpner for nye sykdomsmarkører i første rekke ved forskjellige kreftformer og ved foeto-maternelle problemstillinger. Oversikten gir også en henvisning til metodologiske referanser i disse feltene.</p>

scholarly journals Machines on Genes: Enzymes that Make, Break and Move DNA and RNA

2010 ◽  
Vol 38 (2) ◽  
pp. 381-383 ◽  
Author(s):  
W. Marshall Stark ◽  
Ben F. Luisi ◽  
Richard P. Bowater
Keyword(s):  
Gene Expression ◽  
Molecular Biology ◽  
Nucleic Acids ◽  
Present Article ◽  
Genetic Information ◽  
Clear View ◽  
Dna And Rna ◽  
Repair Enzymes ◽  
University Of Cambridge ◽  
Enzyme Substrates

As the vital information repositories of the cell, the nucleic acids DNA and RNA pose many challenges as enzyme substrates. To produce, maintain and repair DNA and RNA, and to extract the genetic information that they encode, a battery of remarkable enzymes has evolved, which includes translocases, polymerases/replicases, helicases, nucleases, topoisomerases, transposases, recombinases, repair enzymes and ribosomes. An understanding of how these enzymes function is essential if we are to have a clear view of the molecular biology of the cell and aspire to manipulate genomes and gene expression to our advantage. To bring together scientists working in this fast-developing field, the Biochemical Society held a Focused Meeting, ‘Machines on Genes: Enzymes that Make, Break and Move DNA and RNA’, at Robinson College, University of Cambridge, U.K., in August 2009. The present article summarizes the research presented at this meeting and the reviews associated with the talks which are published in this issue of Biochemical Society Transactions.

scholarly journals Graphene Oxide: A Smart (Starting) Material for Natural Methylxanthines Adsorption and Detection

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4247 ◽  
Author(s):  
Rita Petrucci ◽  
Isabella Chiarotto ◽  
Leonardo Mattiello ◽  
Daniele Passeri ◽  
Marco Rossi ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Graphene Oxide ◽  
Nucleic Acids ◽  
Reduced Graphene Oxide ◽  
Electrochemical Sensors ◽  
Enzymatic Digestion ◽  
Biologically Active ◽  
Polar Solvents ◽  
Dna And Rna ◽  
Reduced Graphene

Natural methylxanthines, caffeine, theophylline and theobromine, are widespread biologically active alkaloids in human nutrition, found mainly in beverages (coffee, tea, cocoa, energy drinks, etc.). Their detection is thus of extreme importance, and many studies are devoted to this topic. During the last decade, graphene oxide (GO) and reduced graphene oxide (RGO) gained popularity as constituents of sensors (chemical, electrochemical and biosensors) for methylxanthines. The main advantages of GO and RGO with respect to graphene are the easiness and cheapness of synthesis, the notable higher solubility in polar solvents (water, among others), and the higher reactivity towards these targets (mainly due to – interactions); one of the main disadvantages is the lower electrical conductivity, especially when using them in electrochemical sensors. Nonetheless, their use in sensors is becoming more and more common, with the obtainment of very good results in terms of selectivity and sensitivity (up to 5.4 × 10−10 mol L−1 and 1.8 × 10−9 mol L−1 for caffeine and theophylline, respectively). Moreover, the ability of GO to protect DNA and RNA from enzymatic digestion renders it one of the best candidates for biosensors based on these nucleic acids. This is an up-to-date review of the use of GO and RGO in sensors.

scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

scholarly journals OP0045 NLRP12 INVOLVES IN THE LUPUS WITH POSITIVE INTERFERON SIGNATURE

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 23.2-24
Author(s):  
Y. P. Tsao ◽  
F. Y. Tseng ◽  
C. W. Chao ◽  
M. H. Chen ◽  
S. T. Chen
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Animal Models ◽  
Nucleic Acids ◽  
Disease Activity ◽  
Interferon Signature ◽  
Healthy Donors ◽  
Healthy Control ◽  
Lupus Disease Activity

Background:Systemic lupus erythematous (SLE) is a systemic autoimmune disease with diverse etiological factors. It was recognized that interferon (IFN) signature involved in the progress of SLE. NLRP12 (NOD-like receptor family (NLR) pyrin domain containing 12) is a pyrin containing NLR protein that we had linked its new biological function to the cross-regulation of Toll like receptor (TLRs) and Rig-I like receptor (RIG-I) pathways. NLPR12 acts as an innate immune check-point in regulating type I IFNs expression during TLRs and RIG-I activation. The importance of NLRP12 in lupus disease activity remained to be elucidated.Objectives:To clarify the role of NLRP12 in regulating the interferon signature.Methods:Peripheral blood mononuclear cells (PBMCs) were collected from SLE patients and healthy donors for analysis of NLRP12 and IFN-α gene expression by RT-QPCR. PBMCs were applied for Chromatin immuneprecipitation (ChIP) assay and electrical mobility shift assay (EMSA) to determine the putative transcription factor that regulates NLRP12 expression. An involvement of epigenetic regulation of NLRP12 expression in SLE patients was also analyzed. Bone marrow derived dendritic cells (BMDCs) were collected from wild type mouse and Nlrp12 knocked-out mice. Another CD14+ monocytes were isolated from 10 cases of lupus patients and 8 cases of healthy control, following by stimulating different type of nucleic acids, and IFN-α and IL-6 were measured with ELISA assay. CD14+ monocytes in lupus patients were also pre-treated with IFNAR2 antibody for further nucleic acid stimulation. Two mice models were applied for evaluation the role of Nlrp12: intraperitoneal injection of TMPD (2,6,10,14-tetramethylpentadecane, or pristane) in C57BL/6 mice and Faslpr mice. Both models were conducted with and without Nlrp12 knockout.Results:NLRP12 expression was significantly lower in PBMC isolated from SLE patients compared to healthy donors. The inverse correlation was observed in NLRP12 and IFNA gene expression as well as NLRP12 expression and amount of double-stranded DNA autoantibody in SLE patients. NLRP12 expression showed negative correlations with IFN-α treatment, as well as herpes simplex virus-1 (HSV-1) infection. Results from ChIP and EMSA analysis indicated a potential transcription factor 1 (TF-1) regulating NLRP12 promoter activity. TF-1 lead to transcriptional suppression of NLRP12 in SLE PBMC, and it was gradually induced after IFN treatment. Recruitment of TF-1 to NLRP12 promoter in SLE PBMC compared to the healthy PBMC was detected, and increased when treating with IFN. Human CD14+ monocytes collected from lupus and healthy control stimulating with different type of nucleic acids revealing significant increasing level of IFN-α and IL-6 in lupus patients. Among animal models, both pristine induced mice and Faslpr mice revealed increasing autoantibodies production and severity of glomerulonephritis in Nlrp12-/- group in comparison with Nlrp12+/+ ones, indicating the role of NLRP12 in maintaining positive interferon signature as well as disease activity.Conclusion:Expression level of NLRP1.2 has been demonstrated to be a biomarker of disease activity in SLE patients. The NLRP12 was involved in the interferon signature, which was also negatively regulated by TF-1. Both clinical samples and animal models revealed NLRP12 in maintaining the positive interferon signature, indicating the possible role of exacerbating factor for lupus disease activity.Disclosure of Interests:None declared

scholarly journals Base-edited CAR T cells for combinational therapy against T cell malignancies

Leukemia ◽  
2021 ◽  
Author(s):  
Christos Georgiadis ◽  
Jane Rasaiyaah ◽  
Soragia Athina Gkazi ◽  
Roland Preece ◽  
Aniekan Etuk ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Specific Binding ◽  
Base Editing ◽  
Car T Cells ◽  
Dna And Rna ◽  
Car T ◽  
T Cell Malignancies

AbstractTargeting T cell malignancies using chimeric antigen receptor (CAR) T cells is hindered by ‘T v T’ fratricide against shared antigens such as CD3 and CD7. Base editing offers the possibility of seamless disruption of gene expression of problematic antigens through creation of stop codons or elimination of splice sites. We describe the generation of fratricide-resistant T cells by orderly removal of TCR/CD3 and CD7 ahead of lentiviral-mediated expression of CARs specific for CD3 or CD7. Molecular interrogation of base-edited cells confirmed elimination of chromosomal translocations detected in conventional Cas9 treated cells. Interestingly, 3CAR/7CAR co-culture resulted in ‘self-enrichment’ yielding populations 99.6% TCR−/CD3−/CD7−. 3CAR or 7CAR cells were able to exert specific cytotoxicity against leukaemia lines with defined CD3 and/or CD7 expression as well as primary T-ALL cells. Co-cultured 3CAR/7CAR cells exhibited highest cytotoxicity against CD3 + CD7 + T-ALL targets in vitro and an in vivo human:murine chimeric model. While APOBEC editors can reportedly exhibit guide-independent deamination of both DNA and RNA, we found no problematic ‘off-target’ activity or promiscuous base conversion affecting CAR antigen-specific binding regions, which may otherwise redirect T cell specificity. Combinational infusion of fratricide-resistant anti-T CAR T cells may enable enhanced molecular remission ahead of allo-HSCT for T cell malignancies.

scholarly journals Characterization of nucleic acids from extracellular vesicle-enriched human sweat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Geneviève Bart ◽  
Daniel Fischer ◽  
Anatoliy Samoylenko ◽  
Artem Zhyvolozhnyi ◽  
Pavlo Stehantsev ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Body Fluids ◽  
Lower Percentage ◽  
Rna Seq ◽  
Protein Coding ◽  
Human Sweat ◽  
Dna And Rna ◽  
Ribonucleoprotein Complexes ◽  
Eccrine Glands

Abstract Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles. Results We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7–45%), with 50–60% of those reads mapping to unannotated region of the genome and 30–55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA. Conclusions Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters.

scholarly journals Frequent EPAS1/HIF2α exons 9 and 12 mutations in non-familial pheochromocytoma

2014 ◽  
Vol 21 (3) ◽  
pp. 495-504 ◽  
Author(s):  
Jenny Welander ◽  
Adam Andreasson ◽  
Michael Brauckhoff ◽  
Martin Bäckdahl ◽  
Catharina Larsson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Gene Expression Pattern ◽  
Exon 2 ◽  
Dna And Rna ◽  
Familial Pheochromocytoma ◽  
Predisposing Genes ◽  
Adrenal Pheochromocytoma ◽  
New Gene ◽  
Sporadic Pheochromocytoma

Pheochromocytomas are neuroendocrine tumors arising from the adrenal medulla. While heritable mutations are frequently described, less is known about the genetics of sporadic pheochromocytoma. Mutations in genes involved in the cellular hypoxia response have been identified in tumors, and recentlyEPAS1, encoding HIF2α, has been revealed to be a new gene involved in the pathogenesis of pheochromocytoma and abdominal paraganglioma. The aim of this study was to further characterizeEPAS1alterations in non-familial pheochromocytomas. Tumor DNA from 42 adrenal pheochromocytoma cases with apparently sporadic presentation, without known hereditary mutations in predisposing genes, were analyzed for mutations inEPAS1by sequencing of exons 9 and 12, which contain the two hydroxylation sites involved in HIF2α degradation, and also exon 2. In addition, the copy number at theEPAS1locus as well as transcriptome-wide gene expression were studied by DNA and RNA microarray analyses, respectively. We identified six missenseEPAS1mutations, three in exon 9 and three in exon 12, in five of 42 pheochromocytomas (12%). The mutations were both somatic and constitutional, and had no overlap in 11 cases (26%) with somatic mutations inNF1orRET. One sample had two differentEPAS1mutations, shown by cloning to occur incis, possibly indicating a novel mechanism of HIF2α stabilization through inactivation of both hydroxylation sites. One of the tumors with anEPAS1mutation also had a gain in DNA copy number at theEPAS1locus. AllEPAS1-mutated tumors displayed a pseudo-hypoxic gene expression pattern, indicating an oncogenic role of the identified mutations.

scholarly journals BIOLOGICAL ACTIVITY OF YERSINIA PSEUDOTUBERCULOSIS TOXINS

2016 ◽  
pp. 10-19
Author(s):  
N. A. Terentieva ◽  
N. F. Timchenko ◽  
V. A. Golotin ◽  
V. A. Rasskazov
Keyword(s):  
Nucleic Acids ◽  
Sea Urchin ◽  
Yersinia Pseudotuberculosis ◽  
Protein Biosynthesis ◽  
Sea Urchin Embryos ◽  
Dna And Rna ◽  
Embryo Cells ◽  
Protein Toxins ◽  
Rna Biosynthesis ◽  
High Concentrations

Aim. Study of effect of heat-labile (HLT) and thermostable (HST) lethal toxins of Yersinia pseudotuberculosis on the development of embryos of sea urchin Strongylocentrotus intermedius, processes of biosynthesis of nucleic acids and protein in embryo cells and activity of nucleoside-kinases of sea urchin. Materials and methods. Y. pseudotuberculosis strains 2517 (pYV-) and 512 (pYV48MD, pYV82MD) were used for isolation of HLT and HST. Gametes and embryos of sea urchin S. intermedius were used to carry out the experiments and isolate nucleoside-kinases. Results. Both of the studied toxins of Y. pseudotuberculosis possessed spermiotoxic effect and reduced fertilizing ability of sea urchin spermies. HLT LD50 was 1 (ig/ml, and HST - 2 pg/ml. Toxins affected the development of embryos of sea urchin resulting in severe morphologic damages, cessation of the development of embryos at early stages of embryogenesis, destruction of cells and death of embryos. Wherein, damaging effect of HLT was observed at lower concentrations compared with HST. HLT inhibited DNA and RNA biosynthesis at concentrations of 1-2 pg/ml. HST did not affect biosynthesis of nucleic acids even at high concentrations, but inhibited protein biosynthesis in sea urchin embryos. HLT did not reduce the level of inclusion of labeled amino acids into embryo cells. HLT had inhibiting effect on the activity of thymidine- and uridine-kinase of sea urchin, whereas HST did not affect these enzymes. Conclusion. Both of Y. pseudotuberculosis protein toxins affect the development of sea urchin embryos, however, mechanisms of action of HLT and HST on embryos and processes occurring in them differ.

Sign in / Sign up

Export Citation Format

Share Document