Faculty Opinions recommendation of Ethylenediamine derivatives efficiently react with oxidized RNA 3' ends providing access to mono and dually labelled RNA probes for enzymatic assays and in vivo translation.

2021 ◽  
Author(s):  
Venkat Gopalan ◽  
Walter Zahurancik ◽  
Lien Lai
Keyword(s):  
Enzymatic Assays ◽  
Rna Probes ◽  
Ethylenediamine Derivatives

ATTAAA as well as downstream sequences are required for RNA 3'-end formation in the E3 complex transcription unit of adenovirus

1985 ◽  
Vol 5 (11) ◽  
pp. 3183-3193
Author(s):  
B M Bhat ◽  
W S Wold
Keyword(s):  
Base Pair ◽  
Transcription Unit ◽  
Rna Probes ◽  
Labeled Rna

We mapped the location of the E3A RNA 3' end site in the E3 transcription unit of adenovirus 2. The procedure used was nuclease-gel analysis with 32P-labeled RNA probes. The poly(A) addition sites were microheterogeneous and were located approximately 17 to 29 nucleotides downstream from an ATTAAA sequence. To identify the sequences that make up the E3A RNA 3' end signal, we constructed five viable virus mutants with deletions in or near the E3A RNA 3' end site. The mutants were analyzed for E3A RNA 3' end formation in vivo. No effect was observed from a 47-base-pair (bp) deletion (dl716) or a 72-bp deletion (dl714) located 22 and 19 nucleotides, respectively, upstream of the ATTAAA. In contrast, E3A RNA 3' end formation was abolished by a 554-bp deletion (dl708) that removes both the ATTAAA and the poly(A) addition sites, a 124-bp deletion (dl713) that removes the ATTAAA but leaves the poly(A) addition sites, and a 65-bp deletion (dl719) that leaves the ATTAAA but removes the poly(A) addition sites. These results indicate that the ATTAAA, as well as downstream sequences, including the poly(A) addition sites, are required for E3A RNA 3' end formation.

Quiescent and activated mouse granulocytes do not express granzyme A and B or perforin: similarities or differences with human polymorphonuclear leukocytes?

Blood ◽  
2005 ◽  
Vol 106 (8) ◽  
pp. 2871-2878 ◽  
Author(s):  
Praxedis Martin ◽  
Reinhard Wallich ◽  
Julian Pardo ◽  
Arno Müllbacher ◽  
Markus Munder ◽  
...  
Keyword(s):  
Polymorphonuclear Leukocytes ◽  
Human Neutrophils ◽  
Enzymatic Assays ◽  
Effector Functions ◽  
Healthy Control ◽  
Polymerase Chain ◽  
Human Polymorphonuclear Leukocytes ◽  
Cytotoxic Effector

AbstractPolymorphonuclear leukocytes have been shown to use a multitude of effector functions to combat pathogens and tumors, including enzymes, defensins, and toxic products such as oxygen radicals and nitrogen oxides. Recent studies provided evidence for the expression of granzymes (gzms) and perforin (perf) within the cytotoxic arsenal of human neutrophils, the validity of which was questioned by 2 subsequent studies. We have now used cytology, intracellular flow cytometry, enzymatic assays, immunoelectron microscopy, and quantitative reverse transcriptase-polymerase chain reaction to obtain evidence of the presence of gzms and/or perf in mouse Gr-1+ granulocyte populations. The data obtained clearly demonstrate that neither in vitro- nor in vivo-derived mouse granulocytes synthesize gzmA and gzmB or perf, even following infection/immunization with pathogens or pathogen-derived material. A parallel comparable analysis on the expression of gzmB in human neutrophils from 3 healthy control subjects and 4 patients with diverse diseases failed to detect gzmB expression. The data indicate that polymorphonuclear leukocytes from mice and humans lack the 3 cytotoxic effector molecules, gzmA, gzmB, and perf, generally associated with natural killer and cytotoxic T lymphocytes. (Blood. 2005;106:2871-2878)

Deeper Insight into the Protease-Mediated Formation of Pyronin Dyes and Possible Implications in the Design of Fluorogenic Probes for Bioimaging and Theranostic Prodrugs

2019 ◽  
Author(s):  
Kévin RENAULT ◽  
Sylvain DEBIEU ◽  
Jean-Alexandre RICHARD ◽  
Anthony ROMIEU
Keyword(s):  
Ad Hoc ◽  
Biomedical Application ◽  
Disease Diagnosis ◽  
Structural Features ◽  
Fluorescent Reporter ◽  
Enzymatic Assays ◽  
Fluorogenic Probes ◽  
Image Guided Drug Delivery

We report a rational and systematic study devoted to structural optimisation of a novel class of protease-sensitive fluorescent probes recently reported by us (<i>Org. Biomol. Chem.</i>, 2017, <b>15</b>, 2575-2584), based on the "covalent-assembly" strategy and using the targeted enzyme (penicilin G acylase as model protease) to build a fluorescent pyronin dye by triggering a biocompatible domino cyclisation-aromatisation reaction. The aim is to identify <i>ad hoc</i> probe candidate(s) that might combine fast/reliable fluorogenic "turn-on" response, full stability in complex biological media and ability to release a second molecule of interest (drug or second fluorescent reporter), for applications in disease diagnosis and therapy. We base our strategy on screening a set of active methylene compounds (C-nucleophiles) to convert the parent probe to various pyronin caged precursors bearing Michael acceptor moieties of differing reactivity. <i>In vitro</i> stability and fluorescent enzymatic assays combined to HPLC-fluorescence analyses provide data useful to define the most appropriate structural features for these fluorogenic scaffolds depending on the specifications required by the biomedical application (<i>e.g.</i>, <i>in vivo</i> molecular imaging, image-guided drug delivery and theranostics) for which they will be used.

scholarly journals An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism

2019 ◽  
Vol 116 (32) ◽  
pp. 15907-15913 ◽  
Author(s):  
Hua Wang ◽  
Alexander A. Fedorov ◽  
Elena V. Fedorov ◽  
Debbie M. Hunt ◽  
Angela Rodgers ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Resistance Mechanism ◽  
Infection Model ◽  
Enzymatic Assays ◽  
X Ray Crystallography ◽  
Mouse Infection Model ◽  
Leucine Catabolism ◽  
Global Population

Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis. One-fourth of the global population is estimated to be infected with Mtb, accounting for ∼1.3 million deaths in 2017. As part of the immune response to Mtb infection, macrophages produce metabolites with the purpose of inhibiting or killing the bacterial cell. Itaconate is an abundant host metabolite thought to be both an antimicrobial agent and a modulator of the host inflammatory response. However, the exact mode of action of itaconate remains unclear. Here, we show that Mtb has an itaconate dissimilation pathway and that the last enzyme in this pathway, Rv2498c, also participates in l-leucine catabolism. Our results from phylogenetic analysis, in vitro enzymatic assays, X-ray crystallography, and in vivo Mtb experiments, identified Mtb Rv2498c as a bifunctional β-hydroxyacyl-CoA lyase and that deletion of the rv2498c gene from the Mtb genome resulted in attenuation in a mouse infection model. Altogether, this report describes an itaconate resistance mechanism in Mtb and an l-leucine catabolic pathway that proceeds via an unprecedented (R)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) stereospecific route in nature.

scholarly journals Towards an Improvement of Anticancer Activity of Benzyl Adenosine Analogs

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7146
Author(s):  
Verdiana Covelli ◽  
Manuela Grimaldi ◽  
Rosario Randino ◽  
Mohammad Firoznezhad ◽  
Maria Chiara Proto ◽  
...  
Keyword(s):  
Enzymatic Assays ◽  
Mva Pathway ◽  
Farnesyl Pyrophosphate Synthase ◽  
Anticancer Effects ◽  
Naturally Occurring ◽  
Molecular Action ◽  
Colorectal Cancer Cells ◽  
Key Enzyme

N6-Isopentenyladenosine (i6A) is a naturally occurring modified nucleoside displaying in vitro and in vivo antiproliferative and pro-apoptotic properties. In our previous studies, including an in silico inverse virtual screening, NMR experiments and in vitro enzymatic assays, we demonstrated that i6A targeted farnesyl pyrophosphate synthase (FPPS), a key enzyme involved in the mevalonate (MVA) pathway and prenylation of downstream proteins, which are aberrant in several cancers. Following our interest in the anticancer effects of FPPS inhibition, we developed a panel of i6A derivatives bearing bulky aromatic moieties in the N6 position of adenosine. With the aim of clarifying molecular action of N6-benzyladenosine analogs on the FPPS enzyme inhibition and cellular toxicity and proliferation, herein we report the evaluation of the N6-benzyladenosine derivatives’ (compounds 2a–m) effects on cell viability and proliferation on HCT116, DLD-1 (human) and MC38 (murine) colorectal cancer cells (CRC). We found that compounds 2, 2a and 2c showed a persistent antiproliferative effect on human CRC lines and compound 2f exerted a significant effect in impairing the prenylation of RAS and Rap-1A proteins, confirming that the antitumor activity of 2f was related to the ability to inhibit FPPS activity.

scholarly journals JMJD6 Cleaves MePCE to Release P-TEFb

2019 ◽  
Author(s):  
Schuyler Lee ◽  
Haolin Liu ◽  
Ryan Hill ◽  
Xia Hong ◽  
Xinjian Liu ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Binding Assays ◽  
Enzymatic Assays ◽  
Pol Ii ◽  
Downstream Effects ◽  
Capping Enzyme

AbstractMore than 30% of genes in higher eukaryotes are regulated by promoter-proximal pausing of RNA polymerase II (Pol II). Phosphorylation of Pol II-CTD by positive transcription elongation factor (P-TEFb) is a necessary precursor event that enables productive transcription elongation. The exact mechanism on how the sequestered P-TEFb is released from the 7SK snRNP complex and recruited to Pol II-CTD remains unknown. In this report, we reveal methylphosphate capping enzyme (MePCE), a core component of the 7SK snRNP complex, as the cognate substrate for Jumonji domain-containing 6 (JMJD6)’s novel proteolytic function. Our evidences consist of a crystal structure of JMJD6 bound to methyl-arginine, enzymatic assays of JMJD6 cleaving MePCE in vivo and in vitro, binding assays, and downstream effects of Jmjd6 knockout and overexpression on Pol II-CTD phosphorylation. We propose that JMJD6 assists bromodomain containing 4 (BRD4) to recruit P-TEFb to Pol II-CTD by disrupting the 7SK snRNP complex.

COMPARISON OF IN VITRO ENZYMATIC ASSAYS WITH IN VIVO 31P MRS OF MUSCLE METABOLISM

1999 ◽  
Vol 31 (Supplement) ◽  
pp. S242 ◽  
Author(s):  
M. Eastlack ◽  
G. Walter ◽  
D. Lenrow ◽  
G. Dudley ◽  
A. Swift ◽  
...  
Keyword(s):  
Muscle Metabolism ◽  
Enzymatic Assays ◽  
31P Mrs

scholarly journals Radiolabeled 6-(2, 3-Dichlorophenyl)-N4-methylpyrimidine-2, 4-diamine (TH287): A Potential Radiotracer for Measuring and Imaging MTH1

2020 ◽  
Vol 21 (22) ◽  
pp. 8860
Author(s):  
Huaping Chen ◽  
Sadia Afrin ◽  
Yingqiu Guo ◽  
Wenhua Chu ◽  
Tammie L.S. Benzinger ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Radioligand Binding ◽  
Competitive Binding ◽  
Nudix Hydrolase ◽  
Binding Assays ◽  
Enzymatic Assays ◽  
The Brain ◽  
Competitive Binding Assays

MTH1 (MutT homolog 1) or NUDT1 (Nudix Hydrolase 1), also known as oxidized purine nucleoside triphosphatase, has potential as a biomarker for monitoring cancer progression and quantifying target engagement for relevant therapies. In this study, we validate one MTH1 inhibitor TH287 as a PET MTH1 radiotracer. TH287 was radiolabeled with tritium and the binding of [3H]TH287 to MTH1 was evaluated in live glioblastoma cells (U251MG) through saturation and competitive binding assays, together with in vitro enzymatic assays. Furthermore, TH287 was radiolabeled with carbon-11 for in vivo microPET studies. Saturation binding assays show that [3H]TH287 has a dissociation constant (Kd) of 1.97 ± 0.18 nM, Bmax of 2676 ± 122 fmol/mg protein for U251MG cells, and nH of 0.98 ± 0.02. Competitive binding assays show that TH287 (Ki: 3.04 ± 0.14 nM) has a higher affinity for MTH1 in U251MG cells compared to another well studied MTH1 inhibitor: (S)-crizotinib (Ki: 153.90 ± 20.48 nM). In vitro enzymatic assays show that TH287 has an IC50 of 2.2 nM in inhibiting MTH1 hydrolase activity and a Ki of 1.3 nM from kinetics assays, these results are consistent with our radioligand binding assays. Furthermore, MicroPET imaging shows that [11C]TH287 gets into the brain with rapid clearance from the brain, kidney, and heart. The results presented here indicate that radiolabeled TH287 has favorable properties to be a useful tool for measuring MTH1 in vitro and for further evaluation for in vivo PET imaging MTH1 of brain tumors and other central nervous system disorders.

scholarly journals ATTAAA as well as downstream sequences are required for RNA 3'-end formation in the E3 complex transcription unit of adenovirus.

1985 ◽  
Vol 5 (11) ◽  
pp. 3183-3193 ◽  
Author(s):  
B M Bhat ◽  
W S Wold
Keyword(s):  
Base Pair ◽  
Transcription Unit ◽  
Rna Probes ◽  
Labeled Rna

We mapped the location of the E3A RNA 3' end site in the E3 transcription unit of adenovirus 2. The procedure used was nuclease-gel analysis with 32P-labeled RNA probes. The poly(A) addition sites were microheterogeneous and were located approximately 17 to 29 nucleotides downstream from an ATTAAA sequence. To identify the sequences that make up the E3A RNA 3' end signal, we constructed five viable virus mutants with deletions in or near the E3A RNA 3' end site. The mutants were analyzed for E3A RNA 3' end formation in vivo. No effect was observed from a 47-base-pair (bp) deletion (dl716) or a 72-bp deletion (dl714) located 22 and 19 nucleotides, respectively, upstream of the ATTAAA. In contrast, E3A RNA 3' end formation was abolished by a 554-bp deletion (dl708) that removes both the ATTAAA and the poly(A) addition sites, a 124-bp deletion (dl713) that removes the ATTAAA but leaves the poly(A) addition sites, and a 65-bp deletion (dl719) that leaves the ATTAAA but removes the poly(A) addition sites. These results indicate that the ATTAAA, as well as downstream sequences, including the poly(A) addition sites, are required for E3A RNA 3' end formation.

scholarly journals Two Spx Proteins Modulate Stress Tolerance, Survival, and Virulence in Streptococcus mutans

2010 ◽  
Vol 192 (10) ◽  
pp. 2546-2556 ◽  
Author(s):  
Jessica K. Kajfasz ◽  
Isamar Rivera-Ramos ◽  
Jacqueline Abranches ◽  
Alaina R. Martinez ◽  
Pedro L. Rosalen ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Streptococcus Mutans ◽  
Gram Positive ◽  
Enzymatic Assays ◽  
Stress Genes ◽  
Gram Positive Bacteria ◽  
Underlying Mechanisms ◽  
Controlling Processes ◽  
High Degree

ABSTRACT Previous work suggested that the underlying mechanisms by which the Streptococcus mutans ClpXP protease affects virulence traits are associated with accumulation of two orthologues of the Spx regulator, named SpxA and SpxB. Here, a thorough characterization of strains lacking the spx genes (ΔspxA, ΔspxB, and ΔspxA ΔspxB) revealed that Spx, indeed, participates in the regulation of processes associated with S. mutans pathogenesis. The ΔspxA strain displayed impaired ability to grow under acidic and oxidative stress conditions and had diminished long-term viability at low pH. Although the ΔspxB strain did not show any inherent stress-sensitive phenotype, the phenotypes observed in ΔspxA were more pronounced in the ΔspxA ΔspxB double mutant. By using two in vivo models, we demonstrate for the first time that Spx is required for virulence in a Gram-positive pathogen. Microarrays confirmed the global regulatory role of SpxA and SpxB. In particular, SpxA was shown to positively regulate genes associated with oxidative stress, a finding supported by enzymatic assays. SpxB had a secondary role in regulation of oxidative stress genes but appeared to play a larger role in controlling processes associated with cell wall homeostasis. Given the high degree of conservation between Spx proteins of low-GC Gram-positive bacteria, these results are likely to have broad implications.

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