Log In Sign up
The largest database of trusted experimental protocols
> Chemicals & Drugs > Biologically Active Substance > Deoxyuridine

Deoxyuridine

Deoxyuridine is a nucleoside that serves as a building block for DNA.
It is formed by the attachment of the pyrimidine base uracil to the sugar deoxyribose.
Deoxyuridine plays a critical role in DNA synthesis and repair processes, making it an important target for research in areas such as cancer, viral infections, and genetic disorders.
Studying the properties and functions of deoxyuridine can provide valuable insights into the fundamental mechanisms of cellular processes and lead to the development of novel therapeutic interventions.

Most cited protocols related to «Deoxyuridine»

1
Lifespan and Movement Assays in C. elegans
Lifespan assays were performed as described previously [12 (link)]. Briefly, wild-type (N2) and fat-6-overexpressing worms (IJ508 yhEx112 [ges-1p::fat-6::GFP, odr-1::RFP]) were maintained on Escherichia coli (OP50)-seeded nematode growth medium (NGM) agar plates at 20°C. Synchronized wild-type and fat-6-overexpressing animals were transferred onto OP50-seeded NGM agar plates containing 10 μM 5-fluoro-2′-deoxyuridine (FUdR, Sigma, St Louis, MO, USA) at day 1 adult stage to prevent progeny from hatching. Worms that did not respond to gentle touching by a platinum wire were counted as dead. Animals that crawled off the plates, ruptured, or burrowed were censored but included in the statistical analysis. The movement-capacity data were adopted from our previously published paper [9 (link)].
Han S.K., Lee D., Lee H., Kim D., Son H.G., Yang J.S., Lee S.J, & Kim S. (2016). OASIS 2: online application for survival analysis 2 with features for the analysis of maximal lifespan and healthspan in aging research. Oncotarget, 7(35), 56147-56152.
Publication 2016
Adult Agar Animals Biological Assay Deoxyuridine Epiphyseal Cartilage Escherichia coli Helminths Movement Nematoda Platinum
2
Genetic Manipulation of Bacteroides thetaiotaomicron

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2008
Agar Alleles Bacteria Bacteroides Blood Cloning Vectors Deletion Mutation Deoxyuridine Erythromycin Gene Deletion Genes Genetic Vectors Genome Intergenic Region Nucleotides Oligonucleotide Primers Parent Plasmids Serine-Specific tRNA Strains Thymidine Kinase
3
TUNEL Assay for Detecting DNA Strand Breaks
DNA strand breaks were demonstrated by labeling free 3′-OH termini with FITC-labeled deoxyuridine, which was detected with alkaline phosphatase–coupled, anti-fluorescein antibody, and the formation of a dye precipitate with a phosphatase substrate (In Situ Cell Death Detection Kit, AP; Boehringer Mannheim, Mannheim, Germany). Yeast cells were fixed with 3.7% formaldehyde, digested with lyticase, and applied to a polylysine-coated slide as described for immunofluorescence (Adams and Pringle, 1984 (link)). The slides were rinsed with PBS, incubated in permeabilization solution (0.1% Triton X-100, 0.1% sodium citrate) for 2 min on ice, rinsed twice with PBS, incubated with 10 μl TUNEL reaction mixture (200 U/ml terminal deoxynucleotidyl transferase, 10 mM FITC-labeled dUTP, 25 mM Tris/HCl, 200 mM sodium cacodylate, 5 mM cobalt chloride; Boehringer Mannheim) for 60 min at 37°C, rinsed three times with PBS, incubated with 50 μl Converter AP solution (alkaline phosphatase– labeled, anti-FITC antibody; Boehringer Mannheim) for 30 min at 37°C, rinsed three times with PBS, and stained by incubation with 50 μl naphthol) AS-MX phosphate (Sigma Chemical Co., Munich, Germany), 0.8 mg/ml, fast red TR salt (Sigma Chemical Co.), 1 mg/ml, 2% dimethylformamide, 1 mM levamisole in 100 mM Tris/HCl, pH 8.2, for 30 min at room temperature. A coverslip was mounted with a drop of Kaiser's glycerol gelatin (Merck, Darmstadt, Germany).
Madeo F., Fröhlich E, & Fröhlich K.U. (1997). A Yeast Mutant Showing Diagnostic Markers of Early and Late Apoptosis. The Journal of Cell Biology, 139(3), 729-734.
Publication 1997
Alkaline Phosphatase Antibodies, Anti-Idiotypic Cacodylate Cell Death Cells cobaltous chloride Deoxyuridine deoxyuridine triphosphate Dimethylformamide DNA Breaks DNA Nucleotidylexotransferase fast red TR salt Fluorescein Fluorescein-5-isothiocyanate Fluorescent Antibody Technique Formaldehyde Gelatins Glycerin In Situ Nick-End Labeling Levamisole Hydrochloride lyticase Naphthols Phosphates Phosphoric Monoester Hydrolases Polylysine Sodium Sodium Citrate Triton X-100 Tromethamine Yeast, Dried
4
USER Cloning for Plasmid and Phage Construction
All plasmid and phage materials were constructed via USER cloning33 (link). See Extended Data Table 2. Briefly, primers were designed to include a single internal deoxyuracil base 15–20 bases from the 5′ end of the primer, specifying this region as the “USER junction”. Criteria for design of the USER junction were: it should contain minimal secondary structure, have 45 °C < Tm < 70 °C, and begin with a deoxyadenosine and end with a deoxythymine (to be replaced by deoxyuridine). The USER junction specifies the homology required for correct assembly. We note that PfuTurbo Cx Hotstart DNA polymerase (Agilent Technologies), VeraSeq ULtra DNA polymerase (Enzymatics), or Phusion U Hot Start DNA Polymerase (Life Technologies) are able to use primers carrying deoxyuracil bases, whereas some other polymerases undergo a phenomenon known as PCR poisoning and do not extend the primer.
All PCR products were purified using MinElute PCR Purification Kit (Qiagen) to 10 μL final volume and quantified using a NanoDrop 1000 Spectrophotometer (Thermo Scientific). For assembly, PCR products carrying complementary USER junctions were mixed in an equimolar ratio (up to 1 pmol each) in a 10 μL reaction containing 15 units DpnI (New England Biolabs), 0.75 units USER (Uracil-Specific Excision Reagent) enzyme (Endonuclease VIII and Uracil-DNA Glycosylase, NEB), 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 100 μg/ml BSA at pH 7.9 (1x CutSmart Buffer, New England Biolabs). The reactions were incubated at 37 °C for 45 min, followed by heating to 80 °C and slow cooling to 22 °C at 0.1 °C/s in a temperature-controlled block. The hybridized constructs were directly used for heat-shock transformation of chemically competent NEB Turbo E. coli cells according to the manufacturer’s instructions. Transformants were selected on 1.8% agar-2xYT plates supplemented with the appropriate antibiotic(s).
For SP cloning, the hybridized constructs were purified using EconoSpin purification columns (Epoch Life Sciences), eluted using 25 μL 10% glycerol, and transformed into electrocompetent S2060 cells carrying the phage-responsive AP pJC175e, which produces functional pIII in response to phage infection (this strain is henceforth referred to as S2208). Following recovery for 3–4 h at 37 °C using 2xYT (United States Biological) media, the culture was centrifuged and the supernatant was purified using a 0.22 μm PVDF Ultrafree centrifugal filter (Millipore). The supernatant was diluted serially in 100-fold increments and used in plaque assays using log-phase S2208 cells. Following overnight at 37 °C, single plaques were picked into 2xYT media and grown for 12–18 h in a 37 °C shaker at 230 rpm. The supernatant was purified again to yield clonal phage stocks. In all cases, cloned plasmids and phages were prepared using the TempliPhi 500 Amplification Kit (GE Life Sciences) according to the manufacturers protocol and verified by Sanger sequencing.
Badran A.H., Guzov V.M., Huai Q., Kemp M.M., Vishwanath P., Kain W., Nance A.M., Evdokimov A., Moshiri F., Turner K.H., Wang P., Malvar T, & Liu D.R. (2016). Continuous evolution of B. thuringiensis toxins overcomes insect resistance. Nature, 533(7601), 58-63.
Publication 2016
2'-deoxyadenosine Acetate Agar Antibiotics Bacteriophages Biological Assay Biopharmaceuticals Buffers Cells Dental Plaque Deoxyuridine DNA-Directed DNA Polymerase Enzymes EPOCH protocol Escherichia coli Glycerin Heat-Shock Response Infection magnesium acetate NEIL1 protein, human Oligonucleotide Primers Plasmids polyvinylidene fluoride Potassium Acetate Senile Plaques Strains Tromethamine Uracil Uracil-DNA Glycosylase
5
Transcriptome Analysis of Malaria Parasites
Total RNA was prepared directly from the frozen pellets of parasitized erythrocytes, where approximately 1 ml of cell pellet was lysed in 7.5 ml Trizol (GIBCO) and RNA was extracted according to the manufacturer's instructions. mRNA was isolated from total RNA preparations using the Oligotex mRNA Mini Kit (Qiagen, Valencia, CA). For the hybridization experiments, 12 μg total RNA was used for first-strand cDNA synthesis as follows: RNA was mixed with a mixture of random hexamer (pdN6) oligonucelotides and oligo-(dT20) at final concentration 125 μg/μl for each oligonucleotide. The mixture was heated to 70°C for 10 min and then incubated on ice for 10 min. Reverse transcription was started by adding dNTPs to a final concentration of 1 mM dATP and 500 μM each: dCTP, dGTP, dTTP and 5-(3-aminoallyl)-2'-deoxyuridine-5'-triophosphate, (aa-dUTP) (Sigma), with 150 units of StrataScript (Stratagene, La Jolla, CA). The reaction was carried out at 42°C for 120 min and the residual RNA was hydrolyzed with 0.1 mM EDTA and 0.2 M NaOH at 65°C for 15 min. The resulting aa-dUTP-containing cDNA was coupled to CyScribe Cy3 or Cy5 (Amersham, Piscataway, NJ) monofunctional dye in the presence of 0.1 M NaHCO3 pH 9.0. Coupling reactions were incubated for a minimum of 1 h at room temperature. The labeled product was purified using QIAquick PCR purification system (Qiagen). Hybridizations and final washing procedures were carried out as described [9 (link)] with slight modifications. Briefly, the hybridization medium contained 3 × SSC, 1.5 μg/μl poly(A) DNA (Pharmacia Biotech, Uppsala), and 0.5% SDS. Hybridizations were incubated at 65°C for 8-16 h. Arrays were washed in 2 × SSC/0.2% SDS and then 0.1 × SSC at room temperature. The microarrays were scanned with a GenePix 4000B scanner and the images analyzed using GenePix Pro 3.0 software (Axon Instruments, Union City, CA). Subsequently, the data were normalized using the AMAD microarray database and subjected to the cluster analysis using the CLUSTER and TREEVIEW software, as described [53 (link)]. For the CLUSTER analysis, low-quality features and features with a signal level less than fivefold the background were filtered from the initial raw data set, yielding 4,737 elements. Subsequently, features with an arbitrary twofold fluorescence signal difference in at least four experiments were considered. All programs and microarray-related protocols are available online [55 ].
Bozdech Z., Zhu J., Joachimiak M.P., Cohen F.E., Pulliam B, & DeRisi J.L. (2003). Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology, 4(2), R9.
Publication 2003
2'-deoxycytidine 5'-triphosphate Acid Hybridizations, Nucleic Anabolism AT 125 Axon Bicarbonate, Sodium Cells deoxyguanosine triphosphate Deoxyuridine deoxyuridine triphosphate DNA, Complementary Edetic Acid Erythrocytes Fluorescence Freezing Microarray Analysis Oligonucleotides Pellets, Drug Poly A Reverse Transcription RNA, Messenger thymidine 5'-triphosphate trizol

Most recents protocols related to «Deoxyuridine»

1
Measuring Cell Proliferation with EdU
Samples were labelled with medium containing 5-ethynyl-20-deoxyuridine (EdU; Invitrogen, A10044) at a final concentration of 10 μM for 10 minutes (30 minutes for JARID2 experiments). After labelling, nascent samples were immediately processed. All chased samples were washed twice in PBS and further incubated in fresh, unlabelled medium for the appropriate time interval before collection. For use in ChOR-Seq, Drosophila S2 cells were labelled with 10 μM EdU for 39 hours before further processing.
Flury V., Reverón-Gómez N., Alcaraz N., Stewart-Morgan K.R., Wenger A., Klose R.J, & Groth A. (2023). Recycling of modified H2A-H2B provides short-term memory of chromatin states. Cell, 186(5), 1050-1065.e19.
Publication 2023
Cells Deoxyuridine Drosophila
2
Evaluating Cell Proliferation with EdU Assay
Cell proliferation was determined by 5′-ethynyl-2′-deoxyuridine (EdU) incorporation. EdU labeling was performed with an EdU Assay Kit (Ribobio, Guangzhou, China) according to the manufacturer’s recommendation. Briefly, ∼1 × 104 cells were seeded in 48-well plates at a density of ∼60%. After overnight culture, cells were transfected with siRNA against EP300 or scramble control. Two days after the transfection, the cells were incubated with 20 mM EdU for 4 h at 37°C, then fixed in 4% paraformaldehyde for 30 min at room temperature and permeabilized in 0.5% Triton X-100 for 10 min. After washing with PBS, the cells were incubated with 200 μl 1 × Apollo reaction cocktail for 30 min. DNA was then stained with 1 mg/ml of Hoechst for 10 min and Images were taken and analyzed with the Lionheart FX Automated Live Cell Imager (BioTek®, USA).
Yang L., Tian J., Wang J., Zeng J., Wang T., Lin B., Linneman J., Li L., Niu Y., Gou D, & Zhang Y. (2023). The protective role of EP300 in monocrotaline-induced pulmonary hypertension. Frontiers in Cardiovascular Medicine, 10, 1037217.
Publication 2023
Biological Assay Cell Proliferation Cells Deoxyuridine EP300 protein, human paraform RNA, Small Interfering Transfection Triton X-100
3
Quantifying Cell Proliferation in Knee
For cell proliferation analysis, P1 animals were weighed and injected with 6 μg/g 5-ethynyl-2ʹ-deoxyuridine (EdU) 4 h prior to sacrifice (n = 4 animals). Knees were fixed, sectioned (see “Tissue harvest and sectioning for cryohistology” section), and stained with the Click-&-Go Cell Reaction Buffer Kit (Click Chemistry Tools Cat. No. 1263) and Alexa Fluor 647 Azide (Invitrogen Cat. No. A10277). Stained sections were then coverslipped and imaged (see “Fluorescent imaging” section) and quantified (see “Fluorescent image analysis” section).
Bautista C.A., Srikumar A., Tichy E.D., Qian G., Jiang X., Qin L., Mourkioti F, & Dyment N.A. (2023). CD206+ tendon resident macrophages and their potential crosstalk with fibroblasts and the ECM during tendon growth and maturation. Frontiers in Physiology, 14, 1122348.
Publication 2023
Alexa Fluor 647 Animals Azides Buffers Cell Proliferation Cells Deoxyuridine Knee Tissue Harvesting
4
Cell Proliferation Measurement via EdU Assay
PTr2 cells were seeded at a density of roughly 50,000 cells/well in 24-well plates and cultured overnight. The cells were transfected and incubated for 48 or 72 h at 37 °C with 5% CO2. Each well was incubated for 3 h with 5-ethynyl-20-deoxyuridine agent (EdU; BeyoClick, China). The cells were fixed for 15 min in 4% paraformaldehyde, washed with a washing solution, and permeabilized with 0.3% Triton X-100, followed by three PBS washes. A total of 0.3 mL Click was added onto the plate and incubated at room temperature in the dark for 30 min. The nuclear stain DAPI was added, and the number of EdU-stained cells was photographed and visualized using a confocal laser scanning microscope (Leica, Germany).
Hong L., Zang X., Hu Q., He Y., Xu Z., Xie Y., Gu T., Yang H., Yang J., Shi J., Zheng E., Huang S., Xu Z., Liu D., Cai G., Li Z, & Wu Z. (2023). Uterine luminal-derived extracellular vesicles: potential nanomaterials to improve embryo implantation. Journal of Nanobiotechnology, 21, 79.
Publication 2023
Cells DAPI Deoxyuridine Microscopy, Confocal paraform Triton X-100
5
Quantifying Intestinal Cell Proliferation
7 dpf larvae were immersed overnight in 100 μg/mL 5-ethynyl-2′-deoxyuridine (EdU) solution (A10044; Invitrogen) for 16 h before termination of the experiment at 8 dpf. Larvae were fixed in 4% paraformaldehyde for 24 hr at 4°C, processed for paraffin embedding, and cut into 7-μm sections. For EdU detection, slides were processed according to the Click-iT EdU Cell Proliferation Assay Kit (C35002; Molecular Probes). Samples were imaged on a Nikon Eclipse TE 2000-V inverted microscope equipped with a Photometrics Coolsnap camera. EdU-labeled nuclei within the intestinal epithelium were counted over 30 serial 7-μm sections beginning at the esophageal-intestinal junction and proceeding caudally into the bulb. Analysis of this extended region was necessary because of the stochastic patterns of cell proliferation. The absolute numbers of labeled cells varied between trials. Despite these differences in the absolute numbers of labeled cells, the proportional trends of proliferating cells between treatments were consistent and reproducible between trials.
Banse A.V., VanBeuge S., Smith T.J., Logan S.L, & Guillemin K. (2023). Secreted Aeromonas GlcNAc binding protein GbpA stimulates epithelial cell proliferation in the zebrafish intestine. Gut Microbes, 15(1), 2183686.
Publication 2023
Biological Assay Cell Nucleus Cell Proliferation Deoxyuridine Intestinal Epithelium Intestines Larva Medulla Oblongata Microscopy Molecular Probes paraform Somatostatin-Secreting Cells

Top products related to «Deoxyuridine»

1
5 ethynyl 2 deoxyuridine edu by Thermo Fisher Scientific
Sourced in United States, Germany, Australia
5-ethynyl-2′-deoxyuridine (EdU) is a modified nucleoside that can be incorporated into DNA during DNA synthesis. It contains a terminal alkyne group that can be detected using a copper-catalyzed click chemistry reaction.
2
Click it edu imaging kit by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, France
The Click-iT EdU Imaging Kit is a tool designed for the detection and visualization of DNA synthesis in proliferating cells. It utilizes a chemical labeling technique to incorporate the nucleoside analog EdU (5-ethynyl-2'-deoxyuridine) into newly synthesized DNA, which can then be detected using a fluorescent azide dye. This kit provides the necessary reagents and protocols for this process.
3
Click it edu alexa fluor 488 imaging kit by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom
The Click-iT EdU Alexa Fluor 488 Imaging Kit is a fluorescent labeling system designed for detecting and visualizing DNA synthesis in proliferating cells. It utilizes a thymidine analog, EdU (5-ethynyl-2'-deoxyuridine), which is incorporated into newly synthesized DNA during the S phase of the cell cycle. The incorporated EdU is then covalently labeled with Alexa Fluor 488 dye, allowing for the identification and quantification of proliferating cells through fluorescence microscopy or flow cytometry.
4
5 ethynyl 2 deoxyuridine (edu) by Thermo Fisher Scientific
Sourced in United States, United Kingdom, Germany, Japan
EdU is a synthetic nucleoside analog of thymidine that can be incorporated into the DNA of dividing cells during the S phase of the cell cycle. It can be used to detect and quantify cell proliferation in various cell culture and tissue samples.
5
5 fluoro 2 deoxyuridine by Merck Group
Sourced in United States, Spain, Germany
5-fluoro-2′-deoxyuridine is a synthetic nucleoside analogue. It functions as an antimetabolite, inhibiting the synthesis of DNA.
6
Fluorescence microscope by Olympus
Sourced in Japan, United States, Germany, China, Italy, United Kingdom, Denmark, Switzerland, France
The Olympus Fluorescence Microscope is an optical microscope that uses fluorescence to visualize and analyze samples. It illuminates the specimen with light of a specific wavelength, causing fluorescent molecules within the sample to emit light at a different wavelength, which is then detected and displayed.
7
5 fluoro 2 deoxyuridine fudr by Merck Group
Sourced in United States, Germany
5-fluoro-2′-deoxyuridine (FUdR) is a synthetic nucleoside analogue. It is a white crystalline powder that is soluble in water and dimethyl sulfoxide.
8
5 ethynyl 2 deoxyuridine edu by RiboBio
Sourced in China
5-ethynyl-2′-deoxyuridine (EdU) is a nucleoside analog that can be incorporated into DNA during DNA synthesis. It provides a method for detecting and quantifying DNA replication in living cells.
9
4 6 diamidino 2 phenylindole (dapi) by Merck Group
Sourced in United States, Germany, Japan, United Kingdom, China, Italy, Sao Tome and Principe, France, Macao, Canada, Switzerland, Spain, Australia, Denmark, India, Poland, Israel, Belgium, Sweden, Ireland, Netherlands, Panama, Brazil, Portugal, Czechia, Puerto Rico, Austria, Hong Kong, Singapore
DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
10
Edu cell proliferation assay kit by RiboBio
Sourced in China
The EdU Cell Proliferation Assay Kit is a laboratory tool designed to measure cell proliferation. It utilizes the incorporation of the nucleoside analog EdU (5-ethynyl-2'-deoxyuridine) into the DNA of dividing cells, which can then be detected and quantified using a fluorescent dye. This kit provides a straightforward method for assessing cell proliferation in various experimental settings.

More about "Deoxyuridine"

Deoxyuridine, also known as dUrd or dU, is a critical component in DNA synthesis and repair processes, making it a crucial target for research in various fields, including cancer, viral infections, and genetic disorders.
This pyrimidine nucleoside is formed by the attachment of the base uracil to the sugar deoxyribose, serving as a building block for DNA.
Studying the properties and functions of deoxyuridine can provide valuable insights into the fundamental mechanisms of cellular processes and lead to the development of novel therapeutic interventions.
Related compounds, such as 5-ethynyl-2'-deoxyuridine (EdU), are often used in conjunction with deoxyuridine research, as they can be utilized in imaging and cell proliferation assays to track DNA synthesis.
The Click-iT EdU Imaging Kit and Click-iT EdU Alexa Fluor 488 Imaging Kit, for example, leverage the incorporation of EdU into newly synthesized DNA, allowing for the visualization and quantification of cell proliferation.
Additionally, 5-fluoro-2'-deoxyuridine (FUdR) is another related compound that can inhibit DNA synthesis and is often used in cancer research.
Fluorescence microscopy techniques, such as those employing DAPI (4',6-diamidino-2-phenylindole) staining, are commonly used in conjunction with deoxyuridine and related compounds to study DNA structure and dynamics.
The EdU Cell Proliferation Assay Kit provides a convenient way to measure cell proliferation by detecting the incorporation of EdU into newly synthesized DNA.
By understanding the role of deoxyuridine and its related compounds in cellular processes, researchers can develop more effective strategies for addressing a wide range of health conditions, from cancer and viral infections to genetic disorders.
Leveraging the insights gained from deoxyuridine research can lead to breakthroughs in our understanding of fundamental biological mechanisms and the development of innovative therapeutic interventions.