61135-33-9

Usage

References

1) Salic and Mitchison (2008),?A chemical method for fast and sensitive detection of DNA synthesis in vivo; Proc. Natl. Acad. Sci. USA,?105?2415 2) Zeng?et al. (2010),?Evaluation of 5-ethynyl-2′-deoxyuridine staining as a sensitive and reliable method for studying cell proliferation in the adult nervous system; Brain Res.,?1319C?21

InChI:InChI=1/C11H12N2O5/c1-2-6-4-13(11(17)12-10(6)16)9-3-7(15)8(5-14)18-9/h1,4,7-9,14-15H,3,5H2,(H,12,16,17)/t7-,8+,9+/m0/s1

Upstream product

• 77875-91-3 5-ethynyltrimethylsilyl-3',5'-di-O-p-toluyl-2'-deoxyuridine 
• 78731-54-1 5-(1-chlorovinyl)-2'-deoxy-3',5'-di-O-(p-toluoyl)uridine 
• 151362-01-5 1-(2-deoxy-β-D-ribofuranosyl)-5-[2-(trimethylsilyl)ethynyl]uracil 
• 69075-43-0 5-Ethynyl-3',5'-di-O-p-toluyl-2'-deoxyuridine 
• 31356-86-2 1-[2-deoxy-3,5-di-O-(p-toluoyl)-β-D-erythro-pentofuranosyl]-5-iodouracil 
• 151361-85-2 5-(Trifluoromethanesulfonyloxy)-2'-deoxyuridine 
• 117626-97-8 5'-O-(4,4'-dimethoxytrityl)-5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxyuridine 
• 78731-60-9 5-(1-Chloro-vinyl)-2,4-bis-trimethylsilanyloxy-pyrimidine 
• 59989-18-3 5-ethynyluracil 
• 50-89-5 thymidine 
• 13030-62-1 3',5'-di-O-acetyl-2'-deoxyuridine 
• 1956-30-5 3',5'-O-diacetyl-5-iodo-2'-deoxyuridine 
• 100021-00-9 1-(3,5-di-O-acetyl-2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynyluracil 
• 85267-60-3 1-(3,5-di-O-acetyl-2-deoxy-β-D-erythro-pentofuranosyl)-5-(trimethylsilylethynyl)uracil 

Downstream Products

• 117626-97-8 5'-O-(4,4'-dimethoxytrityl)-5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxyuridine 
• 15176-29-1 edoxudine 
• 55520-67-7 5-vinyl-2'-deoxyuridine 
• 59090-41-4 5-acetyl-1-(2-deoxy-β-D-erythro-pentofuranosyl)uracil 
• 596107-17-4 5-[(4-tert-butylphenyl)ethynyl]-2'-deoxyuridine 

Relevant academic research and scientific papers

Phosphorylated 5-ethynyl-2′-deoxyuridine for advanced DNA labeling

The representative DNA-labeling agent 5-ethynyl-2′-deoxyuridine (EdU) was chemically modified to improve its function. Chemical monophosphorylation was expected to enhance the efficiency of the substrate in DNA polymerization by circumventing the enzymati

Turning Off Transcription with Bacterial RNA Polymerase through CuAAC Click Reactions of DNA Containing 5-Ethynyluracil

Copper(I)-catalyzed azide–alkyne cycloaddition (CuAAC) click reaction in the major groove of DNA containing 5-ethynyluracil (UE) with azides was used for turning off sequence-specific protein–DNA interactions. The concept was first demonstrated

Synthesis of tricarbonyl rhenium and technetium complexes of a 5′-carboxamide 5-ethyl-2′-deoxyuridine for selective inhibition of herpes simplex virus thymidine kinase 1

Herpes simplex virus thymidine kinase type 1 (HSV1-TK) is frequently used as reporter protein in gene therapy. Our aim is to produce single photon emitting reporter probe based on technetium-99m. The synthesis of organometallic technetium and rhenium comp

5-Alkynyl analogs of arabinouridine and 2′-deoxyuridine: Cytostatic activity against herpes simplex virus and varicella-zoster thymidine kinase gene-transfected cells

A group of arabinouridines (TMSEAU, EAU, IEAU-TA) and 2′- deoxyuridines (TMSEDU, EDU, IEDU) having a variety of substituents at the uracil C-5 position (trimethylsilylethynyl, TMSE; ethynyl, E; or iodoethynyl, IE), and the sugar C-2′ position (2′-arabino

Tropolone-Conjugated DNA: Fluorescence Enhancement in the Duplex

Tropolone (2-hydroxycyclohepta-2,4,6-triene-1-one and tautomer) is a non-benzenoid bioactive natural chromophore with pH-dependent fluorescence character and extraordinary metal binding affinities, especially with transition-metal ions Cu2+/Zn

Intermolecular hydrogen-bond interaction to promote thermoreversible 2'-deoxyuridine-based AIE-organogels

Fluorescent supramolecular nucleoside-based organogels or hydrogels have attracted increasing attention owing to their tunable stability, drug delivery, tissue engineering, and inherent biocompatibility for applications in designing sensors. As the temper

Thermodynamic Reaction Control of Nucleoside Phosphorolysis

Nucleoside analogs represent a class of important drugs for cancer and antiviral treatments. Nucleoside phosphorylases (NPases) catalyze the phosphorolysis of nucleosides and are widely employed for the synthesis of pentose-1-phosphates and nucleoside analogs, which are difficult to access via conventional synthetic methods. However, for the vast majority of nucleosides, it has been observed that either no or incomplete conversion of the starting materials is achieved in NPase-catalyzed reactions. For some substrates, it has been shown that these reactions are reversible equilibrium reactions that adhere to the law of mass action. In this contribution, we broadly demonstrate that nucleoside phosphorolysis is a thermodynamically controlled endothermic reaction that proceeds to a reaction equilibrium dictated by the substrate-specific equilibrium constant of phosphorolysis, irrespective of the type or amount of NPase used, as shown by several examples. Furthermore, we explored the temperature-dependency of nucleoside phosphorolysis equilibrium states and provide the apparent transformed reaction enthalpy and apparent transformed reaction entropy for 24 nucleosides, confirming that these conversions are thermodynamically controlled endothermic reactions. This data allows calculation of the Gibbs free energy and, consequently, the equilibrium constant of phosphorolysis at any given reaction temperature. Overall, our investigations revealed that pyrimidine nucleosides are generally more susceptible to phosphorolysis than purine nucleosides. The data disclosed in this work allow the accurate prediction of phosphorolysis or transglycosylation yields for a range of pyrimidine and purine nucleosides and thus serve to empower further research in the field of nucleoside biocatalysis. (Figure presented.).

Direct incorporation and extension of a fluorescent nucleotide through rolling circle DNA amplification for the detection of microRNA 24-3P

We designed and synthesized several fluorescent nucleotides from thiophene, anthracene and pyrene, which have different sizes, and screened their incorporation and extension capability during the rolling circle amplification of DNA. The thiophene-based fluorescent nucleotide (dUthioTP) could highly incorporate and extended into the rolling circle DNA product, while other fluorescent nucleotides (dUanthTP, and dUpyrTP) could not. This dUthioTP fluorescent nucleotide could be used for the detection of miRNA 24-3P, which is related PRRSV. This direct labeling system during rolling circle DNA amplification exhibited an increased fluorescence signal showing gel formation for the detection of miRNA 24-3P. This direct labeling system is a very simple and cost-efficient method for the detection miRNA 24-3P and also exhibited highly sensitive and selective detection properties.

Catalysis of Michael Additions by Covalently Modified G-Quadruplex DNA

Enantioselective catalysis utilizing G-quadruplex DNA-based artificial metalloenzymes has emerged as a new approach in the field of aqueous-phase homogeneous catalysis. Recently, a catalytic asymmetric Michael addition employing a covalently modified G-quadruplex in combination with CuII ions has been reported. Here we assess, by systematic chemical variation and using various spectrometric techniques, a variety of parameters that govern rate acceleration and stereoselectivity of the reaction, such as the position of modification, the topology of the quadruplex, the nature of the ligand, the length of the linker between ligand and DNA, the chemical identity of monovalent ions and transition metal complexes. The DNA quadruplex modified at position 10 (dU10) with hexynyl-linked bpy ligand showed twice the initial reaction rate as compared with the DNA strand derivatized at position 12 (dU12). The strikingly different dependence of the stereoselectivity on the linker length, and their different spectroscopic properties indicate large differences in the architecture of the catalytic centers between the dU10-derivatized and the dU12-modified quadruplexes. Upon addition of CuII, both types of bpy-derivatized DNA strands form defined 1:1 Cu–DNA complexes stable enough for mass spectrometric analysis, while the underivatized strands exhibit weak and unspecific binding, correlated with much lower catalytic rate acceleration. Both dU10- and dU12-derivatized quadruplexes could be reused ten times without reduction of stereoselectivity.

Diverse size approach to incorporate and extend highly fluorescent unnatural nucleotides into DNA

We have prepared a series of size-diverse unnatural nucleotides containing fluorescent (dApyrTP, dUpyrTP, dUantTP, dUthiTP) and quencher (dUazoTP) units, as well as nucleotides presenting small functional groups (dAethTP, dAoctTP, dUethTP, dUiodTP), all based on deoxyadenosine and deoxyuridine, and examined their suitability for use in enzymatic incorporation and extension into DNA. We observed a size-dependence of the incorporation and extension capability (following the order dUiodTP?=?dUethTP?=?dUthiTP?>?dUazoTP?>?dUpyrTP?>?dUantTP) during primer extension. This result was supported by circular dichroism (CD) spectra, which revealed a trend in the different B-form DNA structures depending on the size of the unit at the 5-position of the deoxyuridine (dUiodTP?>?dUethTP?>?dUthiTP?>?dUpyrTP), obtained from the PCR products. Interestingly, dUthiTP could be incorporated and extended into long DNA strands during primer extension and even PCR amplification, with CD spectroscopy confirming a stable secondary B-form duplex DNA structure. We observed full-length extension products even when combining dUthiTP with a template containing 24 continuous dA units during the primer extension. Thus, we believe that dUthiTP is a promising fluorescent nucleotide for a diverse range of biological applications requiring multiple incorporation and extension directly without disruption of B-form DNA structures.