Tag: 100-200

On December 31, 2022, Muller Paul, Hans; Istanto, Dave D.; Heldenbrand, Jacob; Hudson, Matthew E. published an article.Recommanded Product: 5-Methylpyrimidine-2,4(1H,3H)-dione The title of the article was CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation. And the article contained the following:

CRISPR/Cas9 technol. has become an important tool to generate targeted, highly specific genome mutations. The technol. has great potential for crop improvement, as crop genomes are tailored to optimize specific traits over generations of breeding. Many crops have highly complex and polyploid genomes, particularly those used for bioenergy or bioproducts. The majority of tools currently available for designing and evaluating gRNAs for CRISPR experiments were developed based on mammalian genomes that do not share the characteristics or design criteria for crop genomes. We have developed an open source tool for genome-wide design and evaluation of gRNA sequences for CRISPR experiments, CROPSR. The genome-wide approach provides a significant decrease in the time required to design a CRISPR experiment, including validation through PCR, at the expense of an overhead compute time required once per genome, at the first run. To better cater to the needs of crop geneticists, restrictions imposed by other packages on design and evaluation of gRNA sequences were lifted. A new machine learning model was developed to provide scores while avoiding situations in which the currently available tools sometimes failed to provide guides for repetitive, A/T-rich genomic regions. We show that our gRNA scoring model provides a significant increase in prediction accuracy over existing tools, even in non-crop genomes. CROPSR provides the scientific community with new methods and a new workflow for performing CRISPR/Cas9 knockout experiments CROPSR reduces the challenges of working in crops, and helps speed gRNA sequence design, evaluation and validation. We hope that the new software will accelerate discovery and reduce the number of failed experiments The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Recommanded Product: 5-Methylpyrimidine-2,4(1H,3H)-dione

The Article related to grna cas9 crispr cropsr soybean miscanthus, bioinformatics pipelines, crispr, crops, miscanthus, soybean, grna design, Biochemical Genetics: Genetic Engineering and Cloning and other aspects.Recommanded Product: 5-Methylpyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On July 31, 2013, Solomonov, Alexey V.; Rumyantsev, Evgeniy V.; Ivanov, Sergey P.; Kochergin, Boris A.; Antina, Elena V. published an article.Safety of 6-Methylpyrimidine-2,4(1H,3H)-dione The title of the article was Spectroscopic studies of the supramolecular interactions between uracil and 5-hydroxy-6-methyluracil with bovine serum albumin and its bilirubin complex. And the article contained the following:

Using fluorescence and UV-visible absorption spectroscopy, the interaction of bovine serum albumin (BSA) and its bilirubin complex with uracil and 5-hydroxy-6-methyluracil in phosphate buffer at pH 7.4 was investigated. The parameters of forming intermol. complexes (binding constants, quenching rate constants, the radius of the quenching sphere, etc.) were determined The interaction between BSA and the uracils was carried out by static quenching of protein fluorescence and had predominantly hydrophobic character. Using synchronous fluorescence spectroscopy, the influence of uracil and 5-hydroxy-6-methyluracil on the conformational changes of the protein mol. was studied. The uracils effectively bound to the bilirubin-BSA complex compared to the free protein, which was caused by the interaction with the tetrapyrrolic pigment in the macromol. complex. Mol. docking calculations were also performed. The experimental process involved the reaction of 6-Methylpyrimidine-2,4(1H,3H)-dione(cas: 626-48-2).Safety of 6-Methylpyrimidine-2,4(1H,3H)-dione

The Article related to serum albumin interaction uracil hydroxymethyluracil spectroscopy protein conformational change, General Biochemistry: Proteins and Their Constituents and other aspects.Safety of 6-Methylpyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On July 31, 2020, Sakata, Rina C.; Ishiguro, Soh; Mori, Hideto; Tanaka, Mamoru; Tatsuno, Kenji; Ueda, Hiroki; Yamamoto, Shogo; Seki, Motoaki; Masuyama, Nanami; Nishida, Keiji; Nishimasu, Hiroshi; Arakawa, Kazuharu; Kondo, Akihiko; Nureki, Osamu; Tomita, Masaru; Aburatani, Hiroyuki; Yachie, Nozomu published an article.COA of Formula: C5H6N2O2 The title of the article was Base editors for simultaneous introduction of C-to-T and A-to-G mutations. And the article contained the following:

Abstract: We describe base editors that combine both cytosine and adenine base-editing functions. A codon-optimized fusion of the cytosine deaminase PmCDA1, the adenosine deaminase TadA and a Cas9 nickase (Target-ACEmax) showed a high median simultaneous C-to-T and A-to-G editing activity at 47 genomic targets. On-target as well as DNA and RNA off-target activities of Target-ACEmax were similar to those of existing single-function base editors. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).COA of Formula: C5H6N2O2

The Article related to target acemax adenine guanine cytosine thymine mutation base editing, Biochemical Genetics: Gene Structure and Organization and other aspects.COA of Formula: C5H6N2O2

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

Zhang, Jiahui; Fakharzadeh, Ashkan; Pan, Feng; Roland, Christopher; Sagui, Celeste published an article in 2020, the title of the article was Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids.HPLC of Formula: 65-71-4 And the article contains the following content:

Expansion of the GAA/TTC repeats in the first intron of the FXN gene causes Friedreich’s ataxia. Non-canonical structures are linked to this expansion. DNA triplexes and R-loops are believed to arrest transcription, which results in frataxin deficiency and eventual neurodegeneration. We present a systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands; the two hybrid duplexes [r(GAA):d(TTC) and d(GAA):r(UUC)] in an R-loop; and three hybrid triplexes that could form during bidirectional transcription when the non-template DNA strand bonds with the hybrid duplex (collapsed R-loops, where the two DNA strands remain antiparallel). For both Y·R:Y and R·R:Y DNA triplexes, the parallel third strand orientation is more stable; both parallel and antiparallel protonated d(GA+ A)·d(GAA):d(TTC) triplexes are stable. Apparent contradictions in the literature about the R·R:Y triplex stability is probably due to lack of mol. resolution, since shifting the third strand by a single nucleotide alters the stability ranking. In the collapsed R-loops, antiparallel d(TTC+)·d(GAA):r(UUC) is unstable, while parallel d(GAA)·r(GAA):d(TTC) and d(GA+A)·r(GAA):d(TTC) are stable. In addition to providing new structural perspectives for specific therapeutic aims, our results contribute to a systematic structural basis for the emerging field of quant. R-loop biol. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).HPLC of Formula: 65-71-4

The Article related to gaa ttc repeat, friedreich ataxia fxn rna dna triplex hybrid, Biochemical Genetics: Gene Structure and Organization and other aspects.HPLC of Formula: 65-71-4

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

Dvorakova, Zuzana; Renciuk, Daniel; Kejnovska, Iva; kolakova, Petra; Bednarova, Klara; Sagi, Janos; Vorlickova, Michaela published an article in 2018, the title of the article was I-motif of cytosine-rich human telomere DNA fragments containing natural base lesions.COA of Formula: C5H6N2O3 And the article contains the following content:

I-Motif (iM) is a four stranded DNA structure formed by cytosine-rich sequences, which are often present in functionally important parts of the genome such as promoters of genes and telomeres. Using electronic CD and UV absorption spectroscopies and electrophoretic methods, we examined the effect of four naturally occurring DNA base lesions on the folding and stability of the iM formed by the human telomere DNA sequence (C3TAA)3C3T. The results demonstrate that the TAA loop lesions, the apurinic site and 8-oxoadenine substituting for adenine, and the 5-hydroxymethyluracil substituting for thymine only marginally disturb the formation of iM. The presence of uracil, which is formed by enzymic or spontaneous deamination of cytosine, shifts iM formation towards substantially more acidic pH values and simultaneously distinctly reduces iM stability. This effect depends on the position of the damage sites in the sequence. The results have enabled us to formulate addnl. rules for iM formation. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).COA of Formula: C5H6N2O3

The Article related to i motif human telomere dna base pairing lesion substitution, Biochemical Genetics: Gene Structure and Organization and other aspects.COA of Formula: C5H6N2O3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On January 25, 2018, Da, Lin-Tai; Shi, Yi; Ning, Guodong; Yu, Jin published an article.Recommanded Product: 4433-40-3 The title of the article was Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process. And the article contained the following:

Thymine DNA glycosylase (TDG) initiates base excision repair by cleaving the N-glycosidic bond between the sugar and target base. After catalysis, the release of excised base is a requisite step to terminate the catalytic cycle and liberate the TDG for the following enzymic reactions. However, an atomistic-level understanding of the dynamics of the product release process in TDG remains unknown. Here, by employing mol. dynamics simulations combined with the Markov State Model, we reveal the dynamics of the thymine release after the excision at microseconds timescale and all-atom resolution We identify several key metastable states of the thymine and its dominant releasing pathway. Notably, after replacing the TDG residue Gly142 with tyrosine, the thymine release is delayed compared to the wild-type (wt) TDG, as supported by our potential of mean force (PMF) calculations These findings warrant further exptl. tests to potentially trap the excised base in the active site of TDG after the catalysis, which had been unsuccessful by previous attempts. Finally, we extended our studies to other TDG products, including the uracil, 5hmU, 5fC and 5caC bases in order to compare the product release for different targeting bases in the TDG-DNA complex. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Recommanded Product: 4433-40-3

The Article related to mol dynamics base repair tgd gene dna repair complex, Biochemical Genetics: Gene Structure and Organization and other aspects.Recommanded Product: 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On July 31, 2021, Nakazato, Issei; Okuno, Miki; Yamamoto, Hiroshi; Tamura, Yoshiko; Itoh, Takehiko; Shikanai, Toshiharu; Takanashi, Hideki; Tsutsumi, Nobuhiro; Arimura, Shin-ichi published an article.Application of 65-71-4 The title of the article was Targeted base editing in the plastid genome of Arabidopsis thaliana. And the article contained the following:

Bacterial cytidine deaminase fused to the DNA binding domains of transcription activator-like effector nucleases was recently reported to transiently substitute a targeted C to a T in mitochondrial DNA of mammalian cultured cells1. We applied this system to targeted base editing in the Arabidopsis thaliana plastid genome. The targeted Cs were homoplasmically substituted to Ts in some plantlets of the T1 generation and the mutations were inherited by their offspring independently of their nuclear-introduced vectors. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Application of 65-71-4

The Article related to arabidopsis plastid genome base editing, Biochemical Genetics: Genetic Engineering and Cloning and other aspects.Application of 65-71-4

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On December 31, 2019, Yakovlev, Igor A.; Gackowski, Daniel; Abakir, Abdulkadir; Viejo, Marcos; Ruzov, Alexey; Olinski, Ryszard; Starczak, Marta; Fossdal, Carl Gunnar; Krutovsky, Konstantin V. published an article.Electric Literature of 4433-40-3 The title of the article was Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome. And the article contained the following:

5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene expression in metazoans and plants. Iron-(II)/α-ketoglutarate-dependent dioxygenases can oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Although these oxidized forms of 5mC may serve as demethylation intermediates or contribute to transcriptional regulation in animals and fungi, exptl. evidence for their presence in plant genomes is ambiguous. Here, employing reversed-phase HPLC coupled with sensitive mass spectrometry, we demonstrated that, unlike 5caC, both 5hmC and 5fC are detectable in non-negligible quantities in the DNA of a conifer, Norway spruce. Remarkably, whereas 5hmC content of spruce DNA is approx. 100-fold lower relative to human colorectal carcinoma cells, the levels of both – 5fC and a thymine base modification, 5-hydroxymethyluracil, are comparable in these systems. We confirmed the presence of modified DNA bases by immunohistochem. in Norway spruce buds based on peroxidase-conjugated antibodies and tyramide signal amplification. Our results reveal the presence of specific range of noncanonical DNA bases in conifer genomes implying potential roles for these modifications in plant development and homeostasis. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Electric Literature of 4433-40-3

The Article related to picea epigenetic dna modification genome mass spectrometry, Plant Biochemistry: Classical Genetics and Phylogeny and other aspects.Electric Literature of 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On August 7, 2013, Bradley, Stuart Edward; Bell, James Charles; Keily, John; Morrison, Angus; Hanrahan, Patrick Eric; Morgan, Trevor; Rasamison, Chrystelle; Curtis, Eleanor; Smyth, Donald; Bloxham, Jason; Sambrook-Smith, Colin Peter published a patent.Recommanded Product: 596114-50-0 The title of the patent was Preparation of 3-(N-heterocyclylpiperidin-4-yl)butyloxyphenyl derivatives as agonists of GPR119 and GPR40 receptors. And the patent contained the following:

Title compounds I, II and III [R3 = H, F or propyn-1-yl; R5, R6 and R7 = independently H or halogen; E = O, NR8 or S; R8 =H, Me, Et, Pr or i-propyl; V = bond, C(CH3)2, (un)substituted spirocycloalkyl or spiroheterocycle; W = CH2 or form cycloalkyl or heterocyclyl when taken together with V; A = (un)substituted Ph or heteroaryl; B = H, F, OH, propyn-1-yl, etc.; X = O, CH2, N or S; Y = CH2, (CH3)CH, FCH, CH2CH2, etc.; R9 and R10 = independently H, halogen, (un)substituted alkyl, or form azabicyclo[3.3.1]nonane, 3-oxa-7-azabicyclo[ 3.3.1]nonane or azabicyclo[3.2.1]octane when taken together; R11 = H, halogen, alkoxy or (un)substituted alkyl; p and q = 0-2; Z = Ph, benzyl, heteroaryl or CH2-heteroaryl, etc.], and their pharmaceutically acceptable salts, are prepared as agonists of GPR119 and GPR40 receptors. Compound IV was prepared by coupling reaction of compound V (preparation given) and compound VI (preparation given) followed by hydrolysis of the ester group. CompoundIV exhibited activities with EC50 values of less than 1 μM in both GPRl19 cAMP assay and GPR40 FLIPR assay. The invention compounds are useful for the treatment of type II diabetes. The experimental process involved the reaction of 2-Chloro-5-isopropylpyrimidine(cas: 596114-50-0).Recommanded Product: 596114-50-0

The Article related to heterocyclylpiperidinylbutyloxyphenyl derivative preparation gpr119 gpr40 receptor agonist typeii diabetes, Heterocyclic Compounds (One Hetero Atom): Pyridines and other aspects.Recommanded Product: 596114-50-0

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On March 14, 2013, Nagase, Hiroshi; Fujii, Hideaki; Nakata, Eriko; Watanabe, Yoshikazu; Takahashi, Toshihiro published a patent.HPLC of Formula: 596114-50-0 The title of the patent was Preparation of morphinan derivatives as opioid δ receptor agonists. And the patent contained the following:

Title compounds I [R1 = H, alkyl, aryl, etc.; R2 = H, alkyl, cycloalkyl, etc.; R3-R5 = independently H, hydroxy, halo, etc.; R6a, R6b = independently H, F or hydroxy; R6a and R6b may combine to form oxo; R7, R8 = independently H, F or hydroxy; R9, R10 = independently H, alkyl, aryl, etc.; X = O or CH2; Y = C:O, C:S, SO2, etc.; or pharmacol. acceptable salts thereof] were prepared For example, reaction of (1S,3aS,5aS,6R,11bR,11cR)-3-benzyl-14-(cyclopropylmethyl)-3a,11-dihydroxy-10-methoxy-1,3,3a,4,5,6,7,11c-octahydro-2H-6,11b-(iminoethano)-1,5a-expoxynaphtho[1,2-e]indol-2-one with BH3·THF, treatment with PhBr/K2CO3/Cu, exposure to ethylenediamine/sodium silica-gel (stage I), debenzylation, benzoylation, and demethylation using BBr3 afforded compound II. In opioid receptor agonist activity test, the selected invention compounds, e.g., II, showed EC50 of <1 nM for opioid δ receptor. Compounds I are claimed useful for the treatment of pain. The experimental process involved the reaction of 2-Chloro-5-isopropylpyrimidine(cas: 596114-50-0).HPLC of Formula: 596114-50-0

The Article related to morphinan preparation opioid delta receptor agonist, analgesic morphinan opioid delta receptor agonist, Alkaloids: Alkaloids Containing One Nitrogen Atom In A Ring and other aspects.HPLC of Formula: 596114-50-0

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia