Day: November 3, 2022

On December 31, 2021, Hashemkhani Shahnazari, Ghazaleh; Darvish Ganji, Masoud published an article.Safety of 5-Methylpyrimidine-2,4(1H,3H)-dione The title of the article was Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation. And the article contained the following:

The characterization of the complexes of biomols. and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnol. In this work, we have used dispersion corrected d. functional theory (DFT-D) as well as DFT based mol. dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting mols. considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the mol. properties of the nucleobase-Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM anal. indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Safety of 5-Methylpyrimidine-2,4(1H,3H)-dione

The Article related to golden nanocluster dft calculation dna nucleobase mol property, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Safety of 5-Methylpyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On June 24, 2020, Li, Pengfei; Rangadurai, Atul; Al-Hashimi, Hashim M.; Hammes-Schiffer, Sharon published an article.SDS of cas: 65-71-4 The title of the article was Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. And the article contained the following:

DNA bases can adopt energetically unfavorable tautomeric forms that enable the formation of Watson-Crick-like (WC-like) mispairs, which have been proposed to give rise to spontaneous mutations in DNA and misincorporation errors in DNA replication and translation. Previous NMR and computational studies have indicated that the population of WC-like guanine-thymine (G-T) mispairs depends on the environment, such as the local nucleic acid sequence and solvation. To investigate these environmental effects, herein G-T mispair tautomerization processes are studied computationally in aqueous solution, in A-form and B-form DNA duplexes, and within the active site of a DNA polymerase λ variant. The wobble G-T (wG-T), WC-like G-T*, and WC-like G*-T forms are considered, where * indicates the enol tautomer of the base. The min. free energy paths for the tautomerization from the wG-T to the WC-like G-T* and from the WC-like G-T* to the WC-like G*-T are computed with mixed quantum mech./mol. mech. (QM/MM) free energy simulations. The reaction free energies and free energy barriers are found to be significantly influenced by the environment. The wG-T→ G-T* tautomerization is predicted to be endoergic in aqueous solution and the DNA duplexes but slightly exoergic in the polymerase, with Arg517 and Asn513 providing electrostatic stabilization of G-T*. The G-T*→ G*-T tautomerization is also predicted to be slightly more thermodynamically favorable in the polymerase relative to these DNA duplexes. These simulations are consistent with an exptl. driven kinetic misincorporation model suggesting that G-T mispair tautomerization occurs in the ajar polymerase conformation or concertedly with the transition from the ajar to the closed polymerase conformation. Furthermore, the order of the associated two proton transfer reactions is predicted to be different in the polymerase than in aqueous solution and the DNA duplexes. These studies highlight the impact of the environment on the thermodn., kinetics, and fundamental mechanisms of G-T mispair tautomerization, which plays a role in a wide range of biochem. important processes. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).SDS of cas: 65-71-4

The Article related to dsdna guanine thymine mispair tautomerization dna polymerase qm mm, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.SDS of cas: 65-71-4

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On October 1, 2020, Cheng, Yuanlei; Zhang, Yashuo; Gong, Zhou; Zhang, Xinghua; Li, Yutong; Shi, Xiangqian; Pei, Yufeng; You, Huijuan published an article.COA of Formula: C5H6N2O2 The title of the article was High Mechanical Stability and Slow Unfolding Rates Are Prevalent in Parallel-Stranded DNA G-Quadruplexes. And the article contained the following:

Guanine-rich repeat sequences are known to adopt diverse G-quadruplex (G4) topologies. Determining the unfolding rates of individual G4 species is challenging due to the coexistence of multiple G4 conformations in a solution Here, using single-mol. magnetic tweezers, we systematically measured the unfolding force distributions of 4 oncogene promoter G4s, 12 model sequences with two 1-nucleotide (nt) thymine loops that predominantly adopt parallel-stranded G4 structures, and 6 sequences forming multiple G4 structures. All parallel-stranded G4s reveal an unfolding force peak at 40-60 pN, which is associated with extremely slow unfolding rates on the order of 10-5-10-7 s-1. In contrast, nonparallel G4s and partially folded intermediate states reveal an unfolding force peak <40 pN. These results suggest a strong correlation between the parallel-stranded G4s folding topol. and the slow unfolding rates and provide important insights into the mechanism that govern the stability and the transition kinetics of G4s. 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 parallel stranded dna g quadruplex unfolding kinetics mech stability, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.COA of Formula: C5H6N2O2

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On March 18, 2016, Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Weigele, Peter R.; Wanunu, Meni published an article.Safety of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione The title of the article was Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA. And the article contained the following:

Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and mol. dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified mols. Mol. dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA mols., which may account for the differences observed in our nanopore translocation experiments The altered physico-chem. properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Safety of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

The Article related to dna hydroxymethyluracil flexibility hydrophilicity nanopore translocation mol dynamics simulation, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Safety of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On January 31, 2020, Shekaari, Ashkan; Jafari, Mahmoud published an article.COA of Formula: C5H6N2O2 The title of the article was Modeling the action of environment on proton tunneling in the adenine-thymine base pair. And the article contained the following:

Effect of environment coupling on the quantum-biol. phenomenon of proton tunneling in the hydrogen bonds of the adenine-thymine base pair in DNA was modeled within the framework of quantum statistics and perturbation theory. A number of important thermodn. indicators including partition function, free energy, and entropy were then calculated and examined The proton was then assumed to be subject to an attraction represented by a double-well potential energy surface with a small asymmetry, which was considered as the perturbation introduced to the system. The action of environment manifested itself in the form of a global min. in the free energy curve, as an implicit implication of the tendency of the system toward randomness and disorder, at which no spontaneous change such as quantum tunneling will accordingly occur. Furthermore, assuming the free energy to be in a close neighborhood of its min. truly explained the smallness of the contribution of environment coupling to the tunneling probability reported in the literature based on the fact that the closer the free energy to its min., the less the transition probability to this point. 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 adenine thymine base pair proton tunneling environment, adenine–thymine base pair, proton tunneling, quantum statistics, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.COA of Formula: C5H6N2O2

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On March 31, 2017, Smith, Karen E.; House, Christopher H.; Dworkin, Jason P.; Callahan, Michael P. published an article.Recommanded Product: 4433-40-3 The title of the article was Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions. And the article contained the following:

On early Earth, a primitive polymer that could spontaneously form from likely available precursors may have preceded both RNA and DNA as the first genetic material. Here, we report that heated aqueous solutions containing 5-hydroxymethyluracil (HMU) result in oligomers of uracil, heated solutions containing 5-hydroxymethylcytosine (HMC) result in oligomers of cytosine, and heated solutions containing both HMU and HMC result in mixed oligomers of uracil and cytosine. Oligomerization of hydroxymethylated pyrimidines, which may have been abundant on the primitive Earth, might have been important in the development of simple informational polymers. 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 oligomerization nucleotide uracil cytosine hmu hmc, liquid chromatography, mass spectrometry, oligomerization, prebiotic chemistry, pyrimidines, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Recommanded Product: 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On March 26, 2020, Jeong, Ye Eun Rebecca; Lenz, Stefan A. P.; Wetmore, Stacey D. published an article.Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione The title of the article was DFT Study on the Deglycosylation of Methylated, Oxidized, and Canonical Pyrimidine Nucleosides in Water: Implications for Epigenetic Regulation and DNA Repair. And the article contained the following:

D. functional theory (B3LYP) was used to characterize the kinetics and thermodn. of the (nonenzymic) deglycosylation in water for a variety of 2′-deoxycytidine (dC) and 2′-deoxyuridine (dU) nucleoside derivatives that differ in methylation and subsequent oxidation of the C5 substituent. A range of computational models are considered that combine implicit and explicit solvation of the nucleophile and nucleobase. Regardless of the model implemented, our calculations reveal that the glycosidic bond in dC is inherently more stable than that in dU. Furthermore, C5 methylation of either pyrimidine and subsequent oxidation of the Me group yield overall small changes to the Gibbs reaction energy profiles and thereby preserve lower deglycosylation barriers for the dC compared to those for the dU nucleoside derivatives However, hydrolytic deglycosylation becomes significantly more energetically favorable when 5-methyl-dC (5m-dC) undergoes two or three rounds of oxidation, with the Gibbs energy barrier decreasing and the reaction becoming more exergonic by up to 40 kJ/mol. In fact, two or three oxidation reactions from 5m-dC result in a deglycosylation barrier similar to that for dU, as well as those for the associated C5-methylated (2′-deoxythymidine) and oxidized (5-hydroxymethyl-dU) derivatives These predicted trends in the inherent deglycosylation energetics in water directly correlate with the previously reported activity of thymine DNA glycosylase (TDG), which cleaves the glycosidic bond in select dC nucleosides as part of epigenetic regulation and in dU variants as part of DNA repair. Thus, our data suggests that fundamental differences in the intrinsic reactivity of the pyrimidine nucleosides help regulate the function of human enzymes that maintain cellular integrity. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

The Article related to methylated oxidized canonical pyrimidine nucleoside hydrolytic deglycosylation dft, epigenetics dna repair pyrimidine nucleoside hydrolytic deglycosylation dft, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Reference of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On February 9, 2021, Nagpal, Anushka; Dhankhar, Dinesh; Cesario, Thomas C.; Li, Runze; Chen, Jie; Rentzepis, Peter M. published an article.Recommanded Product: 65-71-4 The title of the article was Thymine dissociation and dimer formation: A Raman and synchronous fluorescence spectroscopic study. And the article contained the following:

In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and UV-irradiated thymine solutions were recorded in order to detect thymine dimer formation. The thymine dimer formation, as a function of irradiation dose, was determined by Raman spectroscopy. In addition, the formation of a mutagenic (6-4) photoproduct was identified by its synchronous fluorescence spectrum. Our spectroscopic data suggest that the rate of conversion of thymine to thymine dimer decreases after 20 min of UV irradiation, owing to the formation of an equilibrium between the thymine dimers and monomers. However, the formation of the (6-4) photoproduct continued to increase with UV irradiation In addition, the Raman spectra of nonirradiated and irradiated calf thymus DNA were recorded, and the formation of thymine dimers was detected. The spectroscopic data presented make it possible to determine the mechanism of thymine dimer formation, which is known to be responsible for the inhibition of DNA replication that causes bacteria inactivation. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Recommanded Product: 65-71-4

The Article related to raman synchronous fluorescence spectroscopy thymine dissociation dimer formation, dna, uv inactivation, spectroscopy, thymine dimer, thymine dimer raman spectrum, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Recommanded Product: 65-71-4

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On October 5, 2018, Kozanecka-Okupnik, Weronika; Jasiewicz, Beata; Pospieszny, Tomasz; Jastrzab, Renata; Skrobanska, Monika; Mrowczynska, Lucyna published an article.Safety of 6-Methylpyrimidine-2,4(1H,3H)-dione The title of the article was Spectroscopy, molecular modeling and anti-oxidant activity studies on novel conjugates containing indole and uracil moiety. And the article contained the following:

Herein we describe our results on the synthesis and mol. modeling of new conjugates containing indole and uracil moiety. This group of compounds was synthesized by the reaction of indole alkaloid – gramine with appropriate uracil (uracil, 2-thiouracil, 6-methyl-2-thiouracil, thymine, 6-methyluracil and barbituric acid) using DMF as solvent. The structures of all products were confirmed by spectroscopic (1H NMR, 13C NMR, and FT-IR) anal., mass spectrometry (EI) and PM5 semiempirical methods. Moreover the protonation constants for studied compounds were determined The obtained conjugates were screened in vitro for antioxidant and haemolytic activities, and for the protective effects against 2,2′-azobis (2-methylpropionamidine) dihydrochloride (AAPH)-induced oxidative haemolysis of human erythrocytes. 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 oxidant conjugate indole alkaloid uracil preparation, Alkaloids: Alkaloids Containing One Nitrogen Atom In A Ring and other aspects.Safety of 6-Methylpyrimidine-2,4(1H,3H)-dione

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