Tag: 100-200

On November 19, 2020, Zacharias, Martin published an article.Quality Control of 5-Methylpyrimidine-2,4(1H,3H)-dione The title of the article was Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation. And the article contained the following:

Double-stranded (ds)DNA formation and dissociation are of fundamental biol. importance. The neg. DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence-dependent stability of dsDNA. The stability of a dsDNA mol. can be estimated from empirical nearest-neighbor models based on contributions assigned to base-pair steps along the DNA and addnl. parameters because of DNA termini. In efforts to sep. contributions, it has been concluded that base stacking dominates dsDNA stability, whereas base pairing contributes negligibly. Using a different model for dsDNA formation, we reanalyze dsDNA stability contributions and conclude that base stacking contributes already at the level of sep. ssDNAs but that pairing contributions drive the dsDNA formation. The theor. model also predicts that stability contributions of base-pair steps that contain only guanine/cytosine, mixed steps, and steps with only adenine/thymine follow the order 6:5:4, resp., as expected based on the formed hydrogen bonds. The model is fully consistent with the available stacking data and the nearest-neighbor dsDNA parameters. It allows assigning a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of -0.72 kcal·mol-1 based entirely on the exptl. data. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Quality Control of 5-Methylpyrimidine-2,4(1H,3H)-dione

The Article related to double stranded dna base pairing stacking model, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Quality Control of 5-Methylpyrimidine-2,4(1H,3H)-dione

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On April 28, 2022, Nicy; Chakraborty, Debayan; Wales, David J. published an article.Category: pyrimidines The title of the article was Energy Landscapes for Base-Flipping in a Model DNA Duplex. And the article contained the following:

The authors explore the process of base-flipping for four central bases: adenine, guanine, cytosine, and thymine, in a DNA duplex using the energy landscape perspective. NMR imino-proton exchange and fluorescence correlation studies were used in previous experiments to obtain lifetimes for bases in paired and extrahelical states. However, the difference of almost 4 orders of magnitude in the lifetimes obtained by the two methods implies that they are exploring different pathways, and possibly different open states. The authors’ results support the previous suggestion that minor groove opening may be favored by distortions in the DNA backbone, and reveal links between sequence effects and the direction of opening, i.e., whether the base flips toward the major or the minor groove side. In particular, base flipping along the minor groove pathway was found to align toward the 5′ side of the backbone. Bases align toward the 3′ side of the backbone when flipping along the major groove pathway. However, in some cases for cytosine and thymine, the base flipping along the major groove pathway also aligns toward the 5′ side. The sequence effect may be caused by the polar interactions between the flipping-base and its neighboring bases on either of the strands. For guanine flipping toward the minor groove side, the equilibrium constant for opening is large compared to flipping via the major groove. The estimated rates of base opening, and hence the lifetimes of the closed state, obtained for thymine flipping through small and large angles along the major groove differ by 6 orders of magnitude, whereas for thymine flipping through small angles along the minor groove and large angles along the major groove, the rates differ by 3 orders of magnitude. Potential energy as a function of integrated path length for flipping pathways of (a) adenine, (b) guanine, (c) cytosine and (d) thymine along the major and minor groove. Pos. and neg. path lengths correspond to flipping along the minor and major groove, resp. The pathways are between closed state (as shown within Figure) and open states labeled as [A] and [B] (Figures and) for the base flipped out via major and minor groove, resp. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Category: pyrimidines

The Article related to dna duplex energy landscape base flipping model, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Category: pyrimidines

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On December 31, 2020, Ben Imeddourene, A.; Zargarian, L.; Buckle, M.; Hartmann, B.; Mauffret, O. published an article.Application of 65-71-4 The title of the article was Slow motions in A·T rich DNA sequence. And the article contained the following:

In free B-DNA, slow (microsecond-to-millisecond) motions that involve equilibrium between Watson-Crick (WC) and Hoogsteen (HG) base-pairing expand the DNA dynamic repertoire that could mediate DNA-protein assemblies. R1ρ relaxation dispersion NMR methods are powerful tools to capture such slow conformational exchanges in solution using 13C/15N labeled DNA. Here, these approaches were applied to a dodecamer containing a TTAAA element that was assumed to facilitate nucleosome formation. NMR data and inferred exchange parameters assign HG base pairs as the minor, transient conformers specifically observed in three successive A·T base pairs forming the TAA·TTA segment. The abundance of these HG A·T base pairs can be up to 1.2% which is high compared to what has previously been observed Data analyzes support a scenario in which the three adenines undergo non-simultaneous motions despite their spatial proximity, thus optimizing the probability of having one HG base pair in the TAA·TTA segment. Finally, revisiting previous NMR data on H2 resonance linewidths on the basis of our results promotes the idea of there being a special propensity of A·T base pairs in TAA·TTA tracts to adopt HG pairing. In summary, this study provides an example of a DNA functional element submitted to slow conformational exchange. More generally, it strengthens the importance of the role of the DNA sequence in modulating its dynamics, over a nano- to milli-second time scale. 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 slow motion dna sequence a t protein base pair, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Application of 65-71-4

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On December 31, 2021, Rozalski, Rafal; Gackowski, Daniel; Skalska-Bugala, Aleksandra; Starczak, Marta; Siomek-Gorecka, Agnieszka; Zarakowska, Ewelina; Modrzejewska, Martyna; Dziaman, Tomasz; Szpila, Anna; Linowiecka, Kinga; Guz, Jolanta; Szpotan, Justyna; Gawronski, Maciej; Labejszo, Anna; Gackowska, Lidia; Foksinski, Marek; Olinska, Elwira; Wasilow, Aleksandra; Koltan, Andrzej; Styczynski, Jan; Olinski, Ryszard published an article.Synthetic Route of 4433-40-3 The title of the article was The urinary excretion of epigenetically modified DNA as a marker of pediatric ALL status and chemotherapy response. And the article contained the following:

The active DNA demethylation process may be linked to aberrant methylation and may be involved in leukemogenesis. We investigated the role of epigenetic DNA modifications in childhood acute lymphoblastic leukemia (ALL) diagnostics and therapy monitoring. We analyzed the levels of 5-methyl-2′-deoxycytidine (5-mdC) oxidation products in the cellular DNA and urine of children with ALL (at diagnosis and during chemotherapy, n = 55) using two-dimensional ultra-performance liquid chromatog. with tandem mass spectrometry (2D UPLC-MS/MS). Moreover, the expression of Ten Eleven Translocation enzymes (TETs) at the mRNA and protein levels was determined Addnl., the ascorbate level in the blood plasma was analyzed. Before treatment, the ALL patients had profoundly higher levels of the analyzed modified DNA in their urine than the controls. After chemotherapy, we observed a statistically significant decrease in active demethylation products in urine, with a final level similar to the level characteristic of healthy children. The level of 5-hmdC in the DNA of the leukocytes in blood of the patient group was significantly lower than that of the control group. Our data suggest that urinary excretion of epigenetic DNA modification may be a marker of pediatric ALL status and a reliable marker of chemotherapy response. The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).Synthetic Route of 4433-40-3

The Article related to urinary excretion dna marker pediatric acute lymphoblastic leukemia chemotherapy, Mammalian Pathological Biochemistry: Respiratory Diseases and other aspects.Synthetic Route of 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On November 5, 2020, Piccinni, Viviana; Reiter, Sebastian; Keefer, Daniel; de Vivie-Riedle, Regina published an article.Synthetic Route of 65-71-4 The title of the article was Multiscale Conformational Sampling Reveals Excited-State Locality in DNA Self-Repair Mechanism. And the article contained the following:

UV irradiation is known to be responsible for DNA damage. However, exptl. studies in DNA oligonucleotides have shown that UV light can also induce sequence-specific self-repair. Following charge transfer from a guanine adenine sequence adjacent to a cyclobutane pyrimidine dimer (CPD), the covalent bond between the two thymines could be cleaved, recovering the intact base sequence. Mechanistic details promoting the self-repair remained unclear, however. In our theor. study, we investigated whether optical excitation could directly lead to a charge-transfer state, thereby initiating the repair, or whether the initial excited state remains localized on a single nucleobase. We performed conformational sampling of 200 geometries of the damaged DNA double strand solvated in water and used a hybrid quantum and mol. mechanics approach to compute excited states at the complete active space perturbation level of theory. Anal. of the conformational data set clearly revealed that the excited-state properties are uniformly distributed across the fluctuations of the nucleotide in its natural environment. From the electronic wavefunction, we learned that the electronic transitions remained predominantly local on either adenine or guanine, and no direct charge transfer occurred in the exptl. accessed energy range. The investigated base sequence is not only specific to the CPD repair mechanism but ubiquitously occurs in nucleic acids. Our results therefore give a very general insight into the charge locality of UV-excited DNA, a property that is regarded to have determining relevance in the structural consequences following absorption of UV photons. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Synthetic Route of 65-71-4

The Article related to dna cyclobutane pyrimidine dimer repair excited state uv photoexcitation, Radiation Biochemistry: Effects On Biochemical Substances and other aspects.Synthetic Route of 65-71-4

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On November 30, 2016, Choofong, Surakarn; Cloutier, Pierre; Sanche, Leon; Wagner, J. Richard published an article.SDS of cas: 4433-40-3 The title of the article was Base release and modification in solid-phase DNA exposed to low-energy electrons. And the article contained the following:

Ionization generates a large number of secondary low-energy electrons (LEEs) with a most probable energy of approx. 10 eV, which can break DNA bonds by dissociative electron attachment (DEA) and lead to DNA damage. In this study, we investigated radiation damage to dry DNA induced by X rays (1.5 keV) alone on a glass substrate or X rays combined with extra LEEs (average energy of 5.8 eV) emitted from a tantalum (Ta) substrate under an atm. of N2 and standard ambient conditions of temperature and pressure. The targets included calf-thymus DNA and double-stranded synthetic oligonucleotides. We developed anal. methods to measure the release of non-modified DNA bases from DNA and the formation of several base modifications by LC-MS/MS with isotopic dilution for precise quantification. The results show that the yield of non-modified bases as well as base modifications increase by 20-30% when DNA is deposited on a Ta substrate compared to that on a glass substrate. The order of base release (Gua > Ade > Thy ∼ Cyt) agrees well with several theor. studies indicating that Gua is the most susceptible site toward sugar-phosphate cleavage. The formation of DNA damage by LEEs is explained by DEA leading to the release of non-modified bases involving the initial cleavage of N1-C1′, C3′-O3′ or C5′-O5′ bonds. The yield of base modifications was lower than the release of non-modified bases. The main LEE-induced base modifications include 5,6-dihydrothymine (5,6-dHT), 5,6-dihydrouracil (5-dHU), 5-hydroxymethyluracil (5-HmU) and 5-formyluracil (5-ForU). The formation of base modifications by LEEs can be explained by DEA and cleavage of the C-H bond of the Me group of Thy (giving 5-HmU and 5-ForU) and by secondary reactions of H atoms and hydride anions that are generated by primary LEE reactions followed by subsequent reaction with Cyt and Thy (giving 5,6-dHU and 5,6-dHT). The experimental process involved the reaction of 5-(Hydroxymethyl)pyrimidine-2,4(1H,3H)-dione(cas: 4433-40-3).SDS of cas: 4433-40-3

The Article related to ionizing radiation low energy electron base release modification dna, Radiation Biochemistry: Effects On Biochemical Substances and other aspects.SDS of cas: 4433-40-3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On December 18, 2020, Nguyen, Kim; Kubota, Miles; Arco, Jon del; Feng, Chao; Singha, Monika; Beasley, Samantha; Sakr, Jasmine; Gandhi, Sunil P.; Blurton-Jones, Matthew; Fernandez Lucas, Jesus; Spitale, Robert C. published an article.COA of Formula: C5H6N2O3 The title of the article was A Bump-Hole Strategy for Increased Stringency of Cell-Specific Metabolic Labeling of RNA. And the article contained the following:

Profiling RNA expression in a cell-specific manner continues to be a grand challenge in biochem. research. Bioorthogonal nucleosides can be used to track RNA expression; however, these methods currently have limitations due to background and incorporation of analogs into undesired cells. Herein, the authors design and demonstrate that uracil phosphoribosyltransferase can be engineered to match 5-vinyluracil for cell-specific metabolic labeling of RNA with exceptional specificity and stringency. 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 rna expression vinyl uracil metabolic labeling, Biochemical Methods: Other (Not Covered At Other Subsections) and other aspects.COA of Formula: C5H6N2O3

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On September 30, 2020, Li, Qian; Zhao, Jiemin; Liu, Longfei; Jonchhe, Sagun; Rizzuto, Felix J.; Mandal, Shankar; He, Huawei; Wei, Sansen; Sleiman, Hanadi F.; Mao, Hanbin; Mao, Chengde published an article.Computed Properties of 65-71-4 The title of the article was A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials. And the article contained the following:

Abstract: The diversity of DNA duplex structures is limited by a binary pair of hydrogen-bonded motifs. Here we show that poly(thymine) self-associates into antiparallel, right-handed duplexes in the presence of melamine, a small mol. that presents a triplicate set of the hydrogen-bonding face of adenine. X-ray crystallog. shows that in the complex two poly(thymine) strands wrap around a helical column of melamine, which hydrogen bonds to thymine residues on two of its three faces. The mech. strength of the thymine-melamine-thymine triplet surpasses that of adenine-thymine base pairs, which enables a sensitive detection of melamine at 3 pM. The poly(thymine)-melamine duplex is orthogonal to native DNA base pairing and can undergo strand displacement without the need for overhangs. Its incorporation into two-dimensional grids and hybrid DNA-small-mol. polymers highlights the poly(thymine)-melamine duplex as an addnl. tool for DNA nanotechnol. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Computed Properties of 65-71-4

The Article related to polythymine melamine duplex dna nanomaterial, Biochemical Methods: Other (Not Covered At Other Subsections) and other aspects.Computed Properties of 65-71-4

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On December 6, 2018, Fan, Pingchen; Lange, Christopher W.; Lui, Rebecca M.; Malathong, Viengkham; Mali, Venkat Reddy; Punna, Sreenivas; Zeng, Yibin; Zhang, Penglie published a patent.Related Products of 596114-50-0 The title of the patent was 5-5 Fused ring as C5a inhibitors and their preparation. And the patent contained the following:

The disclosure provides, inter alia, compounds of formula I or pharmaceutically acceptable salts thereof that are modulators of the C5a receptor. Also provided are pharmaceutical compositions and methods of use including the treatment of diseases or disorders involving pathol. activation from C5a and non-pharmaceutical applications. Compounds of formula I wherein A1 is N, CH, CO and CR4; A2 is N, CH and CR4; A3, A4, A5 and A6 are independently CH and CR4; dashed bonds are single and double bonds; n is 0, 1, 2 and 3; R1 is C1-8 alkylene-C6-10 aryl, C1-8 alkylene-heteroaryl, C1-8 alkyl, etc.; each R2a is independently C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, etc.; each R2b is independently H, C1-6 alkyl, C1-6 alkoxy, C1-6 haloalkyl, CN, etc.; each R3 is independently C1-4 alkyl, C1-4 haloalkyl, halo and OH; two R3 groups can be taken together to form oxo or a 3- to 5-membered ring; each R4 is independently C1-6 alkyl, C1-6 alkoxy, C1-6 hydroxyalkyl, halo, etc.; and pharmaceutically acceptable salts thereof, are claimed. Example compound II was prepared by a multistep procedure (procedure given). The invention compounds were evaluated for their C5a inhibitory activity. From the assay, it was determined that compound II exhibited IC50 value of < 5 nM. The experimental process involved the reaction of 2-Chloro-5-isopropylpyrimidine(cas: 596114-50-0).Related Products of 596114-50-0

The Article related to pyrrolopyrazole preparation c5a inhibitor, Heterocyclic Compounds (More Than One Hetero Atom): Pyrazoles and other aspects.Related Products of 596114-50-0

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On December 31, 2017, Akbarzadeh, Marzieh; Bakavoli, Mehdi; Eshghi, Hossein; Shiri, Ali published an article.HPLC of Formula: 626-48-2 The title of the article was Synthesis of novel derivatives of (benz)imidazo[2,1-b]pyrimido[4,5-d][1,3]thiazine. And the article contained the following:

Several derivatives of the novel heterocyclic systems 2-substituted-imidazo- and benzimidazo-[2,1-b]pyrimido[4,5-d][1,3]thiazine were synthesized through the one-pot cyclocondensation of 2,4-dichloro-5-(chloromethyl)-6-methylpyrimidine with imidazolidine-2-thione and 1H-benzimidazole-2(3H)-thione and subsequently substituted by various secondary amines in moderately good yields. The experimental process involved the reaction of 6-Methylpyrimidine-2,4(1H,3H)-dione(cas: 626-48-2).HPLC of Formula: 626-48-2

The Article related to amino imidazopyrimidothiazine preparation, Heterocyclic Compounds (More Than One Hetero Atom): Thiazines and other aspects.HPLC of Formula: 626-48-2

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia