Category: 65-71-4

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 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 March 5, 2020, Umesaki, Keisho; Odai, Kei published an article.Category: pyrimidines The title of the article was A Kinetic Approach to Double Proton Transfer in Watson-Crick DNA Base Pairs. And the article contained the following:

Double proton transfer (DPT) in guanine-cytosine (GC) base pairs and adenine-thymine (AT) base pairs produces tautomeric forms, denoted G*C* and A*T*. To examine DPT, (i) intrinsic reaction coordinates for DPT, (ii) probabilities of change from GC to G*C* and from AT to A*T*, and (iii) IR absorption intensities of GC and G*C* were investigated on the basis of d. functional theory and Eyring’s chem. kinetics. The probabilities of change from GC to G*C* were 3 × 10-8, and those from AT to A*T* were 2 × 10-10. These values are consistent with the rate of mutation previously reported by Drake et al. G*C* exhibited two vibrational modes around 3000 cm-1, whereas GC exhibited no vibrational modes around the same frequency. The IR intensity calculated for G*C* showed that the strong absorption obtained around 3000 cm-1 was caused by one of the two modes. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Category: pyrimidines

The Article related to watson crick dna base pair double proton transfer kinetics, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Category: pyrimidines

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Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

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

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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 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 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

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Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

On June 30, 2022, Bonifacio, Lillian Gonzalez; Melo, Mirele; Ayo, Christiane Maria; Assoni, Leticia Carolina Paraboli; Olimpio, Larissa Martins; Nogueira, Mariana Reis; Spegiorin, Ligia Cosentino Junqueira Franco; Barbosa, Deusenia Machado Ulisses; de Mattos, Luiz Carlos; Pereira-Chioccola, Vera Lucia; Brandao, Cinara Cassia published an article.Formula: C5H6N2O2 The title of the article was TNFalpha rs1799964 TT genotype may be a susceptibility factor for vertical transmission of Toxoplasma gondii and clinical signs in newborns from pregnant women with acute toxoplasmosis. And the article contained the following:

One of the main impacts of Toxoplasma gondii infection occurs during pregnancy and is related to the vertical transmission of the parasite (congenital toxoplasmosis), which can cause severe clin. outcomes and fetal death. During acute infection, in order to control the rapid replication of tachyzoites, different host immune response genes are activated, and these include cytokine-encoding genes. Considering that polymorphisms in cytokine genes may increase susceptibility to vertical transmission of T. gondii by determining the immune status of the pregnant woman, this study evaluated the influence of polymorphisms of tumor necrosis factor alpha (TNFα) rs1799964 (- 1031) and interleukin 1 beta (IL1β) rs16944 (- 511) genes on gestational toxoplasmosis and on the vertical transmission of the parasite and verified the allele and genotype frequency of these polymorphisms in pregnant patients whose resp. newborn did or did not present clin. abnormalities suggestive of congenital toxoplasmosis. Methods and results: A total of 204 pregnant patients with (n = 114) or without (n = 90) infection by T. gondii were enrolled. No associations were found involving the polymorphisms rs1799964 (- 1031) of the TNFα gene and rs16944 (- 511) of the IL1β gene with the increased chance of T. gondii infection during pregnancy. However, it was observed that the maternal TT genotype referring to the polymorphism of the TNFα gene seems to influence the vertical transmission of the parasite (P = 0.01; χ2 = 6.05) and the presence of clin. manifestation in newborns from pregnancies with acute toxoplasmosis (P = 0.007; χ2 = 9.68). Conclusion: The TNFα rs1799964 TT genotype may act as a susceptibility factor for the vertical transmission of parasite and for the presence of clin. signs in newborns from pregnant women with acute toxoplasmosis. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Formula: C5H6N2O2

The Article related to toxoplasma tnfalpha genotype acute toxoplasmosis pregnancy newborn, gestational toxoplasmosis, polymorphisms, tnfα and il1β, toxoplasmosis, Mammalian Pathological Biochemistry: Obstetrics – Gynecology and other aspects.Formula: C5H6N2O2

Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia

D’Antonio, Matteo; Nguyen, Jennifer P.; Arthur, Timothy D.; Matsui, Hiroko; Donovan, Margaret K. R.; D’Antonio-Chronowska, Agnieszka; Frazer, Kelly A. published an article in 2022, the title of the article was In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms.COA of Formula: C5H6N2O2 And the article contains the following content:

Reactivation of fetal-specific genes and isoforms occurs during heart failure. However, the underlying mol. mechanisms and the extent to which the fetal program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal, healthy adult and heart failure have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that reactivation of fetal-specific RNA-binding proteins (RBPs), and the accompanied re-expression of 1,523 fetal-specific isoforms, contribute to the transcriptome differences between heart failure and healthy adult heart. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms encode proteins that tend to have more functions, are more likely to harbor RBP binding sites, have canonical sequences at their splice sites, and contain typical upstream polypyrimidine tracts. Our study suggests that compared with healthy adult, fetal cardiac tissue requires stricter transcriptional regulation, and that during heart failure reversion to this stricter transcriptional regulation occurs. Furthermore, we provide a resource of cardiac developmental stage-specific and heart failure-associated genes and isoforms, which are largely unexplored and can be exploited to investigate novel therapeutics for heart failure. 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 transcriptome mbnl1 fmr1 matr3 ipsc exoc7 heart failure adult, Mammalian Pathological Biochemistry: Cardiovascular Diseases and other aspects.COA of Formula: C5H6N2O2

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Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia