Category: 65-71-4

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

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Pyrimidine | C4H4N2 – PubChem,
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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

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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

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Pyrimidine | C4H4N2 – PubChem,
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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

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Pyrimidine | C4H4N2 – PubChem,
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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

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Pyrimidine | C4H4N2 – PubChem,
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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

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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

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Pyrimidine | C4H4N2 – PubChem,
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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,
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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

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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