Category: 452-06-2

Irla, Marta; Hakvaag, Sigrid; Brautaset, Trygve published the artcile< Developing a riboswitch-mediated regulatory system for metabolic flux control in thermophilic Bacillus methanolicus>, Recommanded Product: 7H-Purin-2-amine, the main research area is thermophilic Bacillus methanolicus riboswitch regulatory system metabolic flux; Bacillus methanolicus; lysine riboswitch; methanol; pbuE riboswitch; thermophile.

Genome-wide transcriptomic data obtained in RNA-seq experiments can serve as a reliable source for identification of novel regulatory elements such as riboswitches and promoters. Riboswitches are parts of the 5′ untranslated region of mRNA mols. that can specifically bind various metabolites and control gene expression. For that reason, they have become an attractive tool for engineering biol. systems, especially for the regulation of metabolic fluxes in industrial microorganisms. Promoters in the genomes of prokaryotes are located upstream of transcription start sites and their sequences are easily identifiable based on the primary transcriptome data. Bacillus methanolicus MGA3 is a candidate for use as an industrial workhorse in methanol-based bioprocesses and its metabolism has been studied in systems biol. approaches in recent years, including transcriptome characterization through RNA-seq. Here, we identify a putative lysine riboswitch in B. methanolicus, and test and characterize it. We also select and exptl. verify 10 putative B. methanolicus-derived promoters differing in their predicted strength and present their functionality in combination with the lysine riboswitch. We further explore the potential of a B. subtilis-derived purine riboswitch for regulation of gene expression in the thermophilic B. methanolicus, establishing a novel tool for inducible gene expression in this bacterium.

International Journal of Molecular Sciences published new progress about 5′-Untranslated region Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Recommanded Product: 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Lim, Gary N.; Ross, Ashley E. published the artcile< Purine Functional Group Type and Placement Modulate the Interaction with Carbon-Fiber Microelectrodes>, Computed Properties of 452-06-2, the main research area is purine functional group interaction carbon fiber microelectrode; adenine; adenosine; carbon-fiber microelectrode; fast-scan cyclic voltammetry; guanine; guanosine.

Purine detection in the brain with fast-scan cyclic voltammetry (FSCV) at carbon-fiber microelectrodes (CFME) has become increasingly popular over the past decade; despite the growing interest, an in-depth anal. of how purines interact with the CFME at fast-scan rates has not been studied. Here, the functional group type and placement in the purine ring modulate sensitivity, electron transfer kinetics, and adsorption on the carbon-fiber surface. Similar studies of catecholamine interaction at CFME with FSCV have informed the development of novel catecholamine-based sensors and is needed for purine-based sensors. The authors tested purine bases with either amino, carbonyl, or both functional groups substituted at different positions on the ring and an unsubstituted purine. Unsubstituted purine showed very little to no interaction with the electrode surface, indicating that functional groups are important for interaction at the CFME. Purine nucleosides and nucleotides, like adenosine, guanosine, and ATP, are most often probed using FSCV due to their rich extracellular signaling modalities in the brain. Because of this, the extent to which the ribose and triphosphate groups affect the purine-CFME interaction was also evaluated. Amino functional groups facilitated the interaction of purine analogs with CFME more than carbonyl groups, permitting strong adsorption and high surface coverage. Ribose and triphosphate groups decreased the oxidative current and slowed the interaction at the electrode which is likely due to steric effects and electrostatic repulsion. This work provides insight into the factors that affect purine-CFME interaction and conditions to consider when developing purine-targeted sensors for FSCV.

ACS Sensors published new progress about Carbon fibers Role: ARU (Analytical Role, Unclassified), BUU (Biological Use, Unclassified), PEP (Physical, Engineering or Chemical Process), TEM (Technical or Engineered Material Use), ANST (Analytical Study), BIOL (Biological Study), USES (Uses), PROC (Process). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Computed Properties of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Padroni, G.; Patwardhan, N. N.; Schapira, M.; Hargrove, A. E. published the artcile< Systematic analysis of the interactions driving small molecule-RNA recognition>, Synthetic Route of 452-06-2, the main research area is small mol RNA interaction therapeutic target.

RNA mols. are becoming an important target class in drug discovery. However, the principles for designing RNA-binding small mols. are yet to be fully uncovered. In this study, we examined the Protein Data Bank (PDB) to highlight privileged interactions underlying small mol.-RNA recognition. By comparing this anal. with previously determined small mol.-protein interactions, we find that RNA recognition is driven mostly by stacking and hydrogen bonding interactions, while protein recognition is instead driven by hydrophobic effects. Furthermore, we analyze patterns of interactions to highlight potential strategies to tune RNA recognition, such as stacking and cation-π interactions that favor purine and guanine recognition, and note an unexpected paucity of backbone interactions, even for cationic ligands. Collectively, this work provides further understanding of RNA-small mol. interactions that may inform the design of small mols. targeting RNA.

RSC Medicinal Chemistry published new progress about Aminoglycosides Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Synthetic Route of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Campagnaro, Gustavo D.; Elati, Hamza A. A.; Balaska, Sofia; Martin Abril, Maria Esther; Natto, Manal J.; Hulpia, Fabian; Lee, Kelly; Sheiner, Lilach; Van Calenbergh, Serge; de Koning, Harry P. published the artcile< A Toxoplasma gondii Oxopurine Transporter Binds Nucleobases and Nucleosides Using Different Binding Modes>, Product Details of C5H5N5, the main research area is Toxoplasma gondii oxopurine transporter nucleobase nucleoside binding mode; Tg244440; Toxoplasma gondii; apicomplexan; nucleobase transporter; purine transporter; substrate binding.

Toxoplasma gondii is unable to synthesize purines de novo, instead salvages them from its environment, inside the host cell, for which they need high affinity carriers. Here, we report the expression of a T. gondii Equilibrative Nucleoside Transporter, Tg244440, in a Trypanosoma brucei strain from which nucleobase transporters have been deleted. Tg244440 transported hypoxanthine and guanine with similar affinity (Km ∼1 μM), while inosine and guanosine displayed Ki values of 4.05 and 3.30 μM, resp. Low affinity was observed for adenosine, adenine, and pyrimidines, classifying Tg244440 as a high affinity oxopurine transporter. Purine analogs were used to probe the substrate-transporter binding interactions, culminating in quant. models showing different binding modes for oxopurine bases, oxopurine nucleosides, and adenosine. Hypoxanthine and guanine interacted through protonated N1 and N9, and through unprotonated N3 and N7 of the purine ring, whereas inosine and guanosine mostly employed the ribose hydroxy groups for binding, in addition to N1H of the nucleobase. Conversely, the ribose moiety of adenosine barely made any contribution to binding. Tg244440 is the first gene identified to encode a high affinity oxopurine transporter in T. gondii and, to the best of our knowledge, the first purine transporter to employ different binding modes for nucleosides and nucleobases.

International Journal of Molecular Sciences published new progress about Affinity. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Product Details of C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Ma, Fei; Wang, Ting-ting; Jiang, Longhe; Zhang, Chun-yang published the artcile< Ultrasensitive detection of telomerase activity in lung cancer cells with quencher-free molecular beacon-assisted quadratic signal amplification>, Recommanded Product: 7H-Purin-2-amine, the main research area is telomerase detection mol beacon quadratic signal amplification; Fluorescence detection; Lung cancer; Molecular beacon; Signal amplification; Telomerase.

Telomerase is an important biomarker for cancer diagnosis and a valuable target for cancer therapy. Most of the reported telomerase assays suffer from the repeating thermal cycles, laborious protocols, expensive instruments and the limited sensitivity. To solve these issues, we develop a new telomerase assay based on telomerization-driven release of fluorescent 2-aminopurine. We designed a 2-aminopurine mol. beacon in which the fluorescence of 2-aminopurine is quenched due to stacking interaction effect without the use of extra quenchers. The presence of target telomerase can open the 2-aminopurine mol. beacon, triggering a quadratic signal amplification reaction to digest abundant 2-aminopurine mol. beacons, releasing large amounts of free 2-aminopurine mols. with strong fluorescence emission. Due to the inherent low background signal of 2-aminopurine mol. beacon and the highly efficient telomerization-driven quadratic signal amplification, this method exhibits high sensitivity with a limit of detection equivalent to 1 human lung cancer A549 cell and a large dynamic range of 4 orders of magnitude from 1 to 10000 cells. Moreover, this method can be further applied for telomerase inhibition assay and the discrimination of cancer cells from normal cells, holding great potential in telomerase-related clin. diagnosis and drug discovery.

Analytica Chimica Acta published new progress about Cancer diagnosis. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Recommanded Product: 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Kuznetsova, A. A.; Kladova, O. A.; Barthes, Nicolas P. F.; Michel, Benoit Y.; Burger, Alain; Fedorova, O. S.; Kuznetsov, N. A. published the artcile< Comparative Analysis of Nucleotide Fluorescent Analogs for Registration of DNA Conformational Changes Induced by Interaction with Formamidopyrimidine-DNA Glycosylase Fpg>, SDS of cas: 452-06-2, the main research area is Escherichia DNA Fpg aPu 3HC Cpy tC0.

Abstract: DNA-substrates containing fluorescent DNA base analogs are widely used to study protein-nucleic acid interactions. In the case of DNA-recognizing enzymes, this approach allows one to register conformational changes in DNA during the formation of enzyme-substrate complexes. An important part of such research is the design of model DNA substrates, which includes both the photophys. properties of the fluorescent groups and their location relative to a specific recognition site, namely, in the same chain on the 5′-, 3′-side or in the complementary chain opposite the specific site. In this work, we report a comparative study of the sensitivity of various fluorescent DNA base analogs, such as 2-aminopurine (aPu), pyrrolocytosine (CPy), 1,3-diaza-2-oxophenoxazine (tCO) and 3-hydroxychromone (3HC), to conformational transformations of DNA in the process of interaction with formamidopyrimidine-DNA glycosylase (Fpg) from Escherichia coli.

Russian Journal of Bioorganic Chemistry published new progress about DNA Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, SDS of cas: 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Paterson, Kyle A.; Arlt, Jochen; Jones, Anita C. published the artcile< Dynamic and static quenching of 2-aminopurine fluorescence by the natural DNA nucleotides in solution>, Related Products of 452-06-2, the main research area is nucleoside monophosphate base stacking fluorescence quenching charge transfer.

2-Aminopurine (2AP)is a responsive fluorescent base analog that is used widely as a probe of the local mol. environment in DNA. The ability of 2AP to report changes in local conformation and base-stacking interactions arises from the efficient quenching of its fluorescence by the natural DNA bases. However, the mechanism of this inter-base quenching remains imperfectly understood. Two previous studies of the collisional quenching of 2AP by the natural bases, in different buffer solutions, showed that dynamic quenching efficiency depends on the identity of the natural base, but disagreed on the relative quenching efficiencies of the bases. We report a comprehensive investigation of interbase quenching of 2AP by the natural nucleoside monophosphates(NMPs), replicating the buffer conditions used in the previous studies. Using time-resolved fluorescence measurements to distinguish between dynamic and static quenching, we find that the dynamic quenching rate constants of the different bases show a consistent trend across both buffers, and this is in line with a charge-transfer mechanism. Time-resolved measurements also provide insight into static quenching, revealing formation of 2AP-NMP ground-state complexes in which 2AP displays a very short fluorescence lifetime, comparable to that seen in oligonucleotides. In these complexes, the dependence of the rate of quenching on the partner base also supports a charge-transfer mechanism.

Methods and Applications in Fluorescence published new progress about Buffers. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Related Products of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Caldero-Rodriguez, Naishka E.; Ortiz-Rodriguez, Luis A.; Gonzalez, Andres A.; Crespo-Hernandez, Carlos E. published the artcile< Photostability of 2,6-diaminopurine and its 2'-deoxyriboside investigated by femtosecond transient absorption spectroscopy>, Application In Synthesis of 452-06-2, the main research area is photostability 26DAP 26DAPd femtosecond transient absorption spectroscopy.

UV radiation (UVR) from the sun is essential for the prebiotic syntheses of nucleotides, but it can also induce photolesions such as the cyclobutane pyrimidine dimers (CPDs) to RNA or DNA oligonucleotide in prebiotic Earth. 2,6-Diaminopurine (26DAP) has been proposed to repair CPDs in high yield under prebiotic conditions and be a key component in enhancing the photostability of higher-order prebiotic DNA structures. However, its electronic relaxation pathways have not been studied, which is necessary to know whether 26DAP could have survived the intense UV fluxes of the prebiotic Earth. We investigate the electronic relaxation mechanism of both 26DAP and its 2′-deoxyribonucleoside (26DAP-d) in aqueous solution using steady-state and femtosecond transient absorption measurements that are complemented with electronic-structure calculations The results demonstrate that both purine derivatives are significantly photostable to UVR. It is shown that upon excitation at 287 nm, the lowest energy 1ππ* state is initially populated. The population then branches following two relaxation coordinates in the 1ππ* potential energy surface, which are identified as the C2- and C6-relaxation coordinates. The population following the C6-coordinate internally converts to the ground state nonradiatively through a nearly barrierless conical intersection within 0.7 ps in 26DAP or within 1.1 ps in 26DAP-d. The population that follows the C2-relaxation coordinate decays back to the ground state by a combination of nonradiative internal conversion via a conical intersection and fluorescence emission from the 1ππ* min. in 43 ps and 1.8 ns for the N9 and N7 tautomers of 26DAP, resp., or in 70 ps for 26DAP-d. Fluorescence quantum yields of 0.037 and 0.008 are determined for 26DAP and 26DAP-d, resp. Collectively, it is demonstrated that most of the excited state population in 26DAP and 26DAP-d decays back to the ground state via both nonradiative and radiative relaxation pathways. This result lends support to the idea that 26DAP could have accumulated in large enough quantities during the prebiotic era to participate in the formation of prebiotic RNA or DNA oligomers and act as a key component in the protection of the prebiotic genetic alphabet.

Physical Chemistry Chemical Physics published new progress about Absorption spectroscopy (Femtosecond Transient). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Application In Synthesis of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Seelam, Preethi P.; Mitra, Abhijit; Sharma, Purshotam published the artcile< Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies>, Formula: C5H5N5, the main research area is nucleobases ligands riboswitches crystal structure.

In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for anal. of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chem. constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. The anal. was further extended to study the biol. importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in the context of RNA:ligand recognition. This can, in turn, contribute toward current efforts to develop antimicrobials that target RNAs.

RNA published new progress about Amino acids Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Formula: C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Patutina, Olga; Chiglintseva, Daria; Bichenkova, Elena; Gaponova, Svetlana; Mironova, Nadezhda; Vlassov, Valentin; Zenkova, Marina published the artcile< Dual miRNases for triple incision of miRNA target: design concept and catalytic performance>, Safety of 7H-Purin-2-amine, the main research area is microRNA21 microRNAR155 microRNA17a oligonucleotide peptide catalysis; RNA cleavage; RNase H; anti-miRNA therapy; artificial ribonuclease; miRNase; oligonucleotide-peptide conjugate; oncogenic miRNA.

Irreversible destruction of disease-associated regulatory RNA sequences offers exciting opportunities for safe and powerful therapeutic interventions against human pathophysiol. In 2017, for the first time we introduced miRNAses-miRNA-targeted conjugates of a catalytic peptide and oligonucleotide capable of cleaving an miRNA target. Herein, we report the development of Dual miRNases against oncogenic miR-21, miR-155, miR-17 and miR-18a, each containing the catalytic peptide placed in-between two short miRNA-targeted oligodeoxyribonucleotide recognition motifs. Substitution of adenines with 2-aminoadenines in the sequence of oligonucleotide “”shoulders”” of the Dual miRNase significantly enhanced the efficiency of hybridization with the miRNA target. It was shown that sequence-specific cleavage of the target by miRNase proceeded metal-independently at pH optimum 5.5-7.5 with an efficiency varying from 15% to 85%, depending on the miRNA sequence. A distinct advantage of the engineered nucleases is their ability to addnl. recruit RNase H and cut miRNA at three different locations. Such cleavage proceeds at the central part by Dual miRNase, and at the 5′- and 3′-regions by RNase H, which significantly increases the efficiency of miRNA degradation Due to increased activity at lowered pH Dual miRNases could provide an addnl. advantage in acidic tumor conditions and may be considered as efficient tumor-selective RNA-targeted therapeutic.

Molecules published new progress about MicroRNA-155 Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Safety of 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem