Tag: M.W=100-150

Czernecki, Dariusz; Bonhomme, Frederic; Kaminski, Pierre-Alexandre; Delarue, Marc published the artcile< Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA>, Recommanded Product: 7H-Purin-2-amine, the main research area is .

Abstract: Cyanophage S-2L is known to profoundly alter the biophys. properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homolog of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their resp. substrates provide a rationale for their specificities. The Z-cluster made of these three genes – datZ, mazZ and purZ – was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.

Nature Communications published new progress about 452-06-2. 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

Chen, Jianzhong; Wang, Xingyu; Pang, Laixue; Zhang, John Z. H.; Zhu, Tong published the artcile< Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations>, Related Products of 452-06-2, the main research area is guanine riboswitch mutation ligand binding mol dynamics simulation.

Riboswitches can regulate gene expression by direct and specific interactions with ligands and have recently attracted interest as potential drug targets for antibacterial. In this work, mol. dynamics (MD) simulations, free energy perturbation (FEP) and mol. mechanics generalized Born surface area (MM-GBSA) methods were integrated to probe the effect of mutations on the binding of ligands to guanine riboswitch (GR). The results not only show that binding free energies predicted by FEP and MMGBSA obtain an excellent correlation, but also indicate that mutations involved in the current study can strengthen the binding affinity of ligands GR. Residue-based free energy decomposition was applied to compute ligand-nucleotide interactions and the results suggest that mutations highly affect interactions of ligands with key nucleotides U22, U51 and C74. Dynamics analyses based on MD trajectories indicate that mutations not only regulate the structural flexibility but also change the internal motion modes of GR, especially for the structures J12, J23 and J31, which implies that the aptamer domain activity of GR is extremely plastic and thus readily tunable by nucleotide mutations. This study is expected to provide useful mol. basis and dynamics information for the understanding of the function of GR and possibility as potential drug targets for antibacterial.

Nucleic Acids Research published new progress about Free energy of binding. 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

Tan, Ying; You, Changjun; Park, Jiyeong; Kim, Hyun Suk; Guo, Su; Scharer, Orlando D.; Wang, Yinsheng published the artcile< Transcriptional Perturbations of 2,6-Diaminopurine and 2-Aminopurine>, Recommanded Product: 7H-Purin-2-amine, the main research area is transcription diaminopurine aminopurine.

2,6-Diaminopurine (Z) is a naturally occurring adenine (A) analog that bacteriophages employ in place of A in their genetic alphabet. Recent discoveries of biogenesis pathways of Z in bacteriophages have stimulated substantial research interest in this DNA modification. Here, the authors systematically examined the effects of Z on the efficiency and fidelity of DNA transcription. The authors’ results showed that Z exhibited no mutagenic yet substantial inhibitory effects on transcription mediated by purified T7 RNA polymerase and by human RNA polymerase II in HeLa nuclear extracts and in human cells. A structurally related adenine analog, 2-aminopurine (2AP), strongly blocked T7 RNA polymerase but did not impede human RNA polymerase ii in vitro or in human cells, where no mutant transcript could be detected. The lack of mutagenic consequence and the presence of a strong blockage effect of Z on transcription suggest a role of Z in transcriptional regulation. Z is also subjected to removal by transcription-coupled nucleotide-excision repair (TC-NER), but not global-genome NER in human cells. The authors’ findings provide new insight into the effects of Z on transcription and its potential biol. functions.

ACS Chemical Biology published new progress about Homo sapiens. 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

Subramani, Vinod Kumar; Ravichandran, Subramaniyam; Bansal, Varun; Kim, Kyeong Kyu published the artcile< Chemical-induced formation of BZ-junction with base extrusion>, Recommanded Product: 7H-Purin-2-amine, the main research area is spermine ethanol methanol cobalt sodium perchlorate; 2-Aminopurine; BZ-Junction; Base-extrusion; Z-DNA; Z-DNA junction; Z-inducer.

The crystal structure of BZ-junction reveals that left-handed Z-DNA stabilized by Z-DNA binding domain (Zα) is continuously stacked to right-handed B-DNA with AT bases’ extrusion in the junction site. However, this structure might not fully represent the BZ-junction in solution due to the possibility of the junction formation either by crystal packing or Zα interaction. Therefore, we investigated BZ-junction in solution with chem. Z-DNA inducers using CD and 2-aminopurine base-extrusion assay. We confirmed the formation of Z-DNA and BZ-junction with base-extrusion by chem. Z-DNA inducers. However, neither typical Z-DNA nor base-extrusion could be detected with some inducers such as spermine, suggesting that the energy barrier for the formation of the BZ junction might vary depending on the Z-DNA induction conditions.

Biochemical and Biophysical Research Communications published new progress about Crystal structure. 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

Ouzon-Shubeita, Hala; Schmaltz, Lillian F.; Lee, Seongmin published the artcile< Insights into the substrate discrimination mechanisms of methyl-CpG-binding domain 4>, SDS of cas: 452-06-2, the main research area is methyl CpG binding domain 4 DNA base excision repair; DNA glycosylase; base excision repair; substrate recognition.

G:T mismatches, the major mispairs generated during DNA metabolism, are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). Mismatch-specific DNA glycosylases must discriminate the mismatches against million-fold excess correct base pairs. MBD4 efficiently removes thymine opposite guanine but not opposite adenine. Previous studies have revealed that the substrate thymine is flipped out and enters the catalytic site of the enzyme, while the estranged guanine is stabilized by Arg468 of MBD4. To gain further insights into the mismatch discrimination mechanism of MBD4, we assessed the glycosylase activity of MBD4 toward various base pairs. In addition, we determined a crystal structure of MBD4 bound to T:O6-methylguanine-containing DNA, which suggests the O6 and N2 of purine and the O4 of pyrimidine are required to be a substrate for MBD4. To understand the role of the Arg468 finger in catalysis, we evaluated the glycosylase activity of MBD4 mutants, which revealed the guanidinium moiety of Arg468 may play an important role in catalysis. D560N/R468K MBD4 bound to T:G mismatched DNA shows that the side chain amine moiety of the Lys stabilizes the flipped-out thymine by a water-mediated phosphate pinching, while the backbone carbonyl oxygen of the Lys engages in hydrogen bonds with N2 of the estranged guanine. Comparison of various DNA glycosylase structures implies the guanidinium and amine moieties of Arg and Lys, resp., may involve in discriminating between substrate mismatches and nonsubstrate base pairs.

Biochemical Journal published new progress about Animal gene Role: BSU (Biological Study, Unclassified), BIOL (Biological Study) (MBD4). 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

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

Zhang, Jianwei; Zhang, Yanshi; Schnatter, Wayne F. K.; Herndon, James W. published the artcile< Coupling of N-heterocycle-fused enyne aldehydes with γ,δ-unsaturated Fischer carbene complexes>, Application In Synthesis of 36947-69-0, the main research area is aldehyde enyne heterocyclic preparation coupling unsaturated Fischer carbene; heterocycle polycyclic preparation.

The coupling of γ,δ-unsaturated Fischer carbene complexes, e.g. H2C:CHCH2CH2C(OMe):Cr(CO)5 with enyne aldehyde derivatives fused to indole, imidazole, and pyrazole ring systems, e.g. I (R1 = Me3Si, n-Bu; R2 = PhCH2, PhCHMe, ribofuranosyl; R3 = H, Me3C, Ph), has been examined The reaction leads to heterocycles fused to the hydronaphthalene ring system, e.g. II, in a single step. The products of the reaction feature heterocycles fused either to benzene rings or to a cyclohexane ring. The product distribution correlates with the electronic richness of the heterocyclic ring. A moderate degree of diastereoselectivity was observed using heterocycles featuring chiral nitrogen substituents.

Organometallics published new progress about Alkenynes Role: RCT (Reactant), SPN (Synthetic Preparation), RACT (Reactant or Reagent), PREP (Preparation). 36947-69-0 belongs to class imidazoles-derivatives, and the molecular formula is C7H12N2, Application In Synthesis of 36947-69-0.

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