Tag: M.W=100-150

Xu, Xiaochen; Egger, Michaela; Chen, Hao; Bartosik, Karolina; Micura, Ronald published the artcile< Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition>, Related Products of 452-06-2, the main research area is xanthine riboswitch NMT1 metal ion mediated ligand recognition.

Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, resp., both are involved in the metabolic pathway of purine degradation Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding anal. to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic anal. of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.

Nucleic Acids Research published new progress about Crystal structure. 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

Brovarets, Ol′ha O.; Hovorun, Dmytro M. published the artcile< Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research>, HPLC of Formula: 452-06-2, the main research area is review quantum 2aminopurine mutagenicity tautomerization; 2-Aminopurine; H-bond: hydrogen bond; Watson–Crick↔wobble mutagenic tautomerization; induced mutation; quantum-chemical calculation; transition; transversion.

A review. As of today, a great amount of exptl. and theor. phenomenol. data have been collected in the literature according the mutagenic action of the classical mutagen – 2-aminopurine (2AP). However, so far they have not received proper explanation and substantiation. In this Opinion Piece, we provide an overview of recent progress in computational design and modeling of the physico-chem. mechanisms of the mutagenic action of 2AP. Results of quantum-chem. studies, aimed at the elucidation of the key microstructural mechanisms of the mutagenicity of 2AP, have been summarized here. In this context, for the first time it was outlined the most important surveys: Why 2AP is incorporated into DNA in trace concentrations? Whether classical mechanisms presented in the literature according the formation of the rare tautomers of canonical DNA bases work also for base analog – 2AP? In what way 2AP induces replication and incorporation errors? Whether the amino-imino tautomerisation of 2AP is related to its mutagenicity, that is whether the 2AP* rare tautomer is mutagenic? It is emphasized that the applied approach has a proper theor. substantiation, since it is based on our microstructural theory of the spontaneous point mutagenesis in DNA, and at the same time it accumulates scenarios of the origin of the induced point errors – transitions and transversions, which the classical Watson-Crick tautomeric hypothesis permits. Moreover, using author′s methodol., the profiles of the main physico-chem. characteristics for the tautomerisation reactions involving 2AP, which are integral parts of the biol. important tautomerically-conformational transformations, have been presented. Obtained results open new perspectives for prediction and design of the mutagenic derivatives of the nucleotide bases of any structure and origin before their synthesis and also for planning of new experiments and interpretation of the existing data. Abbreviations2AP2-AminopurineAadenineCcytosineDPTdouble proton transferGguanineIRCintrinsic reaction coordinateKPkey pointTthyminewwobbleWCWatson-CrickvdWvan der WaalsH-bondhydrogen bondCommunicated by Ramaswamy H. Sarma

Journal of Biomolecular Structure and Dynamics 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, HPLC of Formula: 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Kunz, Peter C.; Klaeui, Wolfgang published the artcile< Zinc and cobalt(II) complexes of tripodal nitrogen ligands of the tris[2-substituted imidazol-4(5)-yl]-phosphane type. Biomimetic hydrolysis of an activated ester>, Category: imidazoles-derivatives, the main research area is tris imidazolyl phosphine ligand preparation zinc cobalt complexation; biomimetic ester hydrolysis zinc enzyme; nitrophenyl pyridine carboxylate hydrolysis kinetics zinc cobalt imidazolylphosphine catalyzed.

Novel tris[2-substituted imidazol-4(5)-yl]phosphane (4-TIPR) ligands 2b (R = Ph) and 2c (R = tBu) were prepared as model ligands for the tris(histidine) motif found in many zinc enzymes. They readily form cobalt and zinc nitrato and chloro complexes in protic solvents. The steric requirements of the substituents R in 4(5)-position of the 4-TIPR ligands (R = iPr (2a), Ph (2b), tBu (2c)) is discussed on the basis of their UV/VIS spectra. Zinc complexes of 2a and 2c were studied due to their ability to promote the hydrolysis of the activated ester 4-nitrophenyl pyridine-2-carboxylate (pNpic).

Collection of Czechoslovak Chemical Communications published new progress about Enzymes Role: BCP (Biochemical Process), BIOL (Biological Study), PROC (Process) (model). 36947-69-0 belongs to class imidazoles-derivatives, and the molecular formula is C7H12N2, Category: imidazoles-derivatives.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

He, Yanping; Zhou, Yibo; Chen, Da; Liu, Juewen published the artcile< Global Folding of a Na+-Specific DNAzyme Studied by FRET>, Name: 7H-Purin-2-amine, the main research area is DNAzymes; FRET; aptamers; protein folding; sodium.

Recently, a few RNA-cleaving DNAzymes have been isolated with excellent specificity for Na+, and some of them contain a Na+-binding aptamer. This metal recognition mechanism is different from that of most previously reported DNAzymes. When using 2-aminopurine (2AP) as a probe, interesting local folding induced by Na+ was recently observed In this work, FRET was used to probe the global folding of the Ce13d DNAzyme; one of the Na+-specific DNAzymes. FRET pairs were at different locations, which yielded a total of five constructs to probe the three-way junction structure with a large loop. With endlabeled DNAzymes, the global structure appears to be quite rigid with little folding upon adding up to 200 mM monovalent metal ions, although some minor differences were observed between Li+, Na+, and K+. This lack of significant conformational change is also consistent with CD spectroscopy data. The loop was then labeled with an internal tetramethylrhodamine fluorophore at the G14 position, and its cleavage activity was partially retained. A clear Na+-dependent folding was observed with spectral crossover. From a biosensing standpoint, global folding based sensors are unlikely to work due to the overall rigid structure of the DNAzyme. Therefore, the best way to use this DNAzyme to discriminate Na+ from K+ is based on cleavage activity, followed by probing local folding, whereas global folding is the least effective for metal discrimination.

ChemBioChem published new progress about 452-06-2. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Name: 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Wickhorst, Peter Jonas; Ihmels, Heiko; Paululat, Thomas published the artcile< Studies on the Interactions of 3,11-Difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium and Insulin with the Quadruplex-Forming Oligonucleotide Sequence a2 from the Insulin-Linked Polymorphic Region>, Quality Control of 452-06-2, the main research area is interaction quadruplex oligonucleotide sequence insulin linked polymorphic region; DNA recognition; ILPR; spectroscopic methods.

Recently, several quadruplex-DNA-forming sequences have been identified in the insulin-linked polymorphic region (ILPR), which is a guanine-rich oligonucleotide sequence in the promoter region of insulin. The formation of this non-canonical quadruplex DNA (G4-DNA) has been shown to be involved in the biol. activity of the ILPR, specifically with regard to its interplay with insulin. In this context, this contribution reports on the investigation of the association of the quadruplex-forming ILPR sequence a2 with insulin as well as with the well-known G4-DNA ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium (1), also named RHPS4, by optical and NMR spectroscopy. CD- and NMR-spectroscopic measurements confirmed the preferential formation of an antiparallel quadruplex structure of a2 with four stacked guanine quartets. Furthermore, ligand 1 has high affinity toward a2 and binds by terminal π stacking to the G1-G11-G15-G25 quartet. In addition, the spectroscopic studies pointed to an association of insulin to the deoxyribose backbone of the loops of a2.

Molecules published new progress about Absorption. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Quality Control of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Shin, Yeonoh; Hedglin, Mark; Murakami, Katsuhiko S. published the artcile< Structural basis of reiterative transcription from the pyrG and Pyrbi promoters by bacterial RNA polymerase>, HPLC of Formula: 452-06-2, the main research area is gene transcription pyrG Pyrbi bacteria RNA polymerase crystal structure.

Reiterative transcription is a non-canonical form of RNA synthesis by RNA polymerase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to the nascent RNA transcript. We previously determined the X-ray crystal structure of the bacterial RNA polymerase engaged in reiterative transcription from the pyrG promoter, which contains eight poly-G RNA bases synthesized using three C bases in the DNA as a template and extends RNA without displacement of the promoter recognition σ factor from the core enzyme. In this study, we determined a series of transcript initiation complex structures from the pyrG promoter using soak-trigger-freeze X-ray crystallog. We also performed biochem. assays to monitor template DNA translocation during RNA synthesis from the pyrG promoter and in vitro transcription assays to determine the length of poly-G RNA from the pyrG promoter variants. Our study revealed how RNA slips on template DNA and how RNA polymerase and template DNA determine length of reiterative RNA product. Lastly, we determined a structure of a transcript initiation complex at the pyrBI promoter and proposed an alternative mechanism of RNA slippage and extension requiring the σ dissociation from the core enzyme.

Nucleic Acids Research published new progress about Bacillus subtilis. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, HPLC of Formula: 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Li, Yue; Liu, Yukang; Singh, Jaideep; Tangprasertchai, Narin S.; Trivedi, Ravi; Fang, Yun; Qin, Peter Z. published the artcile< Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM>, Reference of 452-06-2, the main research area is RNA DNA pairing PAM Cas9.

CRISPR-Cas9 is an RNA-guided nuclease that has been widely adapted for genome engineering. A key determinant in Cas9 target selection is DNA duplex unwinding to form an R-loop, in which the single-stranded RNA guide hybridizes with one of the DNA strands. To advance understanding on DNA unwinding by Cas9, we combined two types of spectroscopic label, 2-aminopurine and nitroxide spin-label, to investigate unwinding at a specific DNA base pair induced by Streptococcus pyogenes Cas9. Data obtained with RNA guide lengths varying from 13 to 20 nucleotide revealed that the DNA segment distal to the protospacer adjacent motif can adopt a “”partial unwinding”” state, in which a mixture of DNA-paired and DNA-unwound populations exist in equilibrium Significant unwinding can occur at positions not supported by RNA/DNA pairing, and the degree of unwinding depends on RNA guide length and modulates DNA cleavage activity. The results shed light on Cas9 target selection and may inform developments of genome-engineering strategies.

CRISPR Journal published new progress about Demography. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Reference of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Remington, Jacob M.; McCullagh, Martin; Kohler, Bern published the artcile< Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics>, Quality Control of 452-06-2, the main research area is mol dynamics simulation aminopurine dinucleoside monophosphate stacking kinetics.

Mol. dynamics (MD) simulations of 2-aminopurine (2Ap)-labeled DNA dinucleoside monophosphates (DNMPs) were performed to investigate the hypothesis that base stacking dynamics occur on timescales sufficiently rapid to influence the emission signals measured in time-resolved fluorescence experiments Anal. of multiple microsecond-length trajectories shows that the DNMPs sample all four coplanar stacking motifs. In addition, three metastable unstacked conformations are detected. A hidden Markov-state model (HMSM) was applied to the simulations to estimate transition rates between the stacked and unstacked states. Transitions between different stacked states generally occur at higher rates when the number of nucleobase faces requiring desolvation is minimized. Time constants for structural relaxation range between 1.6 and 25 ns, suggesting that emission from photoexcited 2Ap, which has an excited-state lifetime of 10 ns, is sensitive to base stacking kinetics. A master equation model for the excited-state population of 2Ap predicts multiexponential emission decays that reproduce the sub-10 ns emission decay lifetimes and amplitudes seen in experiments Combining MD simulations with HMSM anal. is a powerful way to understand the dynamics that influence 2Ap excited-state relaxation and represents an important step toward using observed emission signals to validate MD simulations.

Journal of Physical Chemistry B published new progress about Conformation. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Quality Control of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Hu, Ming-Hao; Lin, Jia-Hong; Huang, Qiong published the artcile< Discovery of a fluorescent, long chain-bridged bispurine that selectively targets the c-MYC G-quadruplex>, SDS of cas: 452-06-2, the main research area is c MYC VEGF HRAS BCL2; Bispurine; Fluorescent; G-quadruplex; Selective; c-MYC.

G-quadruplexes (G4s) are special nucleic acid structures which are involved in the regulation of some key biol. events like transcription and translation, which are now treated as promising therapeutic targets for cancers. Stabilizing the promoter G4 by small-mol. ligands can suppress the c-MYC oncogene transcription, thus inhibiting cancer cell proliferation. So far, targeting the very structure, a number of ligands have been reported. However, most of them showed unsatisfactory specificity to the c-MYC G4 over other G4s, resulting in uncertain side effects. In this contribution, we discovered a new class of bispurines bridged with flexible hydrocarbon chains, which presented somewhat selectivity to the c-MYC G4 possibly by adaptive binding, which then showed clear inhibition on the c-MYC expression rather than other G4-driven oncogenes. Moreover, these novel mols. had the potential to fluorescently label G4s. We believed that this study may shed light on the discovery of new functional small mols. targeting a specific G4 structure.

Bioorganic Chemistry published new progress about Animal gene Role: BSU (Biological Study, Unclassified), PRP (Properties), BIOL (Biological Study) (HRAS). 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

Trzaska, Carole; Amand, Severine; Bailly, Christine; Leroy, Catherine; Marchand, Virginie; Duvernois-Berthet, Evelyne; Saliou, Jean-Michel; Benhabiles, Hana; Werkmeister, Elisabeth; Chassat, Thierry; Guilbert, Romain; Hannebique, David; Mouray, Anthony; Copin, Marie-Christine; Moreau, Pierre-Arthur; Adriaenssens, Eric; Kulozik, Andreas; Westhof, Eric; Tulasne, David; Motorin, Yuri; Rebuffat, Sylvie; Lejeune, Fabrice published the artcile< 2,6-Diaminopurine as a highly potent corrector of UGA nonsense mutations>, Recommanded Product: 7H-Purin-2-amine, the main research area is DAP UGA UAA nonsense mutation potent corrector cancer cell.

Nonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by mols. with nonsense mutation readthrough activity. An extract of the mushroom Lepista inversa has recently shown high-efficiency correction of UGA and UAA nonsense mutations. One active constituent of this extract is 2,6-diaminopurine (DAP). In Calu-6 cancer cells, in which TP53 gene has a UGA nonsense mutation, DAP treatment increases p53 level. It also decreases the growth of tumors arising from Calu-6 cells injected into immunodeficient nude mice. DAP acts by interfering with the activity of a tRNA-specific 2′-O-methyltransferase (FTSJ1) responsible for cytosine 34 modification in tRNATrp. Low-toxicity and high-efficiency UGA nonsense mutation correction make DAP a good candidate for the development of treatments for genetic diseases caused by nonsense mutations.

Nature Communications 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, Recommanded Product: 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem