Category: 452-06-2

Camel, Benjamin R.; Jose, Davis; Meze, Katarina; Dang, Anson; von Hippel, Peter H. published the artcile< Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution>, Electric Literature of 452-06-2, the main research area is DNA binding domain bacteriophage T4 gp32 single nucleotide resolution.

In this study, we use single-stranded DNA (oligo-dT) lattices that have been position-specifically labeled with monomer or dimer 2-aminopurine (2-AP) probes to map the local interactions of the DNA bases with the nucleic acid binding cleft of gp32, the single-stranded binding (ssb) protein of bacteriophage T4. Three complementary spectroscopic approaches are used to characterize these local interactions of the probes with nearby nucleotide bases and amino acid residues at varying levels of effective protein binding cooperativity, as manipulated by changing lattice length. These include: (i) examining local quenching and enhancing effects on the fluorescence spectra of monomer 2-AP probes at each position within the cleft; (ii) using acrylamide as a dynamic-quenching additive to measure solvent access to monomer 2-AP probes at each ssDNA position; and (iii) employing CD spectra to characterize changes in exciton coupling within 2-AP dimer probes at specific ssDNA positions within the protein cleft. The results are interpreted in part by what we know about the topol. of the binding cleft from crystallog. studies of the DNA binding domain of gp32 and provide addnl. insights into how gp32 can manipulate the ssDNA chain at various steps of DNA replication and other processes of genome expression.

Nucleic Acids Research published new progress about Bacteriophage T4 protein Gp32 Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Electric Literature of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Fuechtbauer, Anders F.; Wranne, Moa S.; Sarangamath, Sangamesh; Bood, Mattias; El-Sagheer, Afaf H.; Brown, Tom; Graden, Henrik; Grotli, Morten; Wilhelmsson, L. Marcus published the artcile< Lighting Up DNA with the Environment-Sensitive Bright Adenine Analogue qAN4>, Category: imidazoles-derivatives, the main research area is qAN4 DNA oligonucleotide solid phase synthesis photophys property; DNA; FRET; base pairing; nucleobase analogues; photophysics.

The fluorescent adenine analog qAN4 was recently shown to possess promising photophys. properties, including a high brightness as a monomer. Here we report the synthesis of the phosphoramidite of qAN4 and its successful incorporation into DNA oligonucleotides using standard solid-phase synthesis. CD and thermal melting studies indicate that the qAN4-modification has a stabilizing effect on the B-form of DNA. Moreover, qAN4 base-pairs selectively with thymine with mismatch penalties similar to those of mismatches of adenine. The low energy absorption band of qAN4 inside DNA has its peak around 358 nm and the emission in duplex DNA is partly quenched and blue-shifted (ca. 410 nm), compared to the monomeric form. The spectral properties of the fluorophore also show sensitivity to pH; a property that may find biol. applications. Quantum yields in single-stranded DNA range from 1-29 % and in duplex DNA from 1-7 %. In combination with the absorptive properties, this gives an average brightness inside duplex DNA of 275 M-1 cm-1, more than five times higher than the most used environment-sensitive fluorescent base analog, 2-aminopurine. Finally, we show that qAN4 can be used to advantage as a donor for interbase FRET applications in combination with adenine analog qAnitro as an acceptor.

ChemPlusChem published new progress about Circular dichroism. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Category: imidazoles-derivatives.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

He, Yanping; Chang, Yangyang; Chen, Da; Liu, Juewen published the artcile< Probing Local Folding Allows Robust Metal Sensing Based on a Na+-Specific DNAzyme>, Application of C5H5N5, the main research area is sodium DNAzyme metal sensing probing; DNA; aptamers; biosensors; fluorescence; sodium.

Fluorescent metal sensors based on DNA often rely on changes in end-to-end distance or local environmental near fluorophore labels. Because metal ions can also nonspecifically interact with DNA through various mechanisms, such as charge screening, base binding, and increase or decrease in duplex stability, robust and specific sensing of metal ions has been quite challenging. In this work, a side-by-side comparison of two signaling strategies on a Na+-specific DNAzyme that contained a Na+-binding aptamer was performed. The duplex regions of the DNAzyme was systematically shortened and its effect was studied by using a 2-aminopurine (2AP)-labeled substrate strand. Na+ binding affected the local environmental of the 2AP label and increased its fluorescence. A synergistic process of Na+ binding and forming the duplex on the 5′-end of the enzyme strand was observed, and this end was close to the aptamer loop. The effect on the 3′-end is more continuous, and the stem needs to form first before Na+ can bind. With an optimized substrate binding arm, a FRET-based sensor has been designed by labeling the two ends of a cis form of the DNAzyme with two fluorophores. In this case, Na+ failed to show a distinct difference from that of Li+ or K+; thus indicating that probing changes to the local environment allows more robust sensing of metal ions.

ChemBioChem published new progress about Aptamers. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Application of C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Widom, Julia R.; Hoeher, Janson E. published the artcile< Base-Stacking Heterogeneity in RNA Resolved by Fluorescence-Detected Circular Dichroism Spectroscopy>, Application In Synthesis of 452-06-2, the main research area is .

RNA plays a critical role in many biol. processes, and the structures it adopts are intimately linked to those functions. Among many factors that contribute to RNA folding, van der Waals interactions between adjacent nucleobases stabilize structures in which the bases are stacked on top of one another. Here, we utilize fluorescence-detected CD spectroscopy (FDCD) to investigate base-stacking heterogeneity in RNA labeled with the fluorescent adenine analog 2-aminopurine (2-AP). Comparison of standard (transmission-detected) CD and FDCD spectra reveals that in dinucleotides, 2-AP fluorescence is emitted almost exclusively by unstacked mols. In a trinucleotide, some fluorescence is emitted by a population of stacked and highly quenched mols., but more than half originates from a minor ~10% population of unstacked mols. The combination of FDCD and standard CD measurements reveals the prevalence of stacked and unstacked conformational subpopulations as well as their relative fluorescence quantum yields.

Journal of Physical Chemistry Letters published new progress about 452-06-2. 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

Ishikawa, Ryo; Yasuda, Mizuho; Sasaki, Shogo; Ma, Yue; Nagasawa, Kazuo; Tera, Masayuki published the artcile< Stabilization of telomeric G-quadruplex by ligand binding increases susceptibility to S1 nuclease>, Synthetic Route of 452-06-2, the main research area is stabilization G quadruplex S1 nuclease ligand binding.

The extent of thermodn. stabilization of telomeric G-quadruplex (G4) by isomers of G4 ligand L2H2-6OTD, a telomestatin analog, is inversely correlated with susceptibility to S1 nuclease. L2H2-6OTD facilitated the S1 nuclease activities through the base flipping in G4, unlike the conventional role of G4 ligands which inhibit the protein binding to DNA/RNA upon ligand interactions.

Chemical Communications (Cambridge, United Kingdom) published new progress about Enzyme functional sites, ligand-binding. 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

Liu, Chu-Xiao; Guo, Si-Kun; Nan, Fang; Xu, Yi-Feng; Yang, Li; Chen, Ling-Ling published the artcile< RNA circles with minimized immunogenicity as potent PKR inhibitors>, SDS of cas: 452-06-2, the main research area is RNA immunogenicity PKR inhibitor; PKR; PKR inhibitor; T4 RNA ligase; circular RNA; circular RNA structure; dsRNA; group I intron; immune response; permuted Anabaena pre-tRNA group I intron; phage T4 thymidylate synthase gene.

Exon back-splicing-generated circular RNAs, as a group, can suppress double-stranded RNA (dsRNA)-activated protein kinase R (PKR) in cells. We have sought to synthesize immunogenicity-free, short dsRNA-containing RNA circles as PKR inhibitors. Here, we report that RNA circles synthesized by permuted self-splicing thymidylate synthase (td) introns from T4 bacteriophage or by Anabaena pre-tRNA group I intron could induce an immune response. Autocatalytic splicing introduces ∼74 nt td or ∼186 nt Anabaena extraneous fragments that can distort the folding status of original circular RNAs or form structures themselves to provoke innate immune responses. In contrast, synthesized RNA circles produced by T4 RNA ligase without extraneous fragments exhibit minimized immunogenicity. Importantly, directly ligated circular RNAs that form short dsRNA regions efficiently suppress PKR activation 103- to 106-fold higher than reported chem. compounds C16 and 2-AP, highlighting the future use of circular RNAs as potent inhibitors for diseases related to PKR overreaction.

Molecular Cell published new progress about Anabaena. 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

Novotny, Ales; Novotny, Jan; Kejnovska, Iva; Vorlickova, Michaela; Fiala, Radovan; Marek, Radek published the artcile< Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip>, Category: imidazoles-derivatives, the main research area is homopurine protein motif structural peculiarity.

Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence-structure-stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topol. and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased mol. dynamics simulation. We describe sequence-specific supramol. interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same mol. but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.

Nucleic Acids Research published new progress about Deamination. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Category: imidazoles-derivatives.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Salerno, Domenico; Marrano, Claudia Adriana; Cassina, Valeria; Cristofalo, Matteo; Shao, Qing; Finzi, Laura; Mantegazza, Francesco; Dunlap, David published the artcile< Nanomechanics of negatively supercoiled diaminopurine-substituted DNA>, Related Products of 452-06-2, the main research area is diaminopurine DNA conformation nanomechanics.

Single mol. experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. The particular sequence of a DNA segment defines both base stacking and hydrogen bonding that affect the partitioning and conformations of the two phases. Naturally or artificially modified bases alter H-bonds and base stacking and DNA with diaminopurine (DAP) replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded DAP:T base pairs. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiol. conditions of mild tension and unwinding. This transition avoids writhing and the ease of this transition may prevent cumbersome topol. rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length than B-DNA. However, left-handed DAP-substituted DNA was twice as stiff as unmodified L-DNA. Unmodified DNA and DAP-substituted DNA have very distinct mech. characteristics at physiol. levels of neg. supercoiling and tension.

Nucleic Acids Research published new progress about Electrostatic potential. 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

Kimura, Satoshi; Fujisaka, Aki; Obika, Satoshi published the artcile< Nucleobase derivatives induce in-source decay of oligonucleotides as new matrix-assisted laser desorption/ionization matrices>, Product Details of C5H5N5, the main research area is nucleobase derivative oligonucleotide decay MALDITOF mass spectrometry.

Rationale : For quality control of oligonucleotide therapeutics, accurate and efficient structural characterization using mass spectrometry techniques, such as liquid chromatog./mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), is essential. In MALDI MS anal., matrix selection is critical and a new matrix could enable more efficient and rapid structural anal. Methods : We hypothesized that nucleobase derivatives could act as matrixes more efficiently than the currently used matrixes for oligonucleotides because of structural similarity, which leads to close contact with the analyte. To evaluate their suitability as matrixes, 16 nucleobase derivatives were selected and tested as matrix candidates for oligonucleotide anal. Results : Six of the 16 nucleobase derivatives acted as matrixes for oligonucleotides. Particularly, 6-thioguanine (TG) performed well and induced clear in-source decay fragmentation. When TG or 2-amino-6-chloropurine was used as the matrix, oligonucleotides were ionized, and mainly the w and d fragment ions were observed Conclusions : Herein we demonstrate that a 10-mer RNA or DNA sequence can be successfully characterized using TG as matrix and suggest the possibility of using nucleobase derivatives as novel matrixes in oligonucleotide sequencing.

Rapid Communications in Mass Spectrometry published new progress about DNA Role: ANT (Analyte), BSU (Biological Study, Unclassified), ANST (Analytical Study), BIOL (Biological Study) (6-mer, 10-mer, phosphorothioate 6-mer). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Product Details of C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Xu, Yuancong; Cheng, Nan; Luo, Yunbo; Huang, Kunlun; Chang, Qiaoying; Pang, Guofang; Xu, Wentao published the artcile< An Exo III-assisted catalytic hairpin assembly-based self-fluorescence aptasensor for pesticide detection>, Computed Properties of 452-06-2, the main research area is exonuclease catalytic hairpin assembly fluorescence aptasensor pesticide detection.

This study proposed a self-fluorescence aptasensor (SFA) based on an Exo III-assisted catalytic hairpin assembly (EACHA) for pesticide detection. The aptamer in this sensor can specifically recognize the target due to the favorable biol. binding affinity and also can drive the EACHA by modifying the spatial configuration. EACHA was designed as a cyclic amplification process that improved the rate of reused aptamer beacon fuel, and increased the detection efficiency and sensitivity. The signal was applied using the 2-aminopurine (2AP) mol., the fluorescence of which could be quenched via stacking interaction with the adjacent bases in the beacon. Given its fluorescent properties, this design achieved low background anal. with high sensitivity. Chlorpyrifos was used as a model to explore the SFA proof-of-concept. By replacing the aptamer, this method can be extended to other pesticide mols. Therefore, this study may become a powerful tool for quant. detection of various targets for different purposes.

Sensors and Actuators, B: Chemical published new progress about Aptasensors. 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