Tag: M.W=500-550

Zengeya, Thomas published the artcileTriple-Helical Recognition of RNA Using 2-Aminopyridine-Modified PNA at Physiologically Relevant Conditions, COA of Formula: C26H26N4O7, the publication is Angewandte Chemie, International Edition (2012), 51(50), 12593-12596, database is CAplus and MEDLINE.

It was recently proposed that biol. relevant double-stranded RNAs (dsRNAs) could be recognized by major groove-binding peptide nucleic acids (PNAs), resulting in triple-helix formation. The present work demonstrates that sequence-selective recognition of duplex RNA can be achieved under physiol. relevant conditions by PNAs containing 2-aminopyridine (M). After preliminary studies that confirmed the binding of M-modified PNAs to RNA hairpin structures, pri-miRNA-215 was selected as an example of a biol. relevant RNA duplex for binding studies with M-modified PNA. Using an RNA hairpin model that contains the purine-rich recognition site present in pri-miRNA-215, it was shown that a PNA containing three M bases recognized the model hairpin with high affinity and 1:1 stoichiometry.

Angewandte Chemie, International Edition published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C12H10F2Si, COA of Formula: C26H26N4O7.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Chu, Te-Wei published the artcileHybrid polymeric hydrogels via peptide nucleic acid (PNA)/DNA complexation, Related Products of pyrimidines, the publication is Journal of Controlled Release (2015), 220(Part_B), 608-616, database is CAplus and MEDLINE.

This work presents a new concept in hybrid hydrogel design. Synthetic water-soluble N-(2-hydroxypropyl)methacrylamide (HPMA) polymers grafted with multiple peptide nucleic acids (PNAs) are crosslinked upon addition of the linker DNA. The self-assembly is mediated by the PNA-DNA complexation, which results in the formation of hydrophilic polymer networks. We show that the hydrogels can be produced through two different types of complexations. Type I hydrogel is formed via the PNA/DNA double-helix hybridization. Type II hydrogel utilizes a unique “P-form” oligonucleotide triple-helix that comprises two PNA sequences and one DNA. Microrheol. studies confirm the resp. gelation processes and disclose a higher critical gelation concentration for the type I gel when compared to the type II design. SEM reveals the interconnected microporous structure of both types of hydrogels. Type I double-helix hydrogel exhibits larger pore sizes than type II triple-helix gel. The latter apparently contains denser structure and displays greater elasticity as well. The designed hybrid hydrogels have potential as novel biomaterials for pharmaceutical and biomedical applications.

Journal of Controlled Release published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, Related Products of pyrimidines.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Agramunt, Jordi published the artcileInverse Electron-Demand Diels-Alder Bioconjugation Reactions Using 7-Oxanorbornenes as Dienophiles, Formula: C26H26N4O7, the publication is Journal of Organic Chemistry (2020), 85(10), 6593-6604, database is CAplus and MEDLINE.

Oligonucleotides, peptides, and peptide nucleic acids incorporating 7-oxanorbornene as a dienophile were reacted with tetrazines linked to either a peptide, D-biotin, BODIPY, or N-acetyl-D-galactosamine. The inverse electron-demand Diels-Alder (IEDDA) cycloaddition, which was performed overnight at 37°C, in all cases furnished the target conjugate in good yields. IEDDA reactions with 7-oxanorbornenes produce a lower number of stereoisomers than that of IEDDA cycloadditions with other dienophiles.

Journal of Organic Chemistry published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, Formula: C26H26N4O7.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Alguacil, Javier published the artcileA Straightforward Preparation of Aminoglycoside-Dinucleotide and -diPNA Conjugates via Click Ligation Assisted by Microwaves, Synthetic Route of 169396-92-3, the publication is European Journal of Organic Chemistry (2010), 3102-3109, S3102/1-S3102/30, database is CAplus.

An alternative and straightforward method to prepare aminoglycoside-dinucleotide and -diPNA conjugates is reported, which is based on copper-catalyzed Huisgen azide-alkyne cycloaddition (“click chem.” ligation) assisted by microwave irradiation This method permitted conjugations to be performed in aqueous solution, in very short times and with readily prepared precursors.

European Journal of Organic Chemistry published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, Synthetic Route of 169396-92-3.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Das, Indrajit published the artcileA Peptide Nucleic Acid-Amino-Sugar Conjugate Targeting Transactivation Response Element of HIV-1 RNA Genome Shows a High Bioavailability in Human Cells and Strongly Inhibits Tat-Mediated Transactivation of HIV-1 Transcription, Category: pyrimidines, the publication is Journal of Medicinal Chemistry (2012), 55(13), 6021-6032, database is CAplus and MEDLINE.

The 6-aminoglucosamine ring of the aminoglycoside antibiotic neomycin B (ring II) was conjugated to a 16-mer peptide nucleic acid (PNA) targeting HIV-1 TAR RNA. For this purpose, we prepared the aminoglucosamine monomer I and attached it to the protected PNA prior to its cleavage from the solid support. We found that the resulting PNA-aminoglucosamine conjugate is stable under acidic conditions, efficiently taken up by the human cells and fairly distributed in both cytosol and nucleus without endosomal entrapment because co-treatment with endosome-disrupting agent had no effect on its cellular distribution. The conjugate displayed very high target specificity in vitro and strongly inhibited Tat mediated transactivation of HIV-1 LTR transcription in a cell culture system. The unique properties of this new class of PNA conjugate suggest it to be a potential candidate for therapeutic application.

Journal of Medicinal Chemistry published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, Category: pyrimidines.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Brun, Omar published the artcileOn-Resin Conjugation of Diene-Polyamides and Maleimides via Diels-Alder Cycloaddition, Synthetic Route of 169396-92-3, the publication is Journal of Organic Chemistry (2015), 80(12), 6093-6101, database is CAplus and MEDLINE.

The reaction between maleimides and resin-bound diene-polyamides (polyamides are represented by peptides and peptide nucleic acids or PNAs) allows the latter to be used in the preparation of conjugates. Conjugation takes place by reacting the insoluble, hydrophobic diene component either with water-soluble dienophiles or with dienophiles requiring mixtures of water and organic solvents. Exptl. conditions can be adjusted to furnish the target conjugate in good yield with no need of adding large excesses of soluble reagent. In case protected maleimides are used, maleimide deprotection and Diels-Alder cycloaddition can be simultaneously carried out to render conjugates with different linking positions. On-resin conjugation is followed by an acidic treatment that removes the polyamide protecting groups with no harm to the cycloadduct, in contrast with the unreacted diene that is indeed degraded under these conditions. Cycloadducts incorporating suitable functional groups can undergo subsequent addnl. conjugation reactions in solution to furnish double conjugates.

Journal of Organic Chemistry published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, Synthetic Route of 169396-92-3.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Markus, Tal Z. published the artcileThe Capture of Low-Energy Electrons by PNA versus DNA, Recommanded Product: 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, the publication is Journal of Physical Chemistry Letters (2013), 4(19), 3298-3302, database is CAplus.

This study provides insight into the mechanism of capturing low energy electrons by peptide nucleic acid (PNA) and the role of the oligonucleotide backbone in the capture of low energy electrons. We studied by photoemission self-assembled monolayers of two types of oligonucleotides, DNA and PNA. PNA is a synthetic analog of DNA that has a pseudopeptide backbone and which may have important medical and biotechnol. applications. We found that in both PNA and DNA, the guanine nucleobases capture the electrons more efficiently than thymines. In PNA, once the electrons are captured, their state is at least partially localized on the nucleobases, and the PNA mol. undergoes structural changes that stabilize the electron. This situation is in contrast to DNA, in which the captured electrons are transferred very efficiently to the backbone, and the final state of captured electron is base independent.

Journal of Physical Chemistry Letters published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, Recommanded Product: 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Li, Chengxi published the artcileAutomated Flow Synthesis of Peptide-PNA Conjugates, HPLC of Formula: 169396-92-3, the publication is ACS Central Science (2022), 8(2), 205-213, database is CAplus and MEDLINE.

Antisense peptide nucleic acids (PNAs) have yet to translate to the clinic because of poor cellular uptake, limited solubility, and rapid elimination. Cell-penetrating peptides (CPPs) covalently attached to PNAs may facilitate clin. development by improving uptake into cells. We report an efficient technol. that utilizes a fully automated fast-flow instrument to manufacture CPP-conjugated PNAs (PPNAs) in a single shot. The machine is rapid, with each amide bond being formed in 10 s. Anti-IVS2-654 PPNA synthesized with this instrument presented threefold activity compared to transfected PNA in a splice-correction assay. We demonstrated the utility of this approach by chem. synthesizing eight anti-SARS-CoV-2 PPNAs in 1 day. A PPNA targeting the 5′ untranslated region of SARS-CoV-2 genomic RNA reduced the viral titer by over 95% in a live virus infection assay (IC₅₀ = 0.8 μM). Our technol. can deliver PPNA candidates to further investigate their potential as antiviral agents.

ACS Central Science published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, HPLC of Formula: 169396-92-3.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Fang, Ge-min published the artcileA bright FIT-PNA hybridization probe for the hybridization state specific analysis of a CU RNA edit via FRET in a binary system, Application of 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, the publication is Chemical Science (2018), 9(21), 4794-4800, database is CAplus and MEDLINE.

Given the length required for uniqueness of the targeted segment, the commonly used probes do not provide the level of sequence specificity needed to discriminate single base mismatched hybridization. Herein we introduce a binary probe system based on fluorescence resonance energy transfer (FRET) that distinguishes three possible states i.e. (i) absence of target, (ii) presence of edited (matched) and (iii) unedited (single base mismatched) target. To address the shortcomings of read-out via FRET, we designed donor probes that avoid bleed through into the acceptor channel and nevertheless provide a high intensity of FRET signaling. We show the combined use of thiazole orange (TO) and an oxazolopyridine analog (JO), linked as base surrogates in modified PNA FIT-probes that serve as FRET donor for a second, near-IR (NIR)-labeled strand. In absence of target, donor emission is low and FRET cannot occur in lieu of the lacking co-alignment of probes. Hybridization of the TO/JO-PNA FIT-probe with the (unedited RNA) target leads to high brightness of emission at 540 nm. Co-alignment of the NIR-acceptor strand ensues from recognition of edited RNA inducing emission at 690 nm. We show imaging of mRNA in fixed and live cells and discuss the homogeneous detection and intracellular imaging of a single nucleotide mRNA edit used by nature to post-transcriptionally modify the function of the Glycine Receptor (GlyR).

Chemical Science published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C26H26N4O7, Application of 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia

Sethi, Dalip published the artcileFluorescent Peptide-PNA Chimeras for Imaging Monoamine Oxidase A mRNA in Neuronal Cells, Application In Synthesis of 169396-92-3, the publication is Bioconjugate Chemistry (2012), 23(2), 158-163, database is CAplus and MEDLINE.

Monoamine oxidases (MAO) catalyze the oxidative deamination of many biogenic amines and are integral proteins found in the mitochondrial outer membrane. Changes in MAO-A levels are associated with depression, trait aggression, and addiction. Here we report the synthesis, characterization, and in vitro evaluation of novel fluorescent peptide-peptide nucleic acid (PNA) chimeras for MAOA mRNA imaging in live neuronal cells. The probes were designed to include MAOA-specific PNA dodecamers, separated by an N-terminal spacer to a μ-opioid receptor targeting peptide (DAMGO), with a spacer and a fluorophore on the C-terminus. The probe was successfully delivered into human SH-SY5Y neuroblastoma cells through μ-opioid receptor-mediated endocytosis. The K_d by flow cytometry was 11.6±0.8 nM. Uptake studies by fluorescence microscopy showed ∼5-fold higher signal in human SH-SY5Y neuroblastoma cells than in neg. control CHO-K1 cells that lack μ-opioid receptors. Moreover, a peptide-mismatch control sequence showed no significant uptake in SH-SY5Y cells. Such mRNA imaging agents with near-IR fluorophores might enable real time imaging and quantitation of neuronal mRNAs in live animal models.

Bioconjugate Chemistry published new progress about 169396-92-3. 169396-92-3 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide,Others,PNA, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C7H5Cl2NO, Application In Synthesis of 169396-92-3.

Referemce:
https://pubchem.ncbi.nlm.nih.gov/compound/Pyrimidine,
Pyrimidine – Wikipedia