Day: November 21, 2022

Cheng, Yuan published the artcileSupramolecular structures constructed by 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-dimethylprop-2-yn-1-ol monohydrate and 3-[2-amino-6-(3-hydroxy-3,3-dimethylprop-1-yn-1-yl)pyrimidin-4-yl]-1,1-dimethylprop-2-yn-1-ol, Safety of 2-Amino-4,6-dichloropyrimidine, the publication is Acta Crystallographica, Section C: Crystal Structure Communications (2011), 67(7), o244-o248, database is CAplus and MEDLINE.

The mol. of 3-(2-amino-6-chloropyrimidin-4-yl)-1,1-dimethylprop-2-yn-1-ol monohydrate, C₉H₁₀ClN₃O·H₂O, (I), shows a very polarized mol.-electronic structure, while the polarization is slight for 3-[2-amino-6-(3-hydroxy-3,3-dimethylprop-1-yn-1-yl)pyrimidin-4-yl]-1,1-dimethylprop-2-yn-1-ol, C₁₄H₁₇N₃O₂, (II). In the supramol. structure of (I), a combination of hard N-H…N H bonds and soft C-H…N H bonds creates a mol. column. Aromatic π-π stackings between the pyrimidine rings stabilize the column with perpendicular and centroid-centroid distances of 3.283(3) and 3.588(1) Å, resp. Short Cl…Cl contacts further link neighboring mol. columns, creating a hydrophilic tube in which H₂O mols. are fixed by various H bonds. In the packing of (II), a 1-dimensional mol. chain is formed through several contacts involving hard N-H…O(N) and O-H…O(N) and soft C-H…O H bonds. Interchain O-H…O H bonds link the chains giving a two-dimensional stepped network. It is anticipated that study of the influence of H bonding on the patterns of base pairing and mol. packing in aminopyrimidine structures will shed significant light on nucleic acid structures as well as their functions. Crystallog. data are given.

Acta Crystallographica, Section C: Crystal Structure Communications published new progress about 56-05-3. 56-05-3 belongs to pyrimidines, auxiliary class Pyrimidine,Chloride,Amine,API, name is 2-Amino-4,6-dichloropyrimidine, and the molecular formula is C4H3Cl2N3, Safety of 2-Amino-4,6-dichloropyrimidine.

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, HPLC of Formula: 186046-81-1, 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 186046-81-1. 186046-81-1 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Benzene,Amide,Others,PNA,, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(4-(((benzhydryloxy)carbonyl)amino)-2-oxopyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C6H6N2O, HPLC of Formula: 186046-81-1.

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

Gorai, Ananta published the artcileThiazole Containing PNA Mimic Regulates c-MYC Gene Expression through DNA G-Quadruplex, Application In Synthesis of 186046-81-1, the publication is Bioconjugate Chemistry (2022), 33(6), 1145-1155, database is CAplus and MEDLINE.

Peptide nucleic acids (PNAs), besides hybridization to complementary DNA and RNAs, bind and stabilize DNA secondary structures. Herein, we illustrate the design and synthesis of PNA like scaffolds by incorporating five membered thiazole rings as modified bases instead of nucleobases and their subsequent effects on gene regulation by biophys. and in vitro assays. A thiazole modified PNA trimer selectively recognizes c-MYC G-quadruplex (G4) DNA over other G4s and duplex DNA. It displays high stabilization potential for the c-MYC G4 DNA and shows remarkable fluorescence enhancement with the c-MYC G4. It is flexible enough to bind at 5′ and 3′ ends as well as in the groove region of c-MYC G4. Furthermore, the PNA trimer easily permeates cellular membrane and suppresses c-MYC mRNA expression in HeLa cells by targeting the promoter G4. This study illuminates modified PNAs as flexible mol. tools for selective targeting of noncanonical nucleic acids and modulating gene function.

Bioconjugate Chemistry published new progress about 186046-81-1. 186046-81-1 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Benzene,Amide,Others,PNA,, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(4-(((benzhydryloxy)carbonyl)amino)-2-oxopyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C39H35N5O8, Application In Synthesis of 186046-81-1.

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

Odell, Luke R. published the artcilePyrimidyn-Based Dynamin Inhibitors as Novel Cytotoxic Agents, COA of Formula: C4H3Cl2N3, the publication is ChemMedChem (2022), 17(1), e202100560, database is CAplus and MEDLINE.

Five focused libraries of pyrimidine-based dynamin GTPase inhibitors, in total 69 compounds were synthesized, and their dynamin inhibition and broad-spectrum cytotoxicity examined Dynamin plays a crucial role in mitosis, and as such inhibition of dynamin was expected to broadly correlate with the observed cytotoxicity. The pyrimidines synthesized ranged from mono-substituted to trisubstituted. The highest levels of dynamin inhibition were noted with di- and tri- substituted pyrimidines, especially those with pendent amino alkyl chains. Short chains and simple heterocyclic rings reduced dynamin activity. There were three levels of dynamin activity noted: 1-10, 10-25 and 25-60 μM. Screening of these compounds in a panel of cancer cell lines: SW480 (colon), HT29 (colon), SMA (spontaneous murine astrocytoma), MCF-7 (breast), BE2-C (glioblastoma), SJ-G2 (neuroblastoma), MIA (pancreas), A2780 (ovarian), A431 (skin), H460 (lung), U87 (glioblastoma) and DU145 (prostate) cell lines reveal a good correlation between the observed dynamin inhibition and the observed cytotoxicity. The most active analogs (31 a,b) developed returned average GI₅₀ values of 1.0 and 0.78 μM across the twelve cell lines examined These active analogs were: N²-(3-dimethylaminopropyl)-N⁴-dodecyl-6-methylpyrimidine-2,4-diamine (31 a) and N⁴-(3-dimethylaminopropyl)-N²-dodecyl-6-methylpyrimidine-2,4-diamine (31 b).

ChemMedChem published new progress about 56-05-3. 56-05-3 belongs to pyrimidines, auxiliary class Pyrimidine,Chloride,Amine,API, name is 2-Amino-4,6-dichloropyrimidine, and the molecular formula is C4H3Cl2N3, COA of Formula: C4H3Cl2N3.

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, Name: 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(4-(((benzhydryloxy)carbonyl)amino)-2-oxopyrimidin-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 186046-81-1. 186046-81-1 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Benzene,Amide,Others,PNA,, name is 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(4-(((benzhydryloxy)carbonyl)amino)-2-oxopyrimidin-1(2H)-yl)acetamido)acetic acid, and the molecular formula is C39H35N5O8, Name: 2-(N-(2-((((9H-Fluoren-9-yl)methoxy)carbonyl)amino)ethyl)-2-(4-(((benzhydryloxy)carbonyl)amino)-2-oxopyrimidin-1(2H)-yl)acetamido)acetic acid.

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

Tessier, Romain published the artcile“Doubly Orthogonal” Labeling of Peptides and Proteins, Quality Control of 5738-14-7, the publication is Chem (2019), 5(8), 2243-2263, database is CAplus.

Herein, we report a cysteine bioconjugation methodol. for the introduction of hypervalent iodine compounds onto biomols. Ethynylbenziodoxolones (EBXs) engage thiols in small organic mols. and cysteine-containing peptides and proteins in a fast and selective addition onto the alkynyl triple bond, resulting in stable vinylbenziodoxolone hypervalent iodine conjugates. The conjugation occurs at room temperature in an open flask under physiol. conditions. The use of an azide-bearing EBX reagent enables a “doubly orthogonal” functionalization of the bioconjugate via strain-release-driven cycloaddition and Suzuki-Miyaura cross-coupling of the vinyl hypervalent iodine bond. We successfully applied the methodol. on relevant and complex biomols., such as histone proteins. Through single-mol. experiments, we illustrated the potential of this doubly reactive bioconjugate by introducing a triplet-state quencher close to a fluorophore, which extended its lifetime by suppressing photobleaching. This work is therefore expected to find broad applications for peptide and protein functionalization.

Chem published new progress about 5738-14-7. 5738-14-7 belongs to pyrimidines, auxiliary class Pyrimidine,Amine,Alcohol,Pyrimidine, name is 2-(Dimethylamino)pyrimidine-4,6-diol, and the molecular formula is C3H6O2, Quality Control of 5738-14-7.

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

Tessier, Romain published the artcile“Doubly Orthogonal” Labeling of Peptides and Proteins, Formula: C4H3Cl2N3, the publication is Chem (2019), 5(8), 2243-2263, database is CAplus.

Herein, we report a cysteine bioconjugation methodol. for the introduction of hypervalent iodine compounds onto biomols. Ethynylbenziodoxolones (EBXs) engage thiols in small organic mols. and cysteine-containing peptides and proteins in a fast and selective addition onto the alkynyl triple bond, resulting in stable vinylbenziodoxolone hypervalent iodine conjugates. The conjugation occurs at room temperature in an open flask under physiol. conditions. The use of an azide-bearing EBX reagent enables a “doubly orthogonal” functionalization of the bioconjugate via strain-release-driven cycloaddition and Suzuki-Miyaura cross-coupling of the vinyl hypervalent iodine bond. We successfully applied the methodol. on relevant and complex biomols., such as histone proteins. Through single-mol. experiments, we illustrated the potential of this doubly reactive bioconjugate by introducing a triplet-state quencher close to a fluorophore, which extended its lifetime by suppressing photobleaching. This work is therefore expected to find broad applications for peptide and protein functionalization.

Chem published new progress about 56-05-3. 56-05-3 belongs to pyrimidines, auxiliary class Pyrimidine,Chloride,Amine,API, name is 2-Amino-4,6-dichloropyrimidine, and the molecular formula is C10H2F12NiO4, Formula: C4H3Cl2N3.

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

Segado, Mireia published the artcileUnderstanding the differences in photochemical properties of substituted aminopyrimidines, Product Details of C6H9N3, the publication is Theoretical Chemistry Accounts (2011), 128(4-6), 713-725, database is CAplus.

The luminescent patterns of several members of the aminopyrimidine family are very different, showing not fluorescence at all, only a fluorescence band, normal or anomalous, or dual fluorescence, depending on the substituents and on the environment (gas phase vs. polar solvents). The authors study the lowest excited states of several members of this family that exhibit different fluorescence patterns to try to explain their photochem. and to understand the effect of the substituents and the environment. Several excited states (local excited (LE), charge transfer (CT) and n _N-π^* states) have min. on the lowest excited potential energy surface (S₁), being their relative energy the determinant factor of the luminescent behavior. If the more stable S₁ min. are of n _N-π^* character, a nonradiative deexcitation channel is the most efficient and the system shows no fluorescence. If the CT and/or LE states are the most stable, the nonradiative deactivation channel is not accessible and the system fluoresces. The relative energies of the CT and LE min. (affected by substituents and by the presence of a polar solvent) and the different magnitude of the oscillator strength for the radiative transition to the ground state determine which emission is more efficient, giving place to normal, anomalous or dual fluorescence. The study was carried out by CASSCF/CASPT2 computations, including the solvent effect by the PCM model.

Theoretical Chemistry Accounts published new progress about 31401-45-3. 31401-45-3 belongs to pyrimidines, auxiliary class Pyrimidine,Amine, name is N,N-Dimethylpyrimidin-4-amine, and the molecular formula is C9H21NO3, Product Details of C6H9N3.

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