Day: November 21, 2022

Hong, In Seok published the artcileSequence selective tagging of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) using PNAs, Computed Properties of 186046-81-1, the publication is Bioorganic & Medicinal Chemistry Letters (2015), 25(21), 4918-4921, database is CAplus and MEDLINE.

8-Oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) is a commonly formed DNA lesion that is useful as a biomarker for oxidative stress. Methods for detecting 8-oxodGuo at specific positions within DNA could be useful for correlating DNA damage with mutational hotspots and repair enzyme accessibility. We describe a method for covalently linking (‘tagging’) peptide nucleic acids (PNAs) containing terminal nucleophiles under oxidative conditions to 8-oxodGuo at specific sites within DNA. Several nucleophiles were examined and the ε-amine of lysine was selected for further studies. As little as 10 fmol of 8-oxodGuo were detected by gel shift using ³²P-labeled target DNA and no tagging of dG at the same site or 8-oxodGuo at a distal site was detected when potassium ferricyanide was used as oxidant in substrates as long as 221 bp.

Bioorganic & Medicinal Chemistry Letters 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, Computed Properties of 186046-81-1.

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

Hong, In Seok published the artcileSequence selective tagging of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) using PNAs, 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 Bioorganic & Medicinal Chemistry Letters (2015), 25(21), 4918-4921, database is CAplus and MEDLINE.

8-Oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) is a commonly formed DNA lesion that is useful as a biomarker for oxidative stress. Methods for detecting 8-oxodGuo at specific positions within DNA could be useful for correlating DNA damage with mutational hotspots and repair enzyme accessibility. We describe a method for covalently linking (‘tagging’) peptide nucleic acids (PNAs) containing terminal nucleophiles under oxidative conditions to 8-oxodGuo at specific sites within DNA. Several nucleophiles were examined and the ε-amine of lysine was selected for further studies. As little as 10 fmol of 8-oxodGuo were detected by gel shift using ³²P-labeled target DNA and no tagging of dG at the same site or 8-oxodGuo at a distal site was detected when potassium ferricyanide was used as oxidant in substrates as long as 221 bp.

Bioorganic & Medicinal 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

Taehtinen, Ville published the artcile¹⁹F NMR Spectroscopic Analysis of the Binding Modes in Triple-Helical Peptide Nucleic Acid (PNA)/MicroRNA Complexes, 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 Chemistry – A European Journal (2017), 23(29), 7113-7124, database is CAplus and MEDLINE.

Triplex-forming peptide nucleic acids (TFPNAs) were targeted to double-helical regions of ¹⁹F-labeled RNA hairpin models (a UA-rich duplex with a hexaethylene glycol (heg) loop and a microRNA model, miR-215). In addition to conventional UV- and CD (CD)-based detection, binding was monitored by ¹⁹F NMR spectroscopy. Detailed information on the stoichiometry and transition between the triple-helical peptide nucleic acid (PNA)/RNA and (PNA)₂/RNA binding modes could be obtained. γ-(R)-Hydroxymethyl-modified thymine-1-yl- and 2-aminopyridin-3-yl-acetyl derivatives of TFPNAs were addnl. synthesized, which were targeted to the same RNA models, and the effect of the γ-(R)-hydroxymethyl group on binding was studied. An appropriate pattern of γ-(R)-hydroxymethyl modifications reduced the stability of the ternary complex and preferred stoichiometric binding to the miR-215 model.

Chemistry – A European Journal 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 C15H21BO2, 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

Smets, J. published the artcileFT-IR spectroscopic study of uracil derivatives and their hydrogen-bonded complexes with model proton donors. Part 5. Complexes of uracils with hydrogen chloride in argon matrixes, Recommanded Product: 3-Methylpyrimidine-2,4(1H,3H)-dione, the publication is Journal of Molecular Structure (1994), 318(1-3), 37-53, database is CAplus.

FT-IR spectra are reported for uracils complexed with hydrogen chloride in Ar matrixes. The spectral characteristics demonstrate that uracils form a C₄:O···H-Cl hydrogen bond of intermediate strength in Ar matrixes. The large shift of the proton donor mode ν_s finds support in the vibration correlation diagram for O-base.HCl complexes. For some of the bases a small amount of the C₂:O···HCl species is identified in matrixes containing an excess of HCl. H-bonding of the C:S group plays only a minor role in thiouracils. For all the bases studied here, N-H···Cl-H structures are also identified from the shifts of the uracil N-H modes. The results allow the discussion of particular bonding trends for the basic groups in uracils, these trends being largely consistent with earlier reported results for complexes of uracils with other proton donors.

Journal of Molecular Structure published new progress about 608-34-4. 608-34-4 belongs to pyrimidines, auxiliary class Pyrimidine,Amide, name is 3-Methylpyrimidine-2,4(1H,3H)-dione, and the molecular formula is C14H10O4, Recommanded Product: 3-Methylpyrimidine-2,4(1H,3H)-dione.

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

Herbich, Jerzy published the artcileDual fluorescence of 4-(dialkylamino)pyrimidines. Twisted intramolecular charge transfer state formation favored by hydrogen bond or by coordination to the metal ion, Quality Control of 31401-45-3, the publication is Journal of Physical Chemistry (1989), 93(9), 3439-44, database is CAplus.

4-(N,N-Dimethylamino)pyrimidine did not exhibit any markedly dual luminescence even in highly polar (aprotic) solvents, unless the ortho substituent deviated the NMe₂ group from coplanarity with the ring. Protic solvents or complexation with Zn²⁺ caused the longwave fluorescence to appear distinctly. 4-(N,N-Diethylamino)pyrimidine revealed dual luminescence in sufficiently polar (aprotic) environment. In alc. solutions the intensity of the fluorescence was reduced. Fluorescence properties of this group of compounds fit the twisted intermol. charge transfer model. The importance of nonradiative deactivation increases with the H⁺-donating ability of the solvent.

Journal of Physical Chemistry 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 C6H9N3, Quality Control of 31401-45-3.

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

Rothlingshofer, Manuel published the artcileNucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response, Formula: C39H35N5O8, the publication is Journal of the American Chemical Society (2011), 133(45), 18110-18113, database is CAplus and MEDLINE.

The photocleavage of a nitrobenzyl-type linker (NPPOC) at 405 nm wavelength was enabled by nucleic acid-templated energy transfer from a sensitizer (thioxanthenone) to the linker. This strategy was used to release profluorescent rhodamine, which facilitated monitoring of the reaction via fluorescence measurement in a nonoverlapping window with the sensitizer/photocleavage reaction. The rate acceleration of the templated reaction was greater than 20-fold over the background reaction. The templated reaction was used in conjunction with strand displacement to design four-component systems that responded to an analyte (DNA). Programming a specific hierarchical relationship among the four components enabled the design of a system that responded first pos. and then neg. to increasing levels of an analyte.

Journal of the American Chemical Society 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, Formula: C39H35N5O8.

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

Rothlingshofer, Manuel published the artcileNucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response, Application In Synthesis of 169396-92-3, the publication is Journal of the American Chemical Society (2011), 133(45), 18110-18113, database is CAplus and MEDLINE.

The photocleavage of a nitrobenzyl-type linker (NPPOC) at 405 nm wavelength was enabled by nucleic acid-templated energy transfer from a sensitizer (thioxanthenone) to the linker. This strategy was used to release profluorescent rhodamine, which facilitated monitoring of the reaction via fluorescence measurement in a nonoverlapping window with the sensitizer/photocleavage reaction. The rate acceleration of the templated reaction was greater than 20-fold over the background reaction. The templated reaction was used in conjunction with strand displacement to design four-component systems that responded to an analyte (DNA). Programming a specific hierarchical relationship among the four components enabled the design of a system that responded first pos. and then neg. to increasing levels of an analyte.

Journal of the American Chemical Society 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 In Synthesis of 169396-92-3.

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

Pianowski, Zbigniew published the artcileImaging of mRNA in Live Cells Using Nucleic Acid-Templated Reduction of Azidorhodamine Probes, Name: 2-(4-((tert-Butoxycarbonyl)amino)-2-oxopyrimidin-1(2H)-yl)acetic acid, the publication is Journal of the American Chemical Society (2009), 131(18), 6492-6497, database is CAplus and MEDLINE.

Nucleic acid-templated reactions leading to a fluorescent product represent an attractive strategy for the detection and imaging of cellular nucleic acids. Herein we report the use of a Staudinger reaction to promote the reduction of profluorescent azidorhodamine. The use of two cell-permeable GPNA probes, one labeled with the profluorescent azidorhodamine and the other with trialkylphosphine, enabled the detection of the mRNA encoding O-6-methylguanine-DNA methyltransferase in intact cells.

Journal of the American Chemical Society published new progress about 172405-16-2. 172405-16-2 belongs to pyrimidines, auxiliary class Pyrimidine,Carboxylic acid,Amine,Amide, name is 2-(4-((tert-Butoxycarbonyl)amino)-2-oxopyrimidin-1(2H)-yl)acetic acid, and the molecular formula is C11H15N3O5, Name: 2-(4-((tert-Butoxycarbonyl)amino)-2-oxopyrimidin-1(2H)-yl)acetic acid.

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

Huang, Kuo-Ting published the artcileCombinatorial Self-Assembly of Glycan Fragments into Microarrays, Synthetic Route of 186046-81-1, the publication is ChemBioChem (2011), 12(1), 56-60, database is CAplus and MEDLINE.

We have demonstrated that complex glycan arrays can be accessed through the combinatorial self assembly of PNA-encoded carbohydrate fragments. Although the use of DNA microarrays to sort carbohydrate-DNA conjugates had previously been reported, previous efforts were restricted to monosaccharides and did not explore a broad range of glycan structures, nor their combinatorial assembly. The cooperativity of the fragments in their interaction with carbohydrate-binding proteins was demonstrated with two different lectins. The binding profile showed the strongest interaction for discrete combinations of two fragments. Importantly, the PNA-tagged glycans can be readily prepared from native oligosaccharides obtained from natural or com. sources by conversion of the anomeric position into a thiol on a mg scale by a two- to three-step process. The simplicity of the protocols described should make glycan arrays more broadly accessible. Immobilization of glycans by hybridization offers a reliable approach by which to obtain a homogeneous distribution of ligands within a microarray spot and allows the use of microarrays with higher d. than accessible by contact printing, which is currently the standard practice. Last but not least, combinatorial self assembly of fragments on DNA microarrays should be broadly applicable beyond the glycan fragments described here.

ChemBioChem 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, Synthetic Route of 186046-81-1.

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

Huang, Kuo-Ting published the artcileCombinatorial Self-Assembly of Glycan Fragments into Microarrays, COA of Formula: C26H26N4O7, the publication is ChemBioChem (2011), 12(1), 56-60, database is CAplus and MEDLINE.

We have demonstrated that complex glycan arrays can be accessed through the combinatorial self assembly of PNA-encoded carbohydrate fragments. Although the use of DNA microarrays to sort carbohydrate-DNA conjugates had previously been reported, previous efforts were restricted to monosaccharides and did not explore a broad range of glycan structures, nor their combinatorial assembly. The cooperativity of the fragments in their interaction with carbohydrate-binding proteins was demonstrated with two different lectins. The binding profile showed the strongest interaction for discrete combinations of two fragments. Importantly, the PNA-tagged glycans can be readily prepared from native oligosaccharides obtained from natural or com. sources by conversion of the anomeric position into a thiol on a mg scale by a two- to three-step process. The simplicity of the protocols described should make glycan arrays more broadly accessible. Immobilization of glycans by hybridization offers a reliable approach by which to obtain a homogeneous distribution of ligands within a microarray spot and allows the use of microarrays with higher d. than accessible by contact printing, which is currently the standard practice. Last but not least, combinatorial self assembly of fragments on DNA microarrays should be broadly applicable beyond the glycan fragments described here.

ChemBioChem 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, COA of Formula: C26H26N4O7.

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