Tag: M.W=500-550

Shemesh, Yossi published the artcilePNA-Rose Bengal Conjugates as Efficient DNA Photomodulators, HPLC of Formula: 169396-92-3, the publication is Bioconjugate Chemistry (2015), 26(9), 1916-1922, database is CAplus and MEDLINE.

Selective photoinduced modulation of DNA may provide a powerful therapeutic tool allowing spatial and temporal control of the photochem. reaction. We have explored the photoreactivity of peptide nucleic acid (PNA) conjugates that were conjugated to a highly potent photosensitizer, Rose Bengal (RB). In addition, a short PEGylated peptide (K-PEG₈-K) was conjugated to the C-terminus of the PNA to improve its water solubility A short irradiation (visible light) of PNA conjugates with a synthetic DNA resulted in highly efficient photomodulation of the DNA as evidenced by polyacrylamide gel electrophoresis (PAGE). In addition, a PNA-RB conjugate replacing K-PEG₈-K with four L-glutamic acids (E₄) was found to be photoinactive. Irradiation of active PNA-RB conjugates with synthetic DNA in D₂0 augments the photoactivity; supporting the involvement of singlet oxygen. PAGE, HPLC, and MALDI-TOF analyses indicate that PNA-DNA photo-crosslinking is a significant pathway in the observed photoreactivity. Selective photo-crosslinking of such PNA-RB conjugates may be a novel approach to selective photodynamic therapy (sPDT) as such mols. would be sequence-specific, cell-permeable, and photoactivated in the visible region.

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 C16H18O4, HPLC of Formula: 169396-92-3.

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

Alpturk, Onur published the artcileOptimization of synthetic route to PNA-T-OH monomers, Name: 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 the Turkish Chemical Society, Section A: Chemistry (2018), 5(2), 457-468, database is CAplus.

Peptide nucleic acids are synthetic mols. crafted to mimic natural nucleic acids, and thus, they are widely utilized in many chem., and, biomedical applications. Although there exist many approaches to synthesize monomers to date, there is still room to improve these methodologies. With this motivation, we compared some widely utilized synthetic routes to obtain N-Boc-PNA-T-OH, and N-Fmoc-PNA-T-OH (Fmoc = 9-fluorenyl-methoxycarbonyl). Our results indicate that N-Boc-ethylenediamine (Boc =tert-butoxycarbonyl) is the most pivotal intermediate in the chem. of PNA, and synthetic route commencing with this material affords these two PNA monomers in relatively high yield, and purity, while being very reproducible.

Journal of the Turkish Chemical Society, Section A: 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, Name: 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

Sanders, Jeffrey M. published the artcileEffects of Hypoxanthine Substitution in Peptide Nucleic Acids Targeting KRAS2 Oncogenic mRNA Molecules: Theory and Experiment, SDS of cas: 169396-92-3, the publication is Journal of Physical Chemistry B (2013), 117(39), 11584-11595, database is CAplus and MEDLINE.

Genetic disorders can arise from single base substitutions in a single gene. A single base substitution for wild type guanine in the twelfth codon of KRAS2 mRNA occurs frequently to initiate lung, pancreatic, and colon cancer. We have observed single base mismatch specificity in radioimaging of mutant KRAS2 mRNA in tumors in mice by in vivo hybridization with radiolabeled peptide nucleic acid (PNA) dodecamers. We hypothesized that multimutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick base pairs with adenine, cytosine, thymine, and uracil. Using mol. dynamics simulations and free energy calculations, we show that hypoxanthine substitutions in PNAs are tolerated in KRAS2 RNA:PNA duplexes where wild type guanine is replaced by mutant uracil or adenine in RNA. To validate our predictions, we synthesized PNA dodecamers with hypoxanthine, and then measured the thermal stability of RNA:PNA duplexes. CD thermal melting results showed that hypoxanthine-containing PNAs are more stable in duplexes where hypoxanthine-adenine and hypoxanthine-uracil base pairs are formed than single mismatch duplexes or duplexes containing hypoxanthine-guanine opposition.

Journal of Physical Chemistry B 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, SDS of cas: 169396-92-3.

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

Shigenaga, Akira published the artcileDevelopment of thiol-responsive amide bond cleavage device and its application for peptide nucleic acid-based DNA releasing system, Application In Synthesis of 169396-92-3, the publication is Tetrahedron Letters (2010), 51(18), 2525-2528, database is CAplus.

To develop a thiol-responsive DNA-releasing system, a thiol-responsive amino acid capable of inducing an amide bond cleavage in the presence of a thiol was developed. It was successfully combined with peptide nucleic acid (PNA), and thiol-induced release of DNA from the thiol-responsive PNA/DNA complex was observed

Tetrahedron 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 C14H10O4, Application In Synthesis of 169396-92-3.

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

Inagaki, Masahito published the artcileN-Benzoyl-protected Peptide Nucleic Acid (PNA) Monomers Expand the Range of Nucleobases Available for PNA-DNA Chimera, Application In Synthesis of 169396-92-3, the publication is Chemistry Letters (2019), 48(4), 341-344, database is CAplus.

We synthesized N-benzoyl-protected peptide nucleic acid (PNA) monomers, which are robust under the conditions for deprotecting the 9-fluorenylmethoxycarbonyl (Fmoc) group by piperidine but are removable by aqueous ammonia and hence totally compatible with Fmoc-solid phase synthesis. This new invention expands the range of available nucleobase sequences, allowing us to use acid-sensitive PNA oligomers and purine nucleotides (both of which are difficult to use in the conventional methods) in the preparation of PNA-DNA chimeras to avoid the drawbacks of traditional PNAs.

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, Application In Synthesis of 169396-92-3.

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

Beall, Edward published the artcileEffects of the backbone and chemical linker on the molecular conductance of nucleic acid duplexes, Related Products of pyrimidines, the publication is Journal of the American Chemical Society (2017), 139(19), 6726-6735, database is CAplus and MEDLINE.

Scanning tunneling microscope break junction measurements were used to examine how the mol. conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Mol. conductances of 10 base-pair-long homoduplexes of DNA, aeg-PNA, γ-PNA, and a heteroduplex of DNA/aeg-PNA with identical nucleobase sequence were measured. The mol. conductance was found to vary by 12-13-fold with the change in backbone. Computational studies showed that the mol. conductance differences between nucleic acids of different backbones correlated with differences in backbone structural flexibility. The mol. conductance was also measured for duplexes connected to the electrode through 2 different linkers, one directly to the backbone and one directly to the nucleobase stack. While the linker caused an order-of-magnitude increase in the overall conductance for a particular duplex, the differences in the elec. conductance with backbone composition were preserved. The highest mol. conductance value(0.06G₀) was measured for aeg-PNA duplexes with a base stack linker. These findings revealed an important new strategy for creating longer and more complex electroactive, nucleic acid assemblies.

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, Related Products of pyrimidines.

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

Michaelis, Julia published the artcileDNA-Triggered Dye Transfer on a Quantum Dot, Product Details of C26H26N4O7, the publication is Bioconjugate Chemistry (2014), 25(1), 18-23, database is CAplus and MEDLINE.

Nucleic acid-templated reactions are frequently explored tools in nucleic acid diagnosis. To enable a separation-free DNA detection, the reactive probe mols. require conjugation with reporter groups that provide measurable changes of an observable parameter upon reaction. A widely used, generic read-out method is based on fluorescence resonance energy transfer (FRET) between two appended dyes. Yet, spectral cross-talk usually limits the achievable enhancements of the FRET signal in DNA-directed chemistries. We describe a DNA-triggered transfer reaction which provides for strong increases of a fluorescent signal caused by FRET. The method may involve DNA- and PNA-based probes and is based upon a proximity-triggered transfer reaction which leads to the covalent fixation of a fluorescence dye on the surface of a quantum dot (QD). The transfer reaction brings the dye closer to the QD than hybridization alone. The resulting FRET signal is a specific monitor of the reaction and allows efficient discrimination of single base mismatched templates. Of note, the 35-fold increase of the FRET signal is measured at 310 nm apparent Stokes shift and turnover in template provides a means for signal amplification.

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 C26H26N4O7, Product Details of C26H26N4O7.

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

Nim-anussornkul, Duangrat published the artcileSynthesis and optical properties of pyrrolidinyl peptide nucleic acid bearing a base discriminating fluorescence nucleobase 8-(pyrene-1-yl)-ethynyladenine, Product Details of C26H26N4O7, the publication is Bioorganic & Medicinal Chemistry (2017), 25(24), 6388-6397, database is CAplus and MEDLINE.

A combination of fluorophore and nucleobase through a π-conjugated rigid linker integrates the base pairing and the fluorescence change into a single event. Such base discriminating fluorophore can change its fluorescence as a direct response to the base pairing event and therefore have advantages over tethered labels or base surrogates lacking the hydrogen-bonding ability. 8-(Pyrene-1-yl)ethynyl-adenine (A^PyE) has been extensively used as fluorescence labels in DNA and LNA, but it showed little discrimination between different nucleobases. Herein we investigated the synthesis, base pairing ability and optical properties of A^PyE in pyrrolidinyl peptide nucleic acid – a DNA mimic that shows much stronger affinity and specificity towards DNA than natural oligonucleotides. The A^PyE in PNA pairs specifically with thymine in the DNA strand, and resulted in 1.5-5.2-fold enhanced and blue-shifted fluorescence emission. Fluorescence quenching was observed in the presence of mismatched base or abasic site directly opposite to the A^PyE. The behavior of A^PyE in acpcPNA is distinctively different from DNA whereby a fluorescence was increased selectively upon duplex formation with complementary DNA and therefore emphasizing the unique advantages of using PNA as alternative oligonucleotide probes. Applications as color-shifting probe for detection of trinucleotide repeats in DNA were demonstrated, and the performance of the probe was further improved by combination with reduced graphene oxide as an external nano-quencher.

Bioorganic & 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, Product Details of C26H26N4O7.

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

Dettin, Monica published the artcileSynthesis and chromatography-free purification of PNA-PEO conjugates for the functionalisation of gold sensors, Related Products of pyrimidines, the publication is Molecules (2012), 11026-11045, database is CAplus and MEDLINE.

Peptide Nucleic Acids (PNAs) linked to high mol. weight (MW) poly(ethylene oxide) (PEO) derivatives could be useful conjugates for the direct functionalisation of gold surfaces dedicated to Surface Plasmon Resonance (SPR)-based DNA sensing. However their use is hampered by the difficulty to obtain them through a convenient and economical route. In this work we compared three synthetic strategies to obtain PNA-high MW PEO conjugates composed of (a) a 15-mer PNA sequence as the probe complementary to genomic DNA of Mycobacterium tuberculosis, (b) a PEO moiety (2 or 5 KDa MW) and (c) a terminal trityl-protected thiol necessary (after acidic deprotection) for grafting to gold surfaces. The 15-mer PNA was obtained by solid-phase synthesis. Its amino terminal group was later condensed to bi-functional PEO derivatives (2 and 5 KDa MW) carrying a Trt-cysteine at one end and a carboxyl group at the other end. The reaction was carried out either in solution, using HATU or PyOxim as coupling agents or through the solid-phase approach, with 49.6%, 100% and 5.2% yield, resp. A differential solvent extraction strategy for product purification without the need for chromatog. is described. The ability of the 5 KDa PEO conjugate to function as a probe for complementary DNA detection was demonstrated using a Grating-Coupling Surface Plasmon Resonance (GC-SPR) system. The optimized PEO conjugation and purification protocols are economical and simple enough to be reproduced also within laboratories that are not highly equipped for chem. synthesis.

Molecules 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

Gasser, Gilles published the artcileTowards the Preparation of Novel Re/^99mTc Tricarbonyl-Containing Peptide Nucleic Acid Bioconjugates, Category: pyrimidines, the publication is Australian Journal of Chemistry (2011), 64(3), 265-272, database is CAplus.

A novel azido derivative of the di-(2-picolyl)amide (Dpam) ligand, namely 3-azido-N,N-bis-pyridin-2-ylmethylpropionamide (3), was prepared from 3-bromo-N,N-bis(pyridin-2-ylmethyl)propanamide (2) with an excess of sodium azide in DMSO. 3 Was then reacted, by Cu(I)-catalyzed [3+2] cycloaddition (often referred to as click chem.), with the previously reported alkyne-containing peptide nucleic acid (PNA) monomer Fmoc-1-OBu-t to give the Dpam-containing PNA monomer (Fmoc-4-OBu-t) in 44% yield. It was also demonstrated that 3 could be reacted by click chem., on the solid phase, to an alkyne-containing PNA oligomer (alkyne-PNA) to yield Dpam-PNA. The attempts to complex Dpam-PNA with [NEt₄]₂[ReBr₃(CO)₃] and [^99mTc(CO)₃(H₂O)₃]⁺ are also discussed in detail.

Australian Journal of 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