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Showing 1 to 16 of 16 for “"Phosphodiester bond"”.
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Biotin and Fluorescent Labeling of Ribonucleic Acids Using T4 Rna Ligase (Rna Modification, Rna-Dna Hybridization)
… of an RNA molecule (acceptor) to form a phosphodiester bond and the AMP portion is released. E. coli and D. melanogaster 5S RNA, yeast tRNA('Phe), (Ap)(,3)C, and (Ap)(,3)A serve as acceptors with yields of products varying from 50 to 100%. Analysis of the oligoribonucleotide (Ap)(,3)C …
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The Synthesis of Oligodeoxyribonucleotides With Rna Ligase
… the ATP-dependent formation of a 3' (--->) 5'-phosphodiester bond between one oligonucleotide with a 3'-hydroxyl group (the acceptor molecule) and another with a 5'-phosphate (the donor molecule). The enzyme does not require the alignment of the donor and acceptor molecules onto a complementary …
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Ribozymes of the RNA World: Investigating Ancient Enzymes through Modern Self-Cleaving Ribozymes.
… They catalyze the cleavage of a specific phosphodiester bond in RNA. We investigated the different catalytic strategies used by one such ribozyme, called the hammerhead ribozyme, and uncovered how RNA can utilize tautomerization, divalent metals, and folding to diversify its chemical …
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DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates
… a wide variety of chemical reactions, including phosphodiester bond cleavage, nucleic acid ligation, thymine dimer photoreversion, and the Diels-Alder reaction. However, the majority of deoxyribozyme-catalyzed reactions involve oligonucleotide substrates. To expand the scope of substrates that …
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Nucleotide recognition and metal ion requirements of an RNA ligase ribozyme
… via a Watson-Crick base pair, forming a 3',5'-phosphodiester bond between its 5'-nucleotide and the substrate, and releasing pyrophosphate. The class I ligase forms the catalytic domain of an RNA polymerase ribozyme which is capable of extending a primer by 14 nucleotides. The ability of the …
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Computational studies of the self-cleavage mechanism in the glmS ribozyme
… a self-cleavage reaction. Namely, the GlcN6P bonds to the glmS ribozyme and triggers a cleavage of a phosphodiester bond at a certain position via a general acid-base mechanism. This work explored the following aspects of its self-cleavage mechanism: general acid-base species, multiple roles …
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RAPID COLORIMETRIC IDENTIFICATION OF ESCHERICHIA COLI SHIGA TOXINS 1 AND 2, AS WELL AS EAE AND AGGR, USING LOOP MEDIATED ISOTHERMAL AMPLIFICATION FOLLOWED BY PNA/AUNP DETECTION
… was amplified, hydrogen ion release during phosphodiester bond formation will decrease the pH of the reaction. This causes the pH indicator dye to turn from pink to yellow. There are disadvantages to a visualization method that relies solely on pH changes. This is an indirect measure of DNA …
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Structural studies of enzymes involved in antibiotic resistance and phosphonate degradation
… potential, and stable and degradation resistant bonds that make up the biological polymers which offer structural and functional support. Insights into secondary metabolism in microorganisms have shed light on fascinating arrays of genetically encoded small molecule natural products which have …
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Sensitivity and Species Specificity of Bisulfite Modification and Pyrosequencing Technology Used to Identify Tissue-Specific DNA Methylation Patterns in Common Biofluids Foudn in Crime Scenes
… CpG sites. The "p" in the CpG stands for the phosphodiester bond which connects the two bases. The study of tissue-specific DNA methylation can serve as a means of identifying the source of a biofluid. Recently, it has been observed that epigenetic DNA methylation patterns are specific for …
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In vitro selection and characterization of mono-, di-, and trivalent metal-dependent DNAzymes and their sensing applications
… procedure to catalyze the cleavage of a phosphodiester bond. Since the discovery of the first aptamer and DNAzyme, many more functional nucleic acids have been isolated and engineered to perform various functions, including binding to a wide variety of different ligands and catalysis of …
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Characterization and evolution of artificial RNA ligases
… RNA ligase catalyzes the formation of a phosphodiester bond between two RNA substrates by joining a 5'-triphospate to a 3'-hydroxyl, with the release of pyrophosphate. This activity has not been observed in nature. An initial selection carried out at 23°C yielded variants that were poorly …
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Deoxyribozymes to hydrolyze DNA phosphodiester bonds
… the sequence-specific hydrolysis of a DNA phosphodiester bond. The DNA hydrolysis by 10MD5 proceeds with kobs = 2.7 h-1 and rate enhancement of 1012 over the uncatalyzed P–O bond hydrolysis. However, 10MD5 has a sharp pH optimum near 7.5, with greatly reduced yield and rate when the pH is …
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Nucleobase-modified deoxyribozymes for amide and peptide hydrolysis
… of deoxyribozymes that cleave a DNA phosphodiester bond. Subsequent selection experiments for DNA-catalyzed ester and amide bond hydrolysis employed an additional capture step to avoid identifying deoxyribozymes for phosphodiester cleavage, leading to the identification of …
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I. In vitro selection of aptamers for perchlorate and melamine II. Towards crystallization of DNAzymes III. A highly selective lead sensor based on a classic lead DNAzyme
… vitro selection) to catalyze the cleavage of a phosphodiester bond. Similar in principle, both SELEX and in vitro selection are combinatorial chemistry technique that enables the isolation of nucleic acid sequences with particular functions from an astronomical number of random sequences via …
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DNA catalysts for amide bond cleavage and for lysine side chain modification
… to identify DNA catalysts which cleave peptide bonds. Previous efforts seeking DNA-catalyzed peptide cleavage resulted in DNA catalysts led to the identification of deoxyribozymes that cleave a DNA phosphodiester bond. In order to avoid identifying deoxyribozymes for phosphodiester cleavage in …