The Experts below are selected from a list of 288 Experts worldwide ranked by ideXlab platform
Ronald R Breaker - One of the best experts on this subject based on the ideXlab platform.
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kinetics of rna degradation by specific Base Catalysis of transesterification involving the 2 hydroxyl group
Journal of the American Chemical Society, 1999Co-Authors: Yingfu Li, Ronald R BreakerAbstract:A detailed understanding of the susceptibility of RNA phosphodiesters to specific Base-catalyzed cleavage is necessary to approximate the stability of RNA under various conditions. In addition, quantifying the rate enhancements that can be produced exclusively by this common cleavage mechanism is needed to fully interpret the mechanisms employed by ribonucleases and by RNA-cleaving ribozymes. Chimeric DNA/RNA oligonucleotides were used to examine the rates of hydroxide-dependent degradation of RNA phosphodiesters under reaction conditions that simulate those of biological systems. Under neutral or alkaline pH conditions, the dominant pathway for RNA degradation is an internal phosphoester transfer reaction that is promoted by specific Base Catalysis. As expected, increasing the concentration of hydroxide ion, increasing the concentration of divalent magnesium, or raising the temperature accelerates strand scission. In most instances, the identities of the nucleotide Bases that flank the target RNA linkage...
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Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group
Journal of the American Chemical Society, 1999Co-Authors: Yingfu Li, Ronald R BreakerAbstract:A detailed understanding of the susceptibility of RNA phosphodiesters to specific Base-catalyzed cleavage is necessary to approximate the stability of RNA under various conditions. In addition, quantifying the rate enhancements that can be produced exclusively by this common cleavage mechanism is needed to fully interpret the mechanisms employed by ribonucleases and by RNA-cleaving ribozymes. Chimeric DNA/RNA oligonucleotides were used to examine the rates of hydroxide-dependent degradation of RNA phosphodiesters under reaction conditions that simulate those of biological systems. Under neutral or alkaline pH conditions, the dominant pathway for RNA degradation is an internal phosphoester transfer reaction that is promoted by specific Base Catalysis. As expected, increasing the concentration of hydroxide ion, increasing the concentration of divalent magnesium, or raising the temperature accelerates strand scission. In most instances, the identities of the nucleotide Bases that flank the target RNA linkage...
Yingfu Li - One of the best experts on this subject based on the ideXlab platform.
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kinetics of rna degradation by specific Base Catalysis of transesterification involving the 2 hydroxyl group
Journal of the American Chemical Society, 1999Co-Authors: Yingfu Li, Ronald R BreakerAbstract:A detailed understanding of the susceptibility of RNA phosphodiesters to specific Base-catalyzed cleavage is necessary to approximate the stability of RNA under various conditions. In addition, quantifying the rate enhancements that can be produced exclusively by this common cleavage mechanism is needed to fully interpret the mechanisms employed by ribonucleases and by RNA-cleaving ribozymes. Chimeric DNA/RNA oligonucleotides were used to examine the rates of hydroxide-dependent degradation of RNA phosphodiesters under reaction conditions that simulate those of biological systems. Under neutral or alkaline pH conditions, the dominant pathway for RNA degradation is an internal phosphoester transfer reaction that is promoted by specific Base Catalysis. As expected, increasing the concentration of hydroxide ion, increasing the concentration of divalent magnesium, or raising the temperature accelerates strand scission. In most instances, the identities of the nucleotide Bases that flank the target RNA linkage...
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Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group
Journal of the American Chemical Society, 1999Co-Authors: Yingfu Li, Ronald R BreakerAbstract:A detailed understanding of the susceptibility of RNA phosphodiesters to specific Base-catalyzed cleavage is necessary to approximate the stability of RNA under various conditions. In addition, quantifying the rate enhancements that can be produced exclusively by this common cleavage mechanism is needed to fully interpret the mechanisms employed by ribonucleases and by RNA-cleaving ribozymes. Chimeric DNA/RNA oligonucleotides were used to examine the rates of hydroxide-dependent degradation of RNA phosphodiesters under reaction conditions that simulate those of biological systems. Under neutral or alkaline pH conditions, the dominant pathway for RNA degradation is an internal phosphoester transfer reaction that is promoted by specific Base Catalysis. As expected, increasing the concentration of hydroxide ion, increasing the concentration of divalent magnesium, or raising the temperature accelerates strand scission. In most instances, the identities of the nucleotide Bases that flank the target RNA linkage...
David M Perrin - One of the best experts on this subject based on the ideXlab platform.
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Probing general Base Catalysis in the hammerhead ribozyme.
Journal of the American Chemical Society, 2008Co-Authors: Jason M Thomas, David M PerrinAbstract:Recent structural and computational studies have shed new light on the catalytic mechanism and active site structure of the RNA cleaving hammerhead ribozyme. Consequently, specific ribozyme functional groups have been hypothesized to be directly involved in general/acid Base Catalysis. In order to test this hypothesis, we have developed an affinity label to identify the functional general Base in the S. mansoni hammerhead ribozyme. The ribozyme was reacted with a substrate analogue bearing a 2'-bromoacetamide group in place of the nucleophilic 2'-hydroxyl group which would normally be deprotonated by a general Base. The electrophilic 2'-bromoacetamide group is poised to alkylate the general Base, which is subsequently identified by footprinting analysis. Herein, we demonstrate alkylation of N1 of G12 in the hammerhead ribozyme in a pH and [Mg(2+)] dependent manner that is consistent with the native cleavage reaction. These results provide substantial evidence that deprotonated N1 of G12 functions directly as a general Base in the hammerhead ribozyme; moreover, our experiments provide evidence that the pKa of G12 is perturbed downward in the context of the active site structure. We also observed other pH-independent alkylations, which do not appear to reflect the catalytic mechanism, but offer further insight into ribozyme conformation and structure.
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covalent schiff Base Catalysis and turnover by a dnazyme a m2 independent ap endonuclease mimic
Journal of the American Chemical Society, 2004Co-Authors: Richard Ting, Jason M Thomas, Leonard Lermer, Yoann Roupioz, David M PerrinAbstract:A DNAzyme, synthetically modified with both primary amines and imidazoles, is found to act as a M2+-independent AP lyase-endonuclease. In the course of the cleavage reaction, this DNAzyme forms a covalent Schiff Base intermediate with an abasic site on a complementary oligodeoxyribonucleotide. This intermediate, which is inferred from NaCNBH3 trapping as well as cyanide inhibition, does not evidently accumulate because the second step, dehydrophosphorylative elimination, is fast compared to Schiff Base formation. The 5‘-product that remains linked to the catalyst hydrolyzes slowly to regenerate free catalyst. The use of duly modified DNAzymes to perform Schiff Base Catalysis demonstrates the value of modified nucleotides for enhancing the catalytic repertoire of nucleic acids. This work suggests that DNAzymes will be capable of catalyzing aldol condensation reactions.
Jusuke Hidaka - One of the best experts on this subject based on the ideXlab platform.
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solid Base Catalysis of calcium oxide for a reaction to convert vegetable oil into biodiesel
Advanced Powder Technology, 2010Co-Authors: Masato Kouzu, Michito Tsunomori, Shinya Yamanaka, Jusuke HidakaAbstract:Abstract For the purpose of investigating solid Base Catalysis of calcium oxide for transesterification of soybean oil with refluxing methanol, the catalyst collected after the reaction was characterized by several instrumental methods: X-ray diffraction, scanning electron microscopy, solid state 13 C-NMR. The collected catalyst consisted of calcium glyceroxide, Ca[O(OH) 2 C 3 H 5 ] 2 , due to the direct combination of calcium oxide with glycerol by-produced from soybean oil. Also, the collected catalyst was active in the soybean oil transesterification, and we found that the yield of fatty acid methyl esters reached 70% after 1 h. Although the transformation of the catalytically active phase brought about a slight decrease in the reaction efficiency, calcium glyceroxide was catalytically tolerant to air-exposure.
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solid Base Catalysis of calcium oxide for a reaction to convert vegetable oil into biodiesel
Journal of The Society of Powder Technology Japan, 2009Co-Authors: Masato Kouzu, Michito Tsunomori, Shinya Yamanaka, Jusuke HidakaAbstract:For the purpose of investigating the solid Base Catalysis of calcium oxide for transesterification of soybean oil with refluxing methanol, the catalyst collected after the reaction was characterized by several instrumental methods : X-ray diffraction, scanning electron microscopy, solid-state 13C-NMR. The collected catalyst consisted of calcium glyceroxide, due to the direct combination of calcium oxide with glycerol by-produced from soybean oil. The collected catalyst was reused for the soybean oil transesterification, and we found that the yield of fatty acid methyl esters reached 70% after 1 h. Although the transformation of the catalytically active phase brought a slight decrease in the reaction efficiency, calcium glyceroxide was catalytically tolerant to air-exposure. This is why the collected catalyst could be reused without any deactivation.
David W. Lupton - One of the best experts on this subject based on the ideXlab platform.
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Lewis Base Catalysis of Three n–π* Mediated Reactions with N-Heterocyclic Carbenes (NHCs), Isothioureas, Bicyclic Tertiary Amines, and Electron-Rich Pyridyls
Synthesis, 2014Co-Authors: Lisa Candish, Yuji Nakano, David W. LuptonAbstract:Lewis Base Catalysis by lone pair donation into anti-bonding π orbitals (n–π*) is a growing field with a range of Lewis Bases capable of this type of Catalysis. In this review, Catalysis of the Morita–Baylis–Hillman reaction, the Steglich rearrangement, and the annulation of α,β-unsaturated acyl Lewis adducts are discussed, using N-heterocyclic carbene (NHC), isothiourea, bicyclic tertiary amine and electron-rich pyridyl catalysts. In many cases, each of these popular Lewis Base catalysts is viable for the given reaction, with the degree of utility defined by the catalyst’s nucleophilicity and Lewis basicity. 1 Introduction to Lewis Base Catalysis 2 Enolates from 1,4-Addition: Morita–Baylis–Hillman Reaction 3 O→C Carboxyl Transfer: Steglich Rearrangement 4 Annulations of α,β-Unsaturated Acyl Lewis Base Adducts 5 Summary and Outlook
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lewis Base Catalysis of three n π mediated reactions with n heterocyclic carbenes nhcs isothioureas bicyclic tertiary amines and electron rich pyridyls
Synthesis, 2014Co-Authors: Lisa Candish, Yuji Nakano, David W. LuptonAbstract:Lewis Base Catalysis by lone pair donation into anti-bonding π orbitals (n–π*) is a growing field with a range of Lewis Bases capable of this type of Catalysis. In this review, Catalysis of the Morita–Baylis–Hillman reaction, the Steglich rearrangement, and the annulation of α,β-unsaturated acyl Lewis adducts are discussed, using N-heterocyclic carbene (NHC), isothiourea, bicyclic tertiary amine and electron-rich pyridyl catalysts. In many cases, each of these popular Lewis Base catalysts is viable for the given reaction, with the degree of utility defined by the catalyst’s nucleophilicity and Lewis basicity. 1 Introduction to Lewis Base Catalysis 2 Enolates from 1,4-Addition: Morita–Baylis–Hillman Reaction 3 O→C Carboxyl Transfer: Steglich Rearrangement 4 Annulations of α,β-Unsaturated Acyl Lewis Base Adducts 5 Summary and Outlook
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1,3-Dipolar Cycloaddition of Unstabilized Azomethine Ylides by Lewis Base Catalysis.
ChemInform, 2013Co-Authors: Shveta Pandiancherri, Sarah J. Ryan, David W. LuptonAbstract:The 1,3-dipolar cycloaddition of unstabilized azomethine ylides with electron-poor olefins is achieved using Lewis Base Catalysis.
