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Base Catalysis

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Ronald R Breaker – One of the best experts on this subject based on the ideXlab platform.

  • kinetics of rna degradation by specific Base Catalysis of transesterification involving the 2 hydroxyl group
    Journal of the American Chemical Society, 1999
    Co-Authors: Yingfu Li, Ronald R Breaker

    Abstract:

    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…

  • Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group
    Journal of the American Chemical Society, 1999
    Co-Authors: Yingfu Li, Ronald R Breaker

    Abstract:

    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.

  • kinetics of rna degradation by specific Base Catalysis of transesterification involving the 2 hydroxyl group
    Journal of the American Chemical Society, 1999
    Co-Authors: Yingfu Li, Ronald R Breaker

    Abstract:

    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…

  • Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group
    Journal of the American Chemical Society, 1999
    Co-Authors: Yingfu Li, Ronald R Breaker

    Abstract:

    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.

  • Probing general Base Catalysis in the hammerhead ribozyme.
    Journal of the American Chemical Society, 2008
    Co-Authors: Jason M Thomas, David M Perrin

    Abstract:

    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.

  • covalent schiff Base Catalysis and turnover by a dnazyme a m2 independent ap endonuclease mimic
    Journal of the American Chemical Society, 2004
    Co-Authors: Richard Ting, Jason M Thomas, Leonard Lermer, Yoann Roupioz, David M Perrin

    Abstract:

    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.