Structure and Reactivity of Oligonucleotides. Part I Kinetics of the Non-Enzymatic Transphosphorylation of Adenylyl-(3′-5′)-Adenosine 3′-Phosphate and Other Dinucleotides

Koike, Tatsuro; Inoue, Yasuo

doi:10.1246/cl.1972.569

Cited by 15 publications

(21 citation statements)

References 16 publications

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“…10,11,13,25 In particular, we examine differences in the free energy profile due to variations in the water model and ion atmosphere. The results (Figure 3, Table 2) show no statistically significant variation in the reaction barrier or geometry when the water model is changed from TIP3P to TIP4P-Ew.…”

Section: Resultsmentioning

confidence: 99%

Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution

2012

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We employ quantum mechanical/molecular mechanical umbrella sampling simulations to probe the free energy surfaces of a series of increasingly complex reaction models of RNA 2’-O-transesterification in aqueous solution under alkaline conditions. Such models are valuable for understanding the uncatalyzed processes underlying catalytic cleavage of the phosphodiester backbone of RNA, a reaction of fundamental importance in biology. The chemically reactive atoms are modeled by the AM1/d-PhoT quantum model for phosphoryl transfer, whereas the aqueous solvation environment is modeled with a molecular mechanics force field. Several simulation protocols were compared that used different ionic conditions and force field models. The results provide insight into how variation of the structural environment of the nucleophile and leaving group affects the free energy profile for the transesterification reaction. Results for a simple RNA backbone model are compared with recent experiments by Harris et al. on the specific base catalyzed cleavage of a UpG dinucleotide. The calculated and measured free energies of activation match extremely well (ΔF‡ = 19.9–20.8 versus 19.9 kcal/mol). Solvation is seen to play a crucial role and is characterized by a network of hydrogen bonds that envelopes the pentacoordinate dianionic phosphorane transition state and provides preferential stabilization relative to the reactant state.

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Section: Resultsmentioning

confidence: 99%

Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution

2012

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“…Inversion of configuration of a phosphorothioate at the reactive phosphoryl supports a concerted mechanism under these conditions30. Above pH 13 the reaction becomes pH independent, with an apparent pK a of 13.5 presumed to reflect deprotonation of the 2'O nucleophile5; 19; 20; 21; 38; 39.…”

Section: Introductionmentioning

confidence: 85%

“…RNA 2'- O -transphosphorylation necessarily involves protonation and deprotonation steps; however, it is exceedingly difficult to gain experimental insight into the trajectory and timing of these proton transfer steps, that is, whether they occur before, during or after transfer of the phosphoryl group. Understanding these details of mechanism is important because the 2'- O -transphosphorylation of RNA is catalyzed by both acid and base in solution5; 18; 19; 20; 21; 22; 23, and potential Bronsted acid and base functional groups are key components of phosphoryl transfer enzyme active sites24; 25; 26; 27; 28; 29. Defining the influence of interactions with acid and base catalysts on the reaction mechanisms in solution therefore provides an essential framework for understanding how enzymes achieve their characteristic attribute of tremendous rate enhancement.…”

Section: Introductionmentioning

confidence: 99%

Kinetic Isotope Effects for RNA Cleavage by 2′-O- Transphosphorylation: Nucleophilic Activation by Specific Base

et al. 2010

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To better understand the interactions between catalysts and transition states during RNA strand cleavage, primary 18 O kinetic isotope effects and solvent D 2 O isotope effects were measured to probe the mechanism of base-catalyzed 2'-O-transphosphorylation of the RNA dinucleotide 5'-UpG-3'. The observed 18 O KIEs for the nucleophilic 2'-O and in the 5'-O leaving group at pH 14 are both large relative to reactions of phosphodiesters with good leaving groups, indicating that the reaction catalyzed by hydroxide has a transition state (TS) with advanced phosphorus-oxygen bond fission to the leaving group ( 18 k LG = 1.034 ± 0.004) and phosphorous-nucleophile bond formation ( 18 k NUC = 0.984 ± 0.004). A breakpoint in the pH dependence of the 2'-Otransphosphorylation rate to a pH independent phase above pH 13 has been attributed to the pK a of the 2'-OH nucleophile. A smaller nucleophile KIE is observed at pH 12 ( 18 k NUC = 0.995 ± 0.004) that is interpreted as the combined effect of the equilibrium isotope effect (~1.02) on deprotonation of the 2′-hydroxyl nucleophile and the intrinsic KIE on the nucleophilic addition step (ca. 0.981). An alternative mechanism in which the hydroxide ion acts as a general base is considered unlikely given the lack of a solvent deuterium isotope effect above the breakpoint in the pH versus rate profile. These results represent the first direct analysis of the transition state for RNA strand cleavage. The primary 18 O KIE results and the lack of a kinetic solvent deuterium isotope effect together provide strong evidence for a late transition state and 2'-O nucleophile activation by specific base catalysis.

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“…The mechanistic analysis on the degradation behavior of the ribose phosphodiester bond has been extensively carried out with and without ribonuclease (RNase). The kinetic studies elucidated that the ribose phosphodiester linkage is cleaved to form 3 0 -and 2 0 -phosphate terminals through the transesterification of 2 0 ,3 0 -cyclic phosphate terminal for nonenzymatic and enzymatic reactions (Koike and Inoue, 1972;Eftink and Biltonen, 1983;Anslyn and Breslow, 1989;Kawamura, 2001Kawamura, , 2003a. The hydrolytic degradation of 5 0 -dCrCdGdG can be expressed using Eqs.…”

Section: Reaction Rates Of Oligonucleotides In the Presence Of Tcaamentioning

confidence: 99%

Chemical evolution of RNA under hydrothermal conditions and the role of thermal copolymers of amino acids for the prebiotic degradation and formation of RNA

Kawamura

Nagahama

Kuranoue

2005

Advances in Space Research

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Structure and Reactivity of Oligonucleotides. Part I Kinetics of the Non-Enzymatic Transphosphorylation of Adenylyl-(3′-5′)-Adenosine 3′-Phosphate and Other Dinucleotides

Abstract: Kinetics of the non-enzymatic transphosphorylation of several diribonucleotides have been studied. First-order rate constants for the reactions, which are acid-base-catalyzed, have been obtained. Base-sequence and base composition dependent nature of rates is discussed.

Cited by 15 publications

References 16 publications

Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution

Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution

Kinetic Isotope Effects for RNA Cleavage by 2′-O- Transphosphorylation: Nucleophilic Activation by Specific Base

Chemical evolution of RNA under hydrothermal conditions and the role of thermal copolymers of amino acids for the prebiotic degradation and formation of RNA

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