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Relevant academic research and scientific papers

The stability of trisubstituted internucleotide bond in the presence of the vicinal 2'-hydroxyl. Chemical synthesis of uridyl(2'-phosphate)-(3'-5')- uridine

The effect of eleven different phosphoryl center protecting groups on the stability of trisubstituted internucleotide bond of the dimers (1a-k), in the presence of the vicinal 2'-hydroxyl, was examined. It has been found that electronic properties of the

Interconversion and Phosphoester Hydrolysis of 2',5'- and 3',5'-Dinucleoside Monophosphates: Kinetics and Mechanisms

First-order rate constants for the interconversion and hydrolytic cleavage of several 2',5'- and 3',5'-dinucleoside monophosphates (UpU, UpA, ApU, ApA) have been determined over an acidity range from H0 = -0.2 to H- = 12.4 at 363.2 K.Both reactions proceed at comparable rates at pH a of the phosphate moiety (0.7) and second-order under less acidic conditions (pH 1-2).With dinucleoside monophosphates derived from adenosine, acid-catalyzed depurination of the starting material competes with the phosphate migration and phosphoester hydrolysis at pH 4.Under these conditions the migration is considerably faster than the phosphoester hydrolysis, which exhibits acid catalysis at pH 8).The reaction is first order with respect to hydroxide ion at -> -3 and approaches zero-order dependence at higher alkalinities, where the unesterified 2'- or 3'-hydroxyl group becomes ionized.The mechanisms of different partial reactions, and the effects of base moiety structure (purine vs pyrimidine) on their rates are discussed.The data are compared to the known reaction kinetics of monoalkyl esters of adenosine 2'- and 3'-monophosphates.

On the mechanism of catalysis by ribonuclease: Cleavage and isomerization of the dinucleotide UpU catalyzed by imidazole buffers

Uridylyl(3',5')uridine [(3',5')-UpU] undergo cleavage to uridine 2',3'-cyclic phosphate and uridine, catalyzed by imidazole buffers. Kinetic studies indicate a sequential bifunctional mechanism, with one buffer component catalyzing its forward decomposition to products. From a study of the buffer-catalyzed isomerization of (3',5')-UpU to [2',5']-UpU, the first catalyst is identified as imidazolium ion and the second as imidazole. The resulting detailed mechanism is chemically reasonable. It is also consistent with what is known about bovine pancreatic ribonuclease. Thus, a related multistep mechanism is suggested for the enzymatic reactions as well.

Self Cleavage of C8-Histamino-r(UpA) Promoted by ZnCl2: Mechanistic Studies on a Designed Ribonuclease Mimic

Studies on self cleavage of dinucleotides (2-5) containing conjugated imidazole and ethylenediamine chains indicated that the imidazole conjugated ribonucleotide 4 hydrolyzed in presence of ZnCl2 whereas other dinucleotides 2, 3 and 5 were inert.An acceleration of 10-15 times in rate of hydrolysis of 4 was observed as compared to the unmodified dinucleotide 6.The product analysis by HPLC suggested that the reaction involves cleavage of P-O5' bond with the formation of C8-histamino dA 9 and 2',3'-cUMP 10 which subsequently hydrolyzed to a mixture of 2' and 3' UMP by a slower reaction.The mechanism of hydrolysis of designed model compound 4 is similar to that of the first step of hydrolysis of RNA by RNase A.

Chiral Nanozymes-Gold Nanoparticle-Based Transphosphorylation Catalysts Capable of Enantiomeric Discrimination

Enantioselectivity in RNA cleavage by a synthetic metalloenzyme has been demonstrated for the first time. Thiols containing chiral ZnII-binding head groups have been self-assembled on the surface of gold nanoparticles. This results in the spontaneous formation of chiral bimetallic catalytic sites that display different activities (kcat) towards the enantiomers of an RNA model substrate. Substrate selectivity is observed when the nanozyme is applied to the cleavage of the dinucleotides UpU, GpG, ApA, and CpC, and remarkable differences in reactivity are observed for the cleavage of the enantiomerically pure dinucleotide UpU.

Ribonuclease activity of an artificial catalyst that combines a ligated CuII ion and a guanidinium group at the upper rim of a cone -Calix[4]arene platform

A cone-calix[4]arene derivative, featuring a guanidinium group and a CuII ion ligated to a 1,4,7-triazacyclononane (TACN) ligand at the 1,3-distal positions of the upper rim, effectively catalyzes the cleavage of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) and a number of diribonucleoside 3′,5′-monophosphates (NpN′). Kinetic and potentiometric measurements support the operation of a general-base/general-acid mechanism and demonstrate that the hydroxo form of the ligated CuII ion is the sole catalytically active species. Rate enhancements relative to the background hydrolysis reaction at 1 mM catalyst concentration are 6 × 105-fold for HPNP and cluster around 107-fold with the most favorable catalyst-NpN′ combinations.

Diguanidinocalix[4]arenes as effective and selective catalysts of the cleavage of diribonucleoside monophosphates

Calix[4]arenes derivatives 1 and 2, featuring two guanidine units at the upper rim, catalyze the transesterification of diribonucleoside monophosphates much more effectively than that of HPNP. Rate accelerations relative to the background range from 10su