Compelling evidence for a stepwise mechanism of the alkaline cyclisation of uridine 3'-phosphate esters

Substrate specificity of an active dinuclear Zn(II) catalyst for cleavage of RNA analogues and a dinucleoside

The cleavage of the diribonucleoside UpU (uridylyl-3'-5'-uridine) to form uridine and uridine (2',3')-cyclic phosphate catalyzed by the dinuclear Zn(II) complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (Zn(2)(1)(H(2)O)) has been studied at pH 7-10 and 25 degrees C. The kinetic data are consistent with the accumulation of a complex between catalyst and substrate and were analyzed to give values of k(c) (s(-)(1)), K(d) (M), and k(c)/K(d) (M(-)(1) s(-)(1)) for the Zn(2)(1)(H(2)O)-catalyzed reaction. The pH rate profile of values for log k(c)/K(d) for Zn(2)(1)(H(2)O)-catalyzed cleavage of UpU shows the same downward break centered at pH 7.8 as was observed in studies of catalysis of cleavage of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) and uridine-3'-4-nitrophenyl phosphate (UpPNP). At low pH, where the rate acceleration for the catalyzed reaction is largest, the stabilizing interaction between Zn(2)(1)(H(2)O) and the bound transition states is 9.3, 7.2, and 9.6 kcal/mol for the catalyzed reactions of UpU, UpPNP, and HpPNP, respectively. The larger transition-state stabilization for Zn(2)(1)(H(2)O)-catalyzed cleavage of UpU (9.3 kcal/mol) compared with UpPNP (7.2 kcal/mol) provides evidence that the transition state for the former reaction is stabilized by interactions between the catalyst and the C-5'-oxyanion of the basic alkoxy leaving group.

Kinetics and Mechanisms for the Isomerization of Internucleosidic 3'-O-P-CH2-5' and 3'-O-P-CH(OH)-5' Linkages to Their 2',5'-Counterparts

Isomerization of internucleosidic 3'-O-P-CH2-5' and 3'-O-P-CH(OH)-5' phosphonate linkages to their 2',5'-counterparts has been studied over a wide pH-range. The model compounds employed are phosphonate analogs of adenylyl-(3',5')-adenosine and adenylyl-(2',5')-adenosine having either adenosine ((R,S)-1, (R,S)-2) or 5'-deoxyadenosine (3, 4) bonded to the phosphorus atom through the C5'-atom. For comparative purposes, the hydrolytic stability of C5'-hydroxyphosphonate analogs derived from 2'-deoxyadenosine ((R,S)-5) has also been studied. In addition to the expected acid-catalyzed (pH < 3) and pH-independent reactions (pH 3-9), the diastereomeric C5'-hydroxyphosphonate analogs ((R,S)-1, (R,S)-2), but not their deoxy counterparts (3, 4), have been observed to undergo a hydroxide-ion-catalyzed isomerization around pH 11 (90 °C). Evidently a hydrogen bond between the dianionic phosphorane and the C5'-hydroxy group stabilize the phosphorane to such an extent that isomerization via kinetically invisible protonation to monoanion becomes possible. The mechanisms of the isomerization reactions taking place under various conditions are discussed.

Chemical models for ribozyme action

Mechanistic studies of the action of catalytic ribonucleic acids, ribozymes, are highly challenging, because even a slight structural change can dramatically affect the chain folding. This, in turn, alters the binding properties of the catalytic core, making identification of the real origin of the observed influence on rate difficult. Unambiguous structure-reactivity correlations based on studies with structurally simplified chemical models may help to distinguish between alternative mechanistic interpretations. The results of such model studies are reviewed. The topics include intramolecular cleavage of RNA phosphodiester bonds by solvent-derived species, general acids/bases and metal ions, effect of molecular environment on their hydrolytic stability and trinucleoside monophosphates as models for large ribozymes.

Artificial ribonucleases

Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.

A Highly Reactive Mononuclear Zn(II) Complex for Phosphodiester Cleavage

The activity of a Zn(II) complex of a tetradentate, tripodal ligand for catalyzing phosphodiester cleavage is enhanced 750-fold by introducing three hydrogen bond donors to the ligand. Inhibition studies show that the Zn-aqua complex is the kinetically active form and that it binds the transition state with a formal dissociation constant of 3 x 108 M-1. The effect of these ligand modifications on the transition-state affinity is comparable to the rate acceleration provided by the metal ion itself. Overall, this mononuclear complex is more active than the most reactive dinuclear Zn(II) complexes reported to date.

Phosphodiester cleavage of guanylyl-(3',3')-(2'-amino-2'-deoxyuridine): rate acceleration by the 2'-amino function

Hydrolytic reactions of the structural analogue of guanylyl-(3',3')-uridine, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine), having one of the 2'-hydroxyl groups replaced with an amino function, have been followed by RP HPLC in the pH range 0-13 at 90 degrees C. The results are compared to those obtained earlier with guanylyl-(3',3')-uridine, guanylyl-(3',3')-(2',5'-di-O-methyluridine), and uridylyl-(3',5')-uridine. Under basic conditions (pH > 8), the hydroxide ion-catalyzed cleavage of the P-O3' bond (first-order in [OH(-)]) yields a mixture of 2'-amino-2'-deoxyuridine and guanosine 2',3'-cyclic phosphate which is hydrolyzed to guanosine 2'- and 3'-phosphates. Under these conditions, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is 10 times less reactive than guanylyl-(3',3')-uridine. Under acidic and neutral conditions (pH 3-8), where the pH-rate profile for the cleavage consists of two pH-independent regions (from pH 3 to pH 4 and from 6 to 8), guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is considerably reactive. For example, in the latter pH range, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is more than 2 orders of magnitude more labile than guanylyl-(3',3')-(2',5'-di-O-methyluridine), while in the former pH range the reactivity difference is 1 order of magnitude. Under very acidic conditions (pH < 3), the isomerization giving guanylyl-(2',3')-(2'-amino-2'-deoxyuridine) and depurination yielding guanine (both first-order in [H(+)]) compete with the cleavage. The Zn(2+)-promoted cleavage ([Zn(2+)] = 5 mmol L(-)(1)) is 15 times faster than the uncatalyzed reaction at pH 5.6. The mechanisms of the reactions of guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) are discussed, particularly focusing on the possible stabilization of phosphorane intermediate and/or transition state via an intramolecular hydrogen bonding by the 2'-amino group.