A Ribozyme for the Aldol Reaction

Abstract

Directed in vitro evolution can create RNA catalysts for a variety of organic reactions, supporting the "RNA world" hypothesis, which proposes that metabolic transformations in early life were catalyzed by RNA molecules rather than proteins. Among the most fundamental carbon-carbon bond-forming reactions in nature is the aldol reaction, mainly catalyzed by aldolases that utilize either an enamine mechanism (class I) or a Zn(2+) cofactor (class II). We report on isolation of a Zn(2+)-dependent ribozyme that catalyzes an aldol reaction at its own modified 5' end with a 4300-fold rate enhancement over the uncatalyzed background reaction. The ribozyme can also act as an intermolecular catalyst that transfers a biotinylated benzaldehyde derivative to the aldol donor substrate, coupled to an external hexameric RNA oligonucleotide, supporting the existence of RNA-originated biosynthetic pathways for metabolic sugar precursors and other biomolecules.

A DNA‐Templated Aldol Reaction as a Model for the Formation of Pentose Sugars in the RNA World

“…The observed requirement for high amine concentrations may reflect the slow formation of a Schiff-base intermediate, indicating that precise positioning of the cofactor in the active site will be a crucial feature of enzymatic catalysis. A recent report by Famulok and colleagues [19] described the first example of an aldolase ribozyme, obtained by in vitro evolution, which catalyzes the reaction of a levulinic acid modified RNA and benzaldehyde-4-carboxamide. The ribozyme employs a Zn 2+ cofactor, analogous to biological class II aldolases.…”

Nukleinsäure‐basierte molekulare Werkzeuge

“…[6] Die Substrate der meisten natürlich hervorgegangenen Ribozyme sind ihrerseits ebenfalls RNAStränge. Im Unterschied dazu zeigen die künstlich entwickelten DNA-und RNAzyme die Fähigkeit, eine Vielzahl von Reaktionsarten [76] (wie Diels-Alder-Reaktionen, [77] Aldolreaktionen, [78] Michael-Additionen, [79] die Bildung von Nglycosidischen Bindungen [80] und Acetylierungen [81] ) zu katalysieren. Viele RNA-und DNAzyme ahmen auch die katalytische Funktion von echten Enzymen nach, darunter die der Cholesterol-Esterase, [82] der N-Glycosylase, [83] des sog.…”

Vierzig Jahre Evolution im Reagenzglas

“…B. die Bildung eines RNA-Phosphodiesters, [55] einer Peptidbindung, [56] einer glycosidischen Bindung, [57] eines Diels-Alder-Cycloadditionsprodukts, [58,59] eines Michael-Additionsprodukts [60] und eines Aldolkondensationsprodukts. [61] Weitere Ribozyme wurden erhalten, die Bindungsspaltungen katalysieren, z. B. die Spaltung von DNA-oder RNA-Phosphoestern, [62,63] die Hydrolyse eines Carbonsäureesters, [64] einen Aminoacyl-Transfer [65] und die Hydrolyse eines Thiophosphats.…”