Selection of M2+-independent RNA-cleaving DNAzymes with Sidechains Mimicking Arginine and Lysine.
Chembiochem 2021;
23:e202100600. [PMID:
34881502 DOI:
10.1002/cbic.202100600]
[Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/04/2021] [Indexed: 11/07/2022]
Abstract
Sequence-specific cleavage of RNA by nucleic acid catalysts in the absence of a divalent metal cation (M 2+ ) has remained an important goal in biomimicry with potential therapeutic applications. Given the lack of functional group diversity in canonical nucleotides, modified nucleotides with amino acid-like side chains were used to enhance self-cleavage rates at a single embedded ribonucleoside site. Previous works relied on three functional groups: an amine, a guanidine and an imidazole ensconced on three different nucleosides. However, to date, few studies have systematically addressed the necessity of all three modifications, as the value of any single modified nucleoside is contextualized at the outset of selection. Herein, we report on the use of only two modified dNTPs, excluding an imidazole, i.e. 5-(3-guanidinoallyl)-2'-dUTP (dU ga TP) and 5-aminoallyl-2'-dCTP (dC aa TP), to select in-vitro self-cleaving DNAzymes that cleave in the absence of M 2+ in a pH-independent fashion. Cleavage shows biphasic kinetics with rate constants that are significantly higher than in unmodified DNAzymes and compare favorably to certain DNAzymes involving an imidazole. This work is the first report of a M2+-independent DNAzyme with two cationic modifications; as such it shows appreciable self-cleaving activity in the absence of an imidazole modification.
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