Development of synthetic RNA-targeting catalysts from biostable nucleic acid analogues
type: CreativeWork
description: RNAs are major biomolecular players in biology and disease, and are a rich source of novel drug targets for molecular medicine. However, therapeutic modulation of specific RNAs remains a significant technical challenge. Single-stranded nucleic acids can fold into complex three-dimensional structures capable of catalysis of a wide range of chemical reactions, particularly RNA processing, playing critical roles in biology. RNA endonuclease “ribozymes” and “DNAzymes”, either re-purposed from nature or evolved in vitro, have been an active area of research with the promise of applications as molecular tools for specific RNA knockdown. In principle, they could provide a rich source of specific, modular, ‘programmable’ single agents. However, key challenges remain, mainly due to the limitations of natural DNA and RNA backbones. To enhance the prospects of in vivo applications, modification of oligonucleotide catalysts with synthetic DNA and RNA analogues—known as XNAs—is being explored, as well as the development of catalysts entirely composed of XNAs, “XNAzymes”. Our aim here is to evolve, engineer, and test RNA-cleaving XNAzymes capable of targeting disease-associated RNA under physiological conditions. This approach seeks to overcome the limitations of other RNA knockdown methods, principally the lack of single-nucleotide specificity and off-target effects, and—in the case of ribozyme and DNAzyme catalysts in particular—poor biostability and activity on long, structured all-RNA targets under physiological conditions. To explore the possibility of using XNAzymes to specifically target microRNAs and other non-coding RNAs, we retargeted a previously characterised XNAzyme composed of 2′-deoxy-2′-fluoro-β-D-arabino nucleic acid (FANA). We demonstrated the effectiveness of this approach in generating novel catalysts with high specificity for individual non-coding RNAs within families of similar sequences in in vitro assays under quasi-physiological conditions; however, we no…
abstract: RNAs are major biomolecular players in biology and disease, and are a rich source of novel drug targets for molecular medicine. However, therapeutic modulation of specific RNAs remains a significant technical challenge. Single-stranded nucleic acids can fold into complex three-dimensional structures capable of catalysis of a wide range of chemical reactions, particularly RNA processing, playing critical roles in biology. RNA endonuclease “ribozymes” and “DNAzymes”, either re-purposed from nature or evolved in vitro, have been an active area of research with the promise of applications as molecular tools for specific RNA knockdown. In principle, they could provide a rich source of specific, modular, ‘programmable’ single agents. However, key challenges remain, mainly due to the limitations of natural DNA and RNA backbones. To enhance the prospects of in vivo applications, modification of oligonucleotide catalysts with synthetic DNA and RNA analogues—known as XNAs—is being explored, as well as the development of catalysts entirely composed of XNAs, “XNAzymes”. Our aim here is to evolve, engineer, and test RNA-cleaving XNAzymes capable of targeting disease-associated RNA under physiological conditions. This approach seeks to overcome the limitations of other RNA knockdown methods, principally the lack of single-nucleotide specificity and off-target effects, and—in the case of ribozyme and DNAzyme catalysts in particular—poor biostability and activity on long, structured all-RNA targets under physiological conditions. To explore the possibility of using XNAzymes to specifically target microRNAs and other non-coding RNAs, we retargeted a previously characterised XNAzyme composed of 2′-deoxy-2′-fluoro-β-D-arabino nucleic acid (FANA). We demonstrated the effectiveness of this approach in generating novel catalysts with high specificity for individual non-coding RNAs within families of similar sequences in in vitro assays under quasi-physiological conditions; however, we no…
author: Donde, Maria
language: eng
keywords: Catalytic oligos, Nucleic acids, RNA knockdown, SELEX, XNA, XNAzyme
license: https://www.repository.cam.ac.uk/bitstreams/d9bd2527-c791-4c77-bdab-fb3c8162f447/download
license: http://purl.org/NET/rdflicense/allrightsreserved
date published: 2025-05-27
date modified: 2026-07-22T22:24:16Z
provider: Cambridge University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Cambridge

PropertyValue
property ID: DOI
value: 10.17863/CAM.126840