New chemistries and enzymes for synthetic genetics

Freund, Niklas; Fürst, Maximilian J. L. J.; Holliger, Philipp

doi:10.1016/j.copbio.2021.11.004

Cited by 35 publications

(25 citation statements)

References 77 publications

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“…Future elaboration of catalysts could involve modified nucleobases with the potential to evolve multiple catalytic mechanisms 87 and/or sugar- or backbone-modified chemistries with advantageous biostability and pharmacodynamics 88 . The use of nucleic acid analogues capable of stabilising secondary structures is an established approach to improve RNA target accessibility in the context of microRNA-targeting agents; 2′-O-methyl-RNA (2′OMe-RNA), 2′-methoxyethyl-RNA (2′MOE-RNA) and locked nucleic acids (LNA) have proven to be of particular utility for antimiR and antagomiR development 23 , 89 – 91 and likewise enhance the activity of nucleic acid catalysts 46 , 47 , 92 , 93 .…”

Section: Discussionmentioning

confidence: 99%

Targeting non-coding RNA family members with artificial endonuclease XNAzymes

et al. 2022

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Non-coding RNAs (ncRNAs) offer a wealth of therapeutic targets for a range of diseases. However, secondary structures and high similarity within sequence families make specific knockdown challenging. Here, we engineer a series of artificial oligonucleotide enzymes (XNAzymes) composed of 2’-deoxy-2’-fluoro-β-D-arabino nucleic acid (FANA) that specifically or preferentially cleave individual ncRNA family members under quasi-physiological conditions, including members of the classic microRNA cluster miR-17~92 (oncomiR-1) and the Y RNA hY5. We demonstrate self-assembly of three anti-miR XNAzymes into a biostable catalytic XNA nanostructure, which targets the cancer-associated microRNAs miR-17, miR-20a and miR-21. Our results provide a starting point for the development of XNAzymes as a platform technology for precision knockdown of specific non-coding RNAs, with the potential to reduce off-target effects compared with other nucleic acid technologies.

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Section: Discussionmentioning

confidence: 99%

Targeting non-coding RNA family members with artificial endonuclease XNAzymes

et al. 2022

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“…Thanks to modern synthetic chemistry, new methods have emerged to refine the chemistry of canonical nucleotides, including ribose modifications, [16,17] introduction of new chemical moieties to nucleobases, [12,18–20] and genetic alphabet expansion [21–23] . Recently, chemically modified nucleotides compatible with polymerase‐mediated synthesis and useful in the SELEX method for the identification of modified aptamers are depicted in Figure 1 [10,24] . This also reflects a merit of aptamers over antibodies – structural refinements are permitted in aptamers, whereas such modifications usually result in a loss of activity in antibodies.…”

Section: Molecular Designs Of Novel Aptamersmentioning

confidence: 99%

“…[21][22][23] Recently, chemically modified nucleotides compatible with polymerase-mediated synthesis and useful in the SELEX method for the identification of modified aptamers are depicted in Figure 1. [10,24] This also reflects a merit of aptamers over antibodies -structural refinements are permitted in aptamers, whereas such modifications usually result in a loss of activity in antibodies.…”

Section: Molecular Designs Of Novel Aptamersmentioning

confidence: 99%

Chemical Modifications for a Next Generation of Nucleic Acid Aptamers

et al. 2022

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In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (∼30 %) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre‐SELEX and post‐SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non‐natural chemistries will open up new vistas for function and application of nucleic acids.

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“…Recent work has discovered a number of XNA polymerases capable of synthesizing a range of chemically diverse nucleic acids. 7 A majority of these polymerases are derived from B-family DNA polymerases such as Tgo; mutants such as Tgo:TGK are capable of synthesizing up to 74 bases of supF tRNA in under 30 seconds, with measured error rates across various substrates ranging from 8 × 10 −3 to 2 × 10 −4 . 8 Other mutations found to enable XNA synthesis in Tgo have been found to similarly improve homologous B-family polymerases, showing the broad utility of these findings by enabling RNA and TNA synthesis in 9 N, Tgo, Deep Vent and KOD.…”

Section: Introductionmentioning

confidence: 99%