An L-RNA Aptamer that Binds and Inhibits RNase

Olea, Charles; Weidmann, Joachim; Dawson, Philip E.; Joyce, Gerald F.

doi:10.1016/j.chembiol.2015.09.017

Cited by 24 publications

(16 citation statements)

References 28 publications

(29 reference statements)

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“…In a particularly striking example, an aptamer produced by this process was shown to function in the presence of a strong nucleolytic enzyme, demonstrating a critical aspect of biostability 13 . Similar successes have also been achieved using mirror-image aptamers (i.e., spiegelmers) 14 , but such reagents are restricted to achiral targets or targets with mirror-images that can be generated by chemical synthesis 15 . Since XNA aptamers are not restricted in this way, they can be used to target a broader range of biological molecules, most notably large proteins and cells that cannot be produced by chemical synthesis 16 .…”

Section: Introductionmentioning

confidence: 88%

Evolution of a General RNA-Cleaving FANA Enzyme

et al. 2018

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The isolation of synthetic genetic polymers (XNAs) with catalytic activity demonstrates that catalysis is not limited to natural biopolymers, but it remains unknown whether such systems can achieve robust catalysis with Michaelis-Menten kinetics. Here, we describe an efficient RNA-cleaving 2’-fluoroarabino nucleic acid enzyme (FANAzyme) that functions with a rate enhancement of >106-fold over the uncatalyzed reaction and exhibits substrate saturation kinetics typical of most natural enzymes. The FANAzyme was generated by in vitro evolution using natural polymerases that were found to recognize FANA substrates with high fidelity. The enzyme comprises a small 25 nucleotide catalytic domain flanked by substrate-binding arms that can be engineered to recognize diverse RNA targets. Substrate cleavage occurs at a specific phosphodiester bond located between an unpaired guanine and a paired uracil in the substrate recognition arm. Our results expand the chemical space of nucleic acid enzymes to include nuclease-resistant scaffolds with strong catalytic activity.

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Section: Introductionmentioning

confidence: 88%

Evolution of a General RNA-Cleaving FANA Enzyme

et al. 2018

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“…Over the years, studies have demonstrated that L-RNA aptamers can be used to detect small molecules, peptides and proteins ( 23–29 ), and several of them are currently under clinical trials ( 30 ). More recently, L-RNA aptamers that target RNA structure were also reported ( 26 , 31–33 ); however, they are limited to stem–loop/hairpin structured RNA region.…”

Section: Introductionmentioning

confidence: 99%

Specific suppression of D-RNA G-quadruplex–protein interaction with an L-RNA aptamer

Umar

Kwok

2020

Nucleic Acids Research

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G-quadruplexes (G4s) are nucleic acid structure motifs that are of significance in chemistry and biology. The function of G4s is often governed by their interaction with G4-binding proteins. Few categories of G4-specific tools have been developed to inhibit G4–protein interactions; however, until now there is no aptamer tool being developed to do so. Herein, we present a novel L-RNA aptamer that can generally bind to D-RNA G-quadruplex (rG4) structure, and interfere with rG4–protein interaction. Using hTERC rG4 as the target for in vitro selection, we report the shortest L-aptamer being developed so far, with only 25 nucleotides. Notably, this new aptamer, L-Apt.4-1c, adopts a stem–loop structure with the loop folding into an rG4 motif with two G-quartet, demonstrates preferential binding toward rG4s over non-G4s and DNA G-quadruplexes (dG4s), and suppresses hTERC rG4–nucleolin interactions. We also show that inhibition of rG4–protein interaction using L-RNA aptamer L-Apt.4-1c is comparable to or better than G4-specific ligands such as carboxypyridostatin and QUMA-1 respectively, highlighting that our approach and findings expand the current G4 toolbox, and open a new avenue for diverse applications.

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“…Consequently, most of the spiegelmers have been selected for small molecules, cytokines, and peptide hormones [ 7 , 8 , 9 ]. The only published spiegelmer that was isolated using a full-length D-enantiomer protein as target of SELEX (Systematic Evolution of Ligands by EXponential Enrichment) is selective for a small, 110 amino acid-composed RNase, indicating the limits of this approach [ 10 ]. Notwithstanding, the structural analysis of aptamer- and spiegelmer-protein complexes revealed that these oligonucleotides interact with their target through definite amino acid motifs; thus, theoretically protein-selective spiegelmers can be generated without application of D-enantiomers of complete proteins [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

Spiegelmer-Based Sandwich Assay for Cardiac Troponin I Detection

Tolnai

András

Szeitner

et al. 2020

IJMS

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Two subunits of the ternary troponin complex, I and C, have cardiac muscle specific isoforms, and hence could be applied as highly-selective markers of acute coronary syndrome. We aimed at paving the way for the development of a robust cardiac troponin I-detecting sandwich assay by replacing antibodies with nuclease resistant aptamer analogues, so-called spiegelmers. To complement the previously generated spiegelmers that were specific for the N-terminus of cTnI, spiegelmers were selected for an amino acid stretch in the proximity of the C-terminal part of the protein by using a D-amino acid composed peptide. Following the selection, the oligonucleotides were screened by filter binding assay, and surface plasmon resonance analysis of the most auspicious candidates demonstrated that this approach could provide spiegelmers with subnanomolar dissociation constant. To demonstrate if the selected spiegelmers are functional and suitable for cTnI detection in a sandwich type arrangement, AlphaLisa technology was leveraged and the obtained results demonstrated that spiegelmers with different epitope selectivity are suitable for specific detection of cTnI protein even in human plasma containing samples. These results suggest that spiegelmers could be considered in the development of the next generation cTnI monitoring assays.

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An L-RNA Aptamer that Binds and Inhibits RNase

Cited by 24 publications

References 28 publications

Evolution of a General RNA-Cleaving FANA Enzyme

Evolution of a General RNA-Cleaving FANA Enzyme

Specific suppression of D-RNA G-quadruplex–protein interaction with an L-RNA aptamer

Spiegelmer-Based Sandwich Assay for Cardiac Troponin I Detection

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