Exploiting inosine as a distinctive cleavage site for deriving a highly specific RNA-cleaving DNAzyme.
- 1Central Hospital of Dalian University of Technology, Dalian Medical-Engineering Interdisciplinary Rapid Diagnosis of Major Diseases Laboratory, Dalian University of Technology Dalian 116000 China [email protected] [email protected] [email protected].
- 2School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology Dalian 116024 China.
Abstract
Most RNA-cleaving DNAzymes are limited to cleaving between combinations of the four canonical ribonucleotides. Through in vitro selection, we isolated ICD11-1T, a DNAzyme that selectively cleaves at inosine, a non-canonical RNA modification generated by adenosine deamination. ICD11-1T cleaves inosine-containing substrates with a rate constant of 0.1 min⁻¹ and achieves >10³-fold selectivity over adenosine, discriminating between nucleosides that differ at the C6 and N1 positions of the purine ring. Molecular dynamics simulations revealed that the inosine positions the cleavage site near the catalytic core, whereas the adenosine complex sequesters it away, accounting for the stringent specificity. Using ICD11-1T, we constructed a fluorescent biosensor that enabled imaging of endogenous ADAR (adenosine deaminase acting on RNA) editing activity in fixed and permeabilized cells. This work provides a proof-of-concept tool for studying adenosine-to-inosine (A-to-I) RNA editing and establishes a strategy for expanding the functionality of DNAzymes.
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BibTeX
@article{xiao2026exploiting,
title = {{Exploiting inosine as a distinctive cleavage site for deriving a highly specific RNA-cleaving DNAzyme.}},
author = {Shusen Xiao and Pan Jia and Kai Niu and Xiaoqian Li and Xiaozheng Li and Yangyang Chang and Zijie Zhang and Hong Yuan and Jiuxing Li and Meng Liu},
journal = {Chemical science},
year = {2026},
month = oct,
doi = {10.1039/d6sc06852a},
url = {https://europepmc.org/article/MED/42904253},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Exploiting inosine as a distinctive cleavage site for deriving a highly specific RNA-cleaving DNAzyme.
AU - Shusen Xiao
AU - Pan Jia
AU - Kai Niu
AU - Xiaoqian Li
AU - Xiaozheng Li
AU - Yangyang Chang
AU - Zijie Zhang
AU - Hong Yuan
AU - Jiuxing Li
AU - Meng Liu
PY - 2026
DA - 2026/10/19
JO - Chemical science
DO - 10.1039/d6sc06852a
UR - https://europepmc.org/article/MED/42904253
AB - Most RNA-cleaving DNAzymes are limited to cleaving between combinations of the four canonical ribonucleotides. Through in vitro selection, we isolated ICD11-1T, a DNAzyme that selectively cleaves at inosine, a non-canonical RNA modification generated by adenosine deamination. ICD11-1T cleaves inosine-containing substrates with a rate constant of 0.1 min⁻¹ and achieves >10³-fold selectivity over adenosine, discriminating between nucleosides that differ at the C6 and N1 positions of the purine ring. Molecular dynamics simulations revealed that the inosine positions the cleavage site near the catalytic core, whereas the adenosine complex sequesters it away, accounting for the stringent specificity. Using ICD11-1T, we constructed a fluorescent biosensor that enabled imaging of endogenous ADAR (adenosine deaminase acting on RNA) editing activity in fixed and permeabilized cells. This work provides a proof-of-concept tool for studying adenosine-to-inosine (A-to-I) RNA editing and establishes a strategy for expanding the functionality of DNAzymes.
SN - 2041-6520
SN - 2041-6539
ER -