A complex RNA-cleaving DNAzyme that can efficiently cleave a pyrimidine-pyrimidine junction

Journal of Molecular Biology
Jeffrey C F LamYingfu Li

Abstract

Several RNA-cleaving deoxyribozymes (DNAzymes) have been reported for efficient cleavage of purine-containing junctions, but none is able to efficiently cleave pyrimidine-pyrimidine (Pyr-Pyr) junctions. We hypothesize that a stronger Pyr-Pyr cleavage activity requires larger DNAzymes with complex structures that are difficult to isolate directly from a DNA library; one possible way to obtain such DNAzymes is to optimize DNA sequences with weak activities. To test this, we carried out an in vitro selection study to derive DNAzymes capable of cleaving an rC-T junction in a chimeric DNA/RNA substrate from DNA libraries constructed through chemical mutagenesis of five previous DNAzymes with a k(obs) of approximately 0.001 min-1 for the rC-T junction. After several rounds of selective amplification, DNAzyme descendants with a k(obs) of approximately 0.1 min-1 were obtained from a DNAzyme pool. The most efficient motif, denoted "CT10-3.29," was found to have a catalytic core of approximately 50 nt, larger than other known RNA-cleaving DNAzymes, and its secondary structure contains five short duplexes confined by a four-way junction. Several variants of CT10-3.29 exhibit a k(obs) of 0.3-1.4 min-1 against the rC-T junction. CT10-3.29 a...Continue Reading

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Citations

Jan 25, 2011·Chemical Communications : Chem Comm·Kennedy O Alila, Dana A Baum
Apr 15, 2011·PloS One·Jianzhong Yi, Chengqian Liu
Dec 5, 2012·Journal of Nucleic Acids·Kha TramYingfu Li
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Sep 19, 2020·Chemical Society Reviews·Ronald Micura, Claudia Höbartner
Feb 20, 2020·Talanta·Alessandra C ZimmermannJason D Kahn
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Feb 18, 2021·Communications Biology·Rika InomataMakoto Miyagishi
Jun 30, 2021·Angewandte Chemie·Anam LiaqatClaudia Höbartner
Aug 15, 2017·Accounts of Chemical Research·Meng LiuYingfu Li

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