title: An Efficient Catalytic DNA that Cleaves L-RNA.
abstract: Many DNAzymes have been isolated from synthetic DNA pools to cleave natural RNA (D-RNA) substrates and some have been utilized for the design of aptazyme biosensors for bioanalytical applications. Even though these biosensors perform well in simple sample matrices, they do not function effectively in complex biological samples due to ubiquitous RNases that can efficiently cleave D-RNA substrates. To overcome this issue, we set out to develop DNAzymes that cleave L-RNA, the enantiomer of D-RNA, which is known to be completely resistant to RNases. Through in vitro selection we isolated three L-RNA-cleaving DNAzymes from a random-sequence DNA pool. The most active DNAzyme exhibits a catalytic rate constant ~3 min-1 and has a structure that contains a kissing loop, a structural motif that has never been observed with D-RNA-cleaving DNAzymes. Furthermore we have used this DNAzyme and a well-known ATP-binding DNA aptamer to construct an aptazyme sensor and demonstrated that this biosensor can achieve ATP detection in biological samples that contain RNases. The current work lays the foundation for exploring RNA-cleaving DNAzymes for engineering biosensors that are compatible with complex biological samples.
authors.affiliation: Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Kha
authors.initials: K
authors.lastname: Tram
authors.affiliation: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Jiaji
authors.initials: J
authors.lastname: Xia
authors.affiliation: Department of Biochemistry and Biomedical Sciences and Origins Institute, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Rachel
authors.initials: R
authors.lastname: Gysbers
authors.affiliation: Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, and Origins Institute, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Yingfu
authors.initials: Y
authors.lastname: Li
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D052157:Aptamers, Nucleotide / Q000378:metabolism; D001483:Base Sequence; D055162:Biocatalysis; D015374:Biosensing Techniques; D021881:DNA, Catalytic / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000378:metabolism*
chemical_list: D052157:Aptamers, Nucleotide; D021881:DNA, Catalytic; D012313:RNA; D000255:Adenosine Triphosphate