Parameters of DNA Fingerloop Structured Antisense Probes that Discriminate Against Mismatched Pairing Partners
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Date
2020-05
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The Ohio State University
Abstract
Nanotechnology is a rapidly expanding field of study due to its potential use in several fields, including medicine and industry. Many RNA nanotechnology objects are designed for proof–in–principle, but a few are derived from natural RNAs (1-3). One such natural RNA is the E. coli native antisense regulatory small RNA, DsrA, which can translationally regulate gene expression by antisense RNA interactions with mRNA targets. DsrA contains atypical structured antisense domains in stem-loops called fingerloops, which behave similarly to toehold sequences (4) to initiate seed sequence pairing and form a base–paired complex with a target mRNA. The fingerloop contains antisense sequence in the loop and one side of the stem that can form base pairs with a specific nucleotide sequence. Additionally, the fingerloop has the interesting quality of being able to discriminate against even single base mismatches between the fingerloop loop sequence and the target sequence. It was previously observed that DNA fingerloops function similarly to RNA in single-base mismatch exclusion. With DNA as with RNA, if a mutation between the nucleic acid pairing target and fingerloop probe falls within the loop portions of the fingerloop, some degree of discrimination is seen against pairing with a mismatched target. To better understand this fundamental property, we delineated certain parameters and limitations of the fingerloop. In this study, we evaluated mismatch location, loop size and sequence content contributions to the mismatch exclusion function of fingerloop DNAs. Strikingly, by forcing the entire 18-nt antisense sequence into the loop portion, exclusion of mismatched targets is enhanced.
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nanotechnology, fingerloop, sRNA, DNA