A rapid and simple quantitative method for specific Detection of Smaller Co-terminal RNA by PCR (DeSCo-PCR): Application to the detection of viral subgenomic RNAs

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Kanodia, Pulkit
Prasanth, K. Reddisiva
Roa-Linares, Vicky
Bradrick, Shelton
Garcia-Blanco, Mariano
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Miller, W. Allen
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Plant Pathology and Microbiology
The Department of Plant Pathology and Microbiology and the Department of Entomology officially merged as of September 1, 2022. The new department is known as the Department of Plant Pathology, Entomology, and Microbiology (PPEM). The overall mission of the Department is to benefit society through research, teaching, and extension activities that improve pest management and prevent disease. Collectively, the Department consists of about 100 faculty, staff, and students who are engaged in research, teaching, and extension activities that are central to the mission of the College of Agriculture and Life Sciences. The Department possesses state-of-the-art research and teaching facilities in the Advanced Research and Teaching Building and in Science II. In addition, research and extension activities are performed off-campus at the Field Extension Education Laboratory, the Horticulture Station, the Agriculture Engineering/Agronomy Farm, and several Research and Demonstration Farms located around the state. Furthermore, the Department houses the Plant and Insect Diagnostic Clinic, the Iowa Soybean Research Center, the Insect Zoo, and BugGuide. Several USDA-ARS scientists are also affiliated with the Department.
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RNAs that are 5’-truncated versions of a longer RNA, but share the same 3’ terminus can be generated by alternative promoters in transcription of cellular mRNAs or by replicating RNA viruses. These truncated RNAs cannot be distinguished from the longer RNA by a simple two-primer RT-PCR because primers that anneal to the cDNA from the smaller RNA also anneal to - and amplify - the longer RNA-derived cDNA. Thus, laborious methods, such as northern blot hybridization, are used to distinguish shorter from longer RNAs. For rapid, low-cost and specific detection of these truncated RNAs, we report Detection of Smaller Co-terminal RNA by PCR (DeSCo-PCR). DeSCo-PCR employs a non-extendable blocking primer (BP), which outcompetes a forward primer (FP) for annealing to longer RNA-derived cDNA, while FP outcompetes BP for annealing to shorter RNA-derived cDNA. In the presence of BP, FP and the reverse primer, only cDNA from the shorter RNA is amplified in a single-tube reaction containing both RNAs. Many positive strand RNA viruses generate 5’-truncated forms of the genomic RNA (gRNA) called subgenomic RNAs (sgRNA), which play key roles in viral gene expression and pathogenicity. We demonstrate that DeSCo-PCR is easily optimized to selectively detect relative quantities of sgRNAs of red clover necrotic mosaic virus from plants and Zika virus from human cells, each infected with viral strains that generate different amounts of sgRNA. This technique should be readily adaptable to other sgRNA-producing viruses, and for quantitative detection of any truncated or alternatively spliced RNA.


This is a manuscript of an article published as Kanodia, Pulkit, K. Reddisiva Prasanth, Vicky C. Roa-Linares, Shelton S. Bradrick, Mariano A. Garcia-Blanco, and W. Allen Miller. "A rapid and simple quantitative method for specific Detection of Smaller Co-terminal RNA by PCR (DeSCo-PCR): Application to the detection of viral subgenomic RNAs." RNA (2020). doi: 10.1261/rna.074963.120.

Wed Jan 01 00:00:00 UTC 2020