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Updated: Jan 30, 2026

Simple and Fast Rolling Circle Amplification-Based Detection of Topoisomerase 1 Activity in Crude Biological Samples
Published on: December 2, 2022
Assessment and optimization of rolling circle amplification protocols for the detection and characterization of
Amit C Sukal1, Dawit B Kidanemariam2, James L Dale2
1Centre for Tropical Crops and Biocommodities (CTCB), Faculty of Science and Engineering (SEF), Queensland University of Technology (QUT), Brisbane 4001, Australia; Centre for Pacific Crops and Trees (CePaCT), Land Resource Division (LRD), Pacific Community (SPC), Suva, Fiji.
Abstract:
The genus Badnavirus is characterized by members that are genetically and serologically heterogeneous which presents challenges for their detection and characterization. The presence of integrated badnavirus-like sequences in some host species further complicates detection using PCR-based protocols. To address these challenges, we have assessed and optimized various RCA protocols including random-primed RCA (RP-RCA), primer-spiked random-primed RCA (primer-spiked RP-RCA), directed RCA (D-RCA) and specific-primed RCA (SP-RCA). Using Dioscorea bacilliform AL virus (DBALV) as an example, we demonstrate that viral DNA amplified using the optimized D-RCA and SP-RCA protocols showed an 85-fold increase in badnavirus NGS reads compared with RP-RCA. The optimized RCA techniques described here were used to detect a range of badnaviruses infecting banana, sugar cane, taro and yam demonstrating the utility of RCA for detection of diverse badnaviruses infecting a variety of host plant species.
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