RNA Detection

Capture Probe

CEs

LEs

Mix lysate with

all probes

Add hairpin

Set X

Add hairpin

Set A

Capture Stage

Amplification Stage

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Adaptor

Target RNA

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Fig. 4Schematic illustration of the direct RNA detection assay. For each target

RNA, the capture hybridization method is done with a series of oligonucleotide

probes (CEs and LEs), each of these probes containing a target-specific

sequence which is complementary to a different region of the target, and an

additional “tail” sequence that is independent of the target sequence but can

interact with either the solid support (CEs) or the adaptor (LEs). The CEs and LEs

sandwich the target RNA through target-specific hybridizations. The common CE

tail sequences hybridize to the capture probe conjugate on the surface of each

well in 96-well plate and capture the associated target RNA onto the plate. The

adaptors bind to the common LE tails and initiate the on-site 2D HCR after the

addition of hairpins. Figure adapted from [5] with permission from Elsevier

190 Yao Xu and Zhi Zheng