ArticleMethods in molecular biology (Clifton, N.J.)2026
RAP-RNA: A Methodological Approach to Study Base-Pairing Between Endogenous RNAs.
Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Long non-coding RNAs (lncRNAs) engage in RNA-RNA interactions (RRIs) that shape transcript fate and gene regulation, yet these duplexes are often transient and difficult to capture in cells. This chapter presents RNA Antisense Purification-RNA coupled to psoralen crosslinking (RAP-RNA[AMT]), a targeted method to capture direct RNA-RNA base-paired partners of a chosen lncRNA in its native cellular context. Duplexes are stabilized with 4'-aminomethyltrioxsalen (AMT) and UVA; the bait lncRNA is captured with biotinylated antisense probes under high stringency, and RNA partners associated through direct base pairing are released by RNase H digestion and quantified by RT-qPCR. The protocol provides practical guidance on probe design, crosslinking parameters, essential controls, and quantitative analysis. Together, the step-by-step workflow enables high-specificity mapping of lncRNA-centered RRIs and can be adapted for focused validation across diverse targets and cell types.
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