Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP

Thomas W. Christy, Catherine A. Giannetti, Gillian Houlihan, Matthew J. Smola, Greggory M. Rice, Jian Wang, Nikolay V. Dokholyan, Alain Laederach, Philipp Holliger, Kevin M. Weeks

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


Higher-order structure governs function for many RNAs. However, discerning this structure for large RNA molecules in solution is an unresolved challenge. Here, we present SHAPE-JuMP (selective 2′-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) to interrogate through-space RNA tertiary interactions. A bifunctional small molecule is used to chemically link proximal nucleotides in an RNA structure. The RNA cross-link site is then encoded into complementary DNA (cDNA) in a single, direct step using an engineered reverse transcriptase that “jumps” across cross-linked nucleotides. The resulting cDNAs contain a deletion relative to the native RNA sequence, which can be detected by sequencing, that indicates the sites of cross-linked nucleotides. SHAPE-JuMP measures RNA tertiary structure proximity concisely across large RNA molecules at nanometer resolution. SHAPE-JuMP is especially effective at measuring interactions in multihelix junctions and loop-to-helix packing, enables modeling of the global fold for RNAs up to several hundred nucleotides in length, facilitates ranking of structural models by consistency with through-space restraints, and is poised to enable solution-phase structural interrogation and modeling of complex RNAs.

Original languageEnglish (US)
Pages (from-to)1971-1982
Number of pages12
Issue number25
StatePublished - Jun 29 2021

All Science Journal Classification (ASJC) codes

  • Biochemistry


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