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To interrogate sequence-level drivers of rG4 folding, we applied a reverse-transcriptase stop sequencing strategy to a library of \u223c3000 synthetic rG4s with varied G-tract lengths, loop lengths, and loop compositions, permitting massively parallel quantification of rG4 stability. Our data confirm known sequence-level features and characterize novel combinatorial impacts of these features. We also assessed systematically mutagenized natural rG4s, revealing unexpected mutations that significantly affect rG4 stability, including contributions from flanking sequences outside of the rG4. We further used our strategy to assess rG4 recognition preferences of the model rG4 ligand pyridostatin, revealing a preferential stabilization of rG4s containing mixed-length G-tracts. We additionally demonstrated the potential for large-scale protein-binding assays with our library to reveal rG4 features recognized by RBPs, specifically G3BP1 and FMRP. Our approach and data provide a generalizable framework to study sequence-level drivers of rG4 stability, binding by RBPs, and ligand interactions, defining basic principles of rG4 formation and downstream biology.<\/jats:p>","DOI":"10.1093\/nar\/gkag821","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T11:12:32Z","timestamp":1786101152000},"source":"Crossref","is-referenced-by-count":0,"title":["Massively parallel characterization of RNA G-quadruplex stability and molecular recognition"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0057-5387","authenticated-orcid":false,"given":"Justin G","family":"Martyr","sequence":"first","affiliation":[{"name":"Department of Pharmacology, University of North Carolina , Chapel Hill, NC 27599 ,","place":["United States"]},{"name":"Blood Research Center, University of North Carolina , Chapel Hill, NC 27599 ,","place":["United 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