Hingerty, B., Brown, R. S. & Jack, A. Further refinement of the structure of yeast tRNAPhe. J. Mol. Biol. 124, 523–534 (1978).

Article  CAS  PubMed  Google Scholar 

Chen, Y. & Pollack, L. SAXS studies of RNA: structures, dynamics, and interactions with partners. Wiley Interdiscip. Rev. RNA 7, 512–526 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dagenais, P., Desjardins, G. & Legault, P. An integrative NMR–SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme. Nucleic Acids Res. 49, 11959–11973 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheong, C. & Moore, P. B. Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures. Biochemistry 31, 8406–8414 (1992).

Article  CAS  PubMed  Google Scholar 

Barnwal, R. P., Yang, F. & Varani, G. Applications of NMR to structure determination of RNAs large and small. Arch. Biochem. Biophys. 628, 42–56 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gabashvili, I. S. et al. Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100, 537–549 (2000).

Article  CAS  PubMed  Google Scholar 

Wrede, P., Wurst, R., Vournakis, J. & Rich, A. Conformational changes of yeast tRNAPhe and E. coli tRNA2Glu as indicated by different nuclease digestion patterns. J. Biol. Chem. 254, 9608–9616 (1979).

Article  CAS  PubMed  Google Scholar 

Wurst, R. M., Vournakis, J. N. & Maxam, A. M. Structure mapping of 5′-32P-labeled RNA with S1 nuclease. Biochemistry 17, 4493–4499 (1978).

Article  CAS  PubMed  Google Scholar 

Lockard, R. E. & Kumar, A. Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom. Nucleic Acids Res. 9, 5125–5140 (1981).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lempereur, L. et al. Conformation of yeast 18S rRNA. Direct chemical probing of the 5′ domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible. Nucleic Acids Res. 13, 8339–8357 (1985).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Merino, E. J., Wilkinson, K. A., Coughlan, J. L. & Weeks, K. M. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127, 4223–4231 (2005).

Article  CAS  PubMed  Google Scholar 

Wan, Y., Kertesz, M., Spitale, R. C., Segal, E. & Chang, H. Y. Understanding the transcriptome through RNA structure. Nat. Rev. Genet. 12, 641–655 (2011).

Article  CAS  PubMed  Google Scholar 

Kertesz, M. et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103–107 (2010).

Article  CAS  PubMed  Google Scholar 

Underwood, J. G. et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods 7, 995–1001 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rouskin, S., Zubradt, M., Washietl, S., Kellis, M. & Weissman, J. S. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505, 701–705 (2014).

Article  CAS  PubMed  Google Scholar 

Ding, Y. et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505, 696–700 (2014).

Article  CAS  PubMed  Google Scholar 

Wan, Y. et al. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706–709 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Homan, P. J. et al. Single-molecule correlated chemical probing of RNA. Proc. Natl Acad. Sci. USA 111, 13858–13863 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Spitale, R. C. & Incarnato, D. Probing the dynamic RNA structurome and its functions. Nat. Rev. Genet. 24, 178–196 (2023).

Article  CAS  PubMed  Google Scholar 

Strobel, E. J., Yu, A. M. & Lucks, J. B. High-throughput determination of RNA structures. Nat. Rev. Genet. 19, 615–634 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Corley, M. et al. Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA–protein interfaces. Mol. Cell 80, 903–914.e8 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee, B. et al. Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA 23, 169–174 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Spitale, R. C. et al. RNA SHAPE analysis in living cells. Nat. Chem. Biol. 9, 18–20 (2013).

Article  CAS  PubMed  Google Scholar 

Marinus, T., Fessler, A. B., Ogle, C. A. & Incarnato, D. A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy. Nucleic Acids Res. 49, e34 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. & Weeks, K. M. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat. Methods 11, 959–965 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zubradt, M. et al. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat. Methods 14, 75–82 (2017).

Article  CAS  PubMed  Google Scholar 

Aviran, S. & Incarnato, D. Computational approaches for RNA structure ensemble deconvolution from structure probing data. J. Mol. Biol. 434, 167635 (2022).

Article  CAS  PubMed  Google Scholar 

Busan, S., Weidmann, C. A., Sengupta, A. & Weeks, K. M. Guidelines for SHAPE reagent choice and detection strategy for RNA structure probing studies. Biochemistry 58, 2655–2664 (2019).

Article  CAS  PubMed  Google Scholar 

Guo, L. T. et al. Sequencing and structure probing of long RNAs using MarathonRT: a next-generation reverse transcriptase. J. Mol. Biol. 432, 3338–3352 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mitchell, D., Cotter, J., Saleem, I. & Mustoe, A. M. Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS. Nucleic Acids Res. 51, 8744–8757 (2023).