{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:39:59Z","timestamp":1772156399248,"version":"3.50.1"},"posted":{"date-parts":[[2024,4,11]]},"group-title":"Molecular Biology","reference-count":82,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,4,11]],"date-time":"2024-04-11T00:00:00Z","timestamp":1712793600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,8,19]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.<\/jats:p>","DOI":"10.1101\/2024.04.11.589009","type":"posted-content","created":{"date-parts":[[2024,4,12]],"date-time":"2024-04-12T00:25:16Z","timestamp":1712881516000},"source":"Crossref","is-referenced-by-count":0,"title":["RNA tertiary structure and conformational dynamics revealed by BASH MaP"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6892-9743","authenticated-orcid":false,"given":"Maxim","family":"Oleynikov","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3615-6958","authenticated-orcid":false,"given":"Samie R.","family":"Jaffrey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2024082205050666000_2024.04.11.589009v4.1","doi-asserted-by":"publisher","DOI":"10.1042\/bj0890127"},{"key":"2024082205050666000_2024.04.11.589009v4.2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1905491116"},{"key":"2024082205050666000_2024.04.11.589009v4.3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.77.8.4679"},{"key":"2024082205050666000_2024.04.11.589009v4.4","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.82.3.648"},{"key":"2024082205050666000_2024.04.11.589009v4.5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/13.23.8339"},{"key":"2024082205050666000_2024.04.11.589009v4.6","doi-asserted-by":"crossref","unstructured":"Wells, S.E. , Hughes, J.M. , Igel, A.H. & Ares Jr, M. [32] Use of dimethyl sulfate to probe RNA structure in vivo. (2000).","DOI":"10.1016\/S0076-6879(00)18071-1"},{"key":"2024082205050666000_2024.04.11.589009v4.7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1407306111"},{"key":"2024082205050666000_2024.04.11.589009v4.8","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nmeth.3029","article-title":"RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)","volume":"11","year":"2014","journal-title":"Nature methods"},{"key":"2024082205050666000_2024.04.11.589009v4.9","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nmeth.4057","article-title":"DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo","volume":"14","year":"2017","journal-title":"Nature Methods"},{"key":"2024082205050666000_2024.04.11.589009v4.10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.48.12.2013"},{"key":"2024082205050666000_2024.04.11.589009v4.11","doi-asserted-by":"publisher","DOI":"10.1261\/rna.1001708"},{"key":"2024082205050666000_2024.04.11.589009v4.12","doi-asserted-by":"publisher","DOI":"10.1093\/carcin\/bgq253"},{"key":"2024082205050666000_2024.04.11.589009v4.13","doi-asserted-by":"publisher","DOI":"10.1261\/rna.041442.113"},{"key":"2024082205050666000_2024.04.11.589009v4.14","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz978"},{"key":"2024082205050666000_2024.04.11.589009v4.15","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.ade2035"},{"key":"2024082205050666000_2024.04.11.589009v4.16","doi-asserted-by":"publisher","DOI":"10.1021\/ja805615w"},{"key":"2024082205050666000_2024.04.11.589009v4.17","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M806277200"},{"key":"2024082205050666000_2024.04.11.589009v4.18","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf5371"},{"key":"2024082205050666000_2024.04.11.589009v4.19","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2112677119"},{"key":"2024082205050666000_2024.04.11.589009v4.20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad522"},{"key":"2024082205050666000_2024.04.11.589009v4.21","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm767"},{"key":"2024082205050666000_2024.04.11.589009v4.22","doi-asserted-by":"crossref","first-page":"3306","DOI":"10.1021\/acschembio.2c00792","article-title":"m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine","volume":"17","year":"2022","journal-title":"ACS Chemical Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.23","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz736"},{"key":"2024082205050666000_2024.04.11.589009v4.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2019.03.036"},{"key":"2024082205050666000_2024.04.11.589009v4.25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm855"},{"key":"2024082205050666000_2024.04.11.589009v4.26","doi-asserted-by":"publisher","DOI":"10.1021\/bi00606a015"},{"key":"2024082205050666000_2024.04.11.589009v4.27","doi-asserted-by":"publisher","DOI":"10.1261\/rna.047910.114"},{"key":"2024082205050666000_2024.04.11.589009v4.28","doi-asserted-by":"publisher","DOI":"10.1126\/science.1207339"},{"key":"2024082205050666000_2024.04.11.589009v4.29","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/nchembio.1561","article-title":"A G-quadruplex\u2013containing RNA activates fluorescence in a GFP-like fluorophore","volume":"10","year":"2014","journal-title":"Nature Chemical Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.30","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1038\/nsmb.2865","article-title":"Structural basis for activity of highly efficient RNA mimics of green fluorescent protein","volume":"21","year":"2014","journal-title":"Nature Structural & Molecular Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.31","doi-asserted-by":"publisher","DOI":"10.1261\/rna.063008.117"},{"key":"2024082205050666000_2024.04.11.589009v4.32","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1619897114"},{"key":"2024082205050666000_2024.04.11.589009v4.33","doi-asserted-by":"crossref","unstructured":"\u0160to\u010dek, J.R. & Dra\u010d\u00ednsk\u00fd, M . Tautomerism of Guanine Analogues. Biomolecules 10 (2020).","DOI":"10.3390\/biom10020170"},{"key":"2024082205050666000_2024.04.11.589009v4.34","doi-asserted-by":"publisher","DOI":"10.1038\/nature12894"},{"key":"2024082205050666000_2024.04.11.589009v4.35","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2022.02.009"},{"key":"2024082205050666000_2024.04.11.589009v4.36","doi-asserted-by":"publisher","DOI":"10.1021\/ja043822v"},{"key":"2024082205050666000_2024.04.11.589009v4.37","doi-asserted-by":"publisher","DOI":"10.1126\/science.7690496"},{"key":"2024082205050666000_2024.04.11.589009v4.38","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/s41594-022-00854-z","article-title":"An atypical RNA quadruplex marks RNAs as vectors for gene silencing","volume":"29","year":"2022","journal-title":"Nature Structural & Molecular Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.39","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/nmeth.3965","article-title":"rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome","volume":"13","year":"2016","journal-title":"Nature Methods"},{"key":"2024082205050666000_2024.04.11.589009v4.40","doi-asserted-by":"crossref","first-page":"9104","DOI":"10.1002\/ange.201603562","article-title":"Structural analysis using SHALiPE to reveal RNA G-quadruplex formation in human precursor microRNA","volume":"128","year":"2016","journal-title":"Angewandte Chemie"},{"key":"2024082205050666000_2024.04.11.589009v4.41","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/s41467-023-35811-x","article-title":"Stress promotes RNA G-quadruplex folding in human cells","volume":"14","year":"2023","journal-title":"Nature Communications"},{"key":"2024082205050666000_2024.04.11.589009v4.42","doi-asserted-by":"publisher","DOI":"10.1261\/rna.058586.116"},{"key":"2024082205050666000_2024.04.11.589009v4.43","doi-asserted-by":"crossref","first-page":"e3000393","DOI":"10.1371\/journal.pbio.3000393","article-title":"Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells","volume":"17","year":"2019","journal-title":"PLoS biology"},{"key":"2024082205050666000_2024.04.11.589009v4.44","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl253"},{"key":"2024082205050666000_2024.04.11.589009v4.45","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-62703-667-2_4"},{"key":"2024082205050666000_2024.04.11.589009v4.46","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq793"},{"key":"2024082205050666000_2024.04.11.589009v4.47","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0806929106"},{"key":"2024082205050666000_2024.04.11.589009v4.48","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0401799101"},{"key":"2024082205050666000_2024.04.11.589009v4.49","doi-asserted-by":"publisher","DOI":"10.1021\/bi3008802"},{"key":"2024082205050666000_2024.04.11.589009v4.50","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg595"},{"key":"2024082205050666000_2024.04.11.589009v4.51","doi-asserted-by":"crossref","unstructured":"Sato, K. & Kato, Y . Prediction of RNA secondary structure including pseudoknots for long sequences. Briefings in Bioinformatics 23 (2021).","DOI":"10.1093\/bib\/bbab395"},{"key":"2024082205050666000_2024.04.11.589009v4.52","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/nprot.2014.001","article-title":"Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria","volume":"9","year":"2014","journal-title":"Nat Protoc"},{"key":"2024082205050666000_2024.04.11.589009v4.53","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl246"},{"key":"2024082205050666000_2024.04.11.589009v4.54","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-129"},{"key":"2024082205050666000_2024.04.11.589009v4.55","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2700"},{"key":"2024082205050666000_2024.04.11.589009v4.56","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/s41586-022-05135-9","article-title":"In vivo single-molecule analysis reveals COOLAIR RNA structural diversity","volume":"609","year":"2022","journal-title":"Nature"},{"key":"2024082205050666000_2024.04.11.589009v4.57","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1038\/s41592-022-01605-0","article-title":"RNA secondary structure packages evaluated and improved by high-throughput experiments","volume":"19","year":"2022","journal-title":"Nature Methods"},{"key":"2024082205050666000_2024.04.11.589009v4.58","doi-asserted-by":"publisher","DOI":"10.1261\/rna.078238.120"},{"key":"2024082205050666000_2024.04.11.589009v4.59","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1038\/nmeth.2701","article-title":"A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat\u2013containing RNA","volume":"10","year":"2013","journal-title":"Nature Methods"},{"key":"2024082205050666000_2024.04.11.589009v4.60","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1038\/s41586-020-2253-5","article-title":"Determination of RNA structural diversity and its role in HIV-1 RNA splicing","volume":"582","year":"2020","journal-title":"Nature"},{"key":"2024082205050666000_2024.04.11.589009v4.61","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2015.04.018"},{"key":"2024082205050666000_2024.04.11.589009v4.62","doi-asserted-by":"crossref","unstructured":"Thiel, B.C. , Beckmann, I.K. , Kerpedjiev, P. & Hofacker, I.L . 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. F1000Research 8 (2019).","DOI":"10.12688\/f1000research.18458.2"},{"key":"2024082205050666000_2024.04.11.589009v4.63","doi-asserted-by":"publisher","DOI":"10.1021\/ja508478x"},{"key":"2024082205050666000_2024.04.11.589009v4.64","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2014.07.041"},{"key":"2024082205050666000_2024.04.11.589009v4.65","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/nchembio.2228","article-title":"Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA","volume":"13","year":"2017","journal-title":"Nat Chem Biol"},{"key":"2024082205050666000_2024.04.11.589009v4.66","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/s41589-019-0459-3","article-title":"Keth-seq for transcriptome-wide RNA structure mapping","volume":"16","year":"2020","journal-title":"Nature Chemical Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.67","doi-asserted-by":"publisher","DOI":"10.1261\/rna.044578.114"},{"key":"2024082205050666000_2024.04.11.589009v4.68","doi-asserted-by":"publisher","DOI":"10.1021\/ja310251r"},{"key":"2024082205050666000_2024.04.11.589009v4.69","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s41592-021-01075-w","article-title":"Genome-scale deconvolution of RNA structure ensembles","volume":"18","year":"2021","journal-title":"Nature Methods"},{"key":"2024082205050666000_2024.04.11.589009v4.70","doi-asserted-by":"publisher","DOI":"10.1261\/rna.061945.117"},{"key":"2024082205050666000_2024.04.11.589009v4.71","doi-asserted-by":"crossref","first-page":"3306","DOI":"10.1021\/acschembio.2c00792","article-title":"m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine","volume":"17","year":"2022","journal-title":"ACS Chemical Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.72","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nmeth.3029","article-title":"RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)","volume":"11","year":"2014","journal-title":"Nature methods"},{"key":"2024082205050666000_2024.04.11.589009v4.73","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad522"},{"key":"2024082205050666000_2024.04.11.589009v4.74","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1905491116"},{"key":"2024082205050666000_2024.04.11.589009v4.75","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2022.02.009"},{"key":"2024082205050666000_2024.04.11.589009v4.76","doi-asserted-by":"publisher","DOI":"10.1261\/rna.061945.117"},{"key":"2024082205050666000_2024.04.11.589009v4.77","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1407306111"},{"key":"2024082205050666000_2024.04.11.589009v4.78","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1619897114"},{"key":"2024082205050666000_2024.04.11.589009v4.79","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/s41586-022-05135-9","article-title":"In vivo single-molecule analysis reveals COOLAIR RNA structural diversity","volume":"609","year":"2022","journal-title":"Nature"},{"key":"2024082205050666000_2024.04.11.589009v4.80","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1038\/nsmb.2865","article-title":"Structural basis for activity of highly efficient RNA mimics of green fluorescent protein","volume":"21","year":"2014","journal-title":"Nature Structural & Molecular Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.81","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/s41594-022-00854-z","article-title":"An atypical RNA quadruplex marks RNAs as vectors for gene silencing","volume":"29","year":"2022","journal-title":"Nature Structural & Molecular Biology"},{"key":"2024082205050666000_2024.04.11.589009v4.82","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2015.04.018"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2024.04.11.589009","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T06:15:32Z","timestamp":1768457732000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2024.04.11.589009"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,11]]},"references-count":82,"URL":"https:\/\/doi.org\/10.1101\/2024.04.11.589009","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.7554\/elife.98540","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.98540.3","asserted-by":"object"}],"has-version":[{"id-type":"doi","id":"10.7554\/eLife.98540.2","asserted-by":"object"},{"id-type":"doi","id":"10.7554\/eLife.98540.1","asserted-by":"object"}]},"subject":[],"published":{"date-parts":[[2024,4,11]]},"subtype":"preprint"}}