{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:04:38Z","timestamp":1791219878423,"version":"4.1.0"},"reference-count":74,"publisher":"Cold Spring Harbor Laboratory","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["RNA"],"published-print":{"date-parts":[[2011,10]]},"abstract":"<jats:p>\n                    Biological RNAs, like their DNA counterparts, contain helical stretches, which have standard Watson-Crick base pairs in the\n                    <jats:italic>anti<\/jats:italic>\n                    conformation. Most functional RNAs also adopt geometries with far greater complexity such as bulges, loops, and multihelical junctions. Occasionally, nucleobases in these regions populate the\n                    <jats:italic>syn<\/jats:italic>\n                    conformation wherein the base resides close to or over the ribose sugar, which leads to a more compact state. The importance of the\n                    <jats:italic>syn<\/jats:italic>\n                    conformation to RNA function is largely unknown. In this study, we analyze 51 RNAs with tertiary structure, including aptamers, riboswitches, ribozymes, and ribosomal RNAs, for number, location, and properties of\n                    <jats:italic>syn<\/jats:italic>\n                    nucleobases. These RNAs represent the set of nonoverlapping, moderate- to high-resolution structures available at present. We find that\n                    <jats:italic>syn<\/jats:italic>\n                    nucleobases are much more common among purines than pyrimidines, and that they favor C2\u2032-endo-like conformations especially among those nucleobases in the intermediate\n                    <jats:italic>syn<\/jats:italic>\n                    conformation. Strikingly, most\n                    <jats:italic>syn<\/jats:italic>\n                    nucleobases participate in tertiary stacking and base-pairing interactions: Inspection of RNA structures revealed that the majority of the\n                    <jats:italic>syn<\/jats:italic>\n                    nucleobases are in regions assigned to function, with many\n                    <jats:italic>syn<\/jats:italic>\n                    nucleobases interacting directly with a ligand or ribozyme active site. These observations suggest that judicious placement of conformationally restricted nucleotides biased into the\n                    <jats:italic>syn<\/jats:italic>\n                    conformation could enhance RNA folding and catalysis. Such changes could also be useful for locking RNAs into functionally competent folds for use in X-ray crystallography and NMR.\n                  <\/jats:p>","DOI":"10.1261\/rna.2759911","type":"journal-article","created":{"date-parts":[[2011,8,27]],"date-time":"2011-08-27T01:02:14Z","timestamp":1314406934000},"page":"1775-1787","source":"Crossref","is-referenced-by-count":63,"title":["Prevalence of\n                    <i>syn<\/i>\n                    nucleobases in the active sites of functional RNAs"],"prefix":"10.1261","volume":"17","author":[{"given":"Joshua E.","family":"Sokoloski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie A.","family":"Godfrey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah E.","family":"Dombrowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip C.","family":"Bevilacqua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2011,8,26]]},"reference":[{"key":"2021112105513820000_17.10.1775.1","doi-asserted-by":"publisher","DOI":"10.1261\/rna.853208"},{"key":"2021112105513820000_17.10.1775.2","doi-asserted-by":"publisher","DOI":"10.1038\/nature02642"},{"key":"2021112105513820000_17.10.1775.3","unstructured":"Anderson TW , Sclove SL . 1986. The statistical analysis of data. Scientific Press, Palo Alto, CA."},{"key":"2021112105513820000_17.10.1775.4","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0308014101"},{"key":"2021112105513820000_17.10.1775.5","doi-asserted-by":"publisher","DOI":"10.1038\/nature03037"},{"key":"2021112105513820000_17.10.1775.6","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3951"},{"key":"2021112105513820000_17.10.1775.7","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.1016\/j.str.2005.10.003","article-title":"Syn-full behavior by T7 DNA polymerase","volume":"13","year":"2005","journal-title":"Structure"},{"key":"2021112105513820000_17.10.1775.8","doi-asserted-by":"publisher","DOI":"10.1111\/j.1432-1033.1977.tb11885.x"},{"key":"2021112105513820000_17.10.1775.9","doi-asserted-by":"publisher","DOI":"10.1021\/bi027273m"},{"key":"2021112105513820000_17.10.1775.10","unstructured":"Bloomfield VA , Crothers DM , Tinoco I Jr . 2000. Nucleic acids: Structures, properties, and functions. 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