PMC:549404 / 39262-40909 JSONTXT

{"project":"2_test","denotations":[{"id":"15722480-8614641-77356741","span":{"begin":460,"end":462},"obj":"8614641"},{"id":"15722480-10385001-77356741","span":{"begin":460,"end":462},"obj":"10385001"},{"id":"15722480-12198171-77356741","span":{"begin":460,"end":462},"obj":"12198171"},{"id":"15722480-10385001-77356742","span":{"begin":629,"end":631},"obj":"10385001"},{"id":"15722480-12952464-77356743","span":{"begin":1387,"end":1389},"obj":"12952464"}],"text":"Reactivity of photo-crosslinkers\nIn addition to allowing us to explore structural and dynamic properties of the hairpin ribozyme in aqueous solutions, our data provide information about the reactive properties of the photo-crosslinkers themselves. We found that decreasing tether length results in fewer crosslinks and lower yields. ‘Zero-length’ photo-crosslinkers such as 4-thio uridine, have been used extensively in investigations of the structure of RNA (36–39). Although fewer crosslinks are obtained, they give higher resolution structural data because the distance constraints they provide can be confined to within 4 Å (38). Similarly, we observe fewer crosslinks with the shorter crosslinkers, but the distance constraints they provide are confined to a smaller range.\nFluorine substitution decreases crosslinking yields. Phenylazide 2, which has the same structure as 1 except for the fluorine substitutions in the aromatic ring, crosslinks with about an order of magnitude less efficiency than 1. This could be due to higher reactivity of the nitrene formed upon irradiation of 2, which could decrease its lifetime due to reactions with solvent and buffer molecules. In addition, the nitrene generated by photolysis of unsubstituted aryl azides can rearrange to an electrophilic dehydroazepine intermediate, providing a photo-crosslinking mechanism by nucleophilic addition (27,28). An important result from this study is that no new crosslinks were formed by 2 compared to 1, showing that the determinant of photo-crosslinking sites for these phenylazide crosslinkers is the length, rather than the chemistry of the photo-crosslinker."}