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. 2006 Mar 17;34(5):1581–1587. doi: 10.1093/nar/gkl075

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© The Author 2006. Published by Oxford University Press. All rights reserved

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Binding kinetics of processed (closed symbols) and unprocessed (open symbols) output strands to the aptamer beacon APT, measured by FRET. The three strand designs differ in stem length and loop sizes (triangles, OUT-1, 14 bp stem/10 nt loop, OUT-1*, 6 bp stem/10 nt loop; squares, OUT-2, 11 bp stem/20 nt loop, OUT-2*, 3 bp stem/20 nt loop; circles, OUT-3, 11 bp stem/7 nt loop, OUT-3*, 3 bp stem/7 nt loop). Larger loop sizes lead to stronger unwanted interactions with the aptamer. The stem size further regulates the hybridization rate after output strand cleavage.