Abstract
Fluorescent base analogues (FBAs) are widely used as spectroscopic tools to probe RNA and DNA structure. Because of their chemical similarity with the naturally occurring bases, they are typically assumed to exert minimal perturbations on the systems they are used to study. However, this cannot be taken for granted. We have systematically investigated the effects of FBA substitution on the folding of the preQ1 riboswitch, which regulates gene expression in response to the ligand preQ1. We placed a popular FBA, the adenine analogue 2-aminopurine (2-AP), at different locations within a stretch of six adenine residues termed “L3”.
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