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Molecular beacon design and interactions. (a) MB binding to target mRNA; (b) MB opened by non-specific mRNA that binds to MB stem; (c) MB mis-folds into non-hairpin structure through the hybridization of loop sequence with stem sequence. (d) A newly designed MB using l-DNA for the stem (red) to enforce a hairpin structure,, and d-DNA for the loop (blue) for nucleic acid recognition effectively avoids the situations depicted in (b) and (c).
