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Stable RNA stem-loops were designed using mfold (Mathews, D. H.; Sabrina, J.; Zuker, M.; Turner, D. H. J. Mol. Biol. 1999, 288, 911). The corresponding pentaloop showed multiple structures in mfold and was thus not utilized in this study.
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note
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Absence of aminoglycoside binding was also confirmed by RNase I footprinting.
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For examples of such an approach, see: (a) Lee, J.; Kwon, M.; Lee, K. H.; Jeong, S.; Hyun, S.; Shin, K. J.; Yu, J. J. Am. Chem. Soc. 2004, 126, 1956.
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