A Novel Stable RNA Pentaloop that Interacts Specifically with A Motif Peptide of Lambda-N Protein |
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| Authors: | Junji Kawakami Naoki Sugimoto Hisanori Tokitoh Yoshiatsu Tanabe |
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| Institution: | 1. Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , Higashinada-ku , Kobe , Japan;2. Department of Chemistry, Faculty of Science and Technology , Konan University , Higashinada-ku , Kobe , Japan;3. Department of Chemistry, Faculty of Science and Technology , Konan University , Higashinada-ku , Kobe , Japan |
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| Abstract: | To achieve a novel specific peptide–nucleic acid binding model, we designed an in vitro selection procedure to decrease the energetic contribution of the electrostatic interaction in the total binding energy and to increase the contribution of hydrogen bonding and π–π stacking. After the selection of hairpin-loop RNAs that specifically bound to a model peptide of lambda N protein (N peptide), a new thermostable pentaloop RNA motif (N binding thermostable RNA hairpin: NTS RNA) was revealed. The obtained NTS RNA was able to bind to the N peptide with superior specificity to the boxB RNA, which is the naturally occurring partner of the lambda N protein. |
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| Keywords: | Lambda N protein Stable RNA hairpin Specific binding Thermodynamic analysis |
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