Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction

详细信息    查看全文

• 作者：Tamaki Endoh ; Naoki Sugimoto
• 刊名：Analytical Chemistry
• 出版年：2015
• 出版时间：August 4, 2015
• 年：2015
• 卷：87
• 期：15
• 页码：7628-7635
• 全文大小：573K
• ISSN：1520-6882

文摘

Conformational transitions of biomolecules in response to specific stimuli control many biological processes. In natural functional RNA switches, often called riboswitches, a particular RNA structure that has a suppressive or facilitative effect on gene expression transitions to an alternative structure with the opposite effect upon binding of a specific metabolite to the aptamer region. Stability of RNA secondary structure (鈭捨?i>G掳) can be predicted based on thermodynamic parameters and is easily tuned by changes in nucleobases. We envisioned that tuning of a functional RNA switch that causes an allosteric interaction between an RNA and a peptide would be possible based on a predicted switching energy (螖螖G掳) that corresponds to the energy difference between the RNA secondary structure before (鈭捨?i>G掳_before) and after (鈭捨?i>G掳_after) the RNA conformational transition. We first selected functional RNA switches responsive to neomycin with predicted 螖螖G掳 values ranging from 5.6 to 12.2 kcal mol^鈥?. We then demonstrated a simple strategy to rationally convert the functional RNA switch to switches responsive to natural metabolites thiamine pyrophosphate, S-adenosyl methionine, and adenine based on the predicted 螖螖G掳 values. The 螖螖G掳 values of the designed RNA switches proportionally correlated with interaction energy (螖G掳_interaction) between the RNA and peptide, and we were able to tune the sensitivity of the RNA switches for the trigger molecule. The strategy demonstrated here will be generally applicable for construction of functional RNA switches and biosensors in which mechanisms are based on conformational transition of nucleic acids.