研究目的
Investigating the binding dynamics and mechanism of neomycin to its RNA aptamer using a cytidine analog as a fluorescent label.
研究成果
The study demonstrates that C? m f is a sensitive probe for RNA dynamics and can be used to study the binding mechanism of neomycin to its aptamer. The two-step binding mechanism was identified, with conformational selection playing a dominant role.
研究不足
The study is limited by the specific RNA sequences and conditions used, and the potential effects of the fluorescent label on RNA structure and dynamics.
1：Experimental Design and Method Selection:
The study utilized steady-state and time-resolved fluorescence spectroscopy to evaluate the photophysical properties of C? m f in RNA and to investigate the binding of neomycin to its aptamer.
2：Sample Selection and Data Sources:
RNA model sequences and neomycin aptamers were synthesized and labeled with C? m f at specific positions.
3：List of Experimental Equipment and Materials:
Instruments included a JASCO V-650 spectrometer for absorption spectra, a JASCO FP 8500 fluorescence spectrometer for emission spectra, and a stopped-flow setup for binding kinetics.
4：Experimental Procedures and Operational Workflow:
Samples were annealed before measurements. Thermal denaturation experiments were conducted to assess the effect of C? m f on duplex stability.
5：Data Analysis Methods:
Fluorescence lifetimes were measured with a time-correlated single photon counting setup. Binding kinetics were analyzed using DynaFit software.
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