Surface Plasmon Resonance for Investigating Molecular Interactions with RNA

Area of Science:

• Biochemistry
• Molecular Biology
• Biophysics

Background:

• Surface plasmon resonance (SPR) is a label-free technology widely used for real-time monitoring of molecular interactions.
• SPR instruments offer high sensitivity to mass changes, enabling the analysis of diverse molecular complexes, including small molecules and macromolecules.
• Nucleic acids, particularly RNA, are well-suited for SPR analysis due to their low non-specific binding to sensor surfaces.

Purpose of the Study:

• To present and illustrate methods for analyzing RNA-protein and RNA-RNA interactions using SPR.
• To demonstrate the adaptability of SPR for studying molecular recognition involving RNA molecules.
• To quantify binding kinetics and equilibrium constants for specific RNA-involved complexes.

Main Methods:

• Utilized SPR spectroscopy to monitor binding events in real-time.
• Immobilized protein or RNA molecules onto SPR sensor chips.
• Analyzed the interaction between the protein Rop and two distinct RNA-RNA loop-loop complexes: RNAI-RNAII and a TAR-TAR* complex.

Main Results:

• Successfully monitored and characterized the molecular interactions between Rop and RNA complexes using SPR.
• Determined binding kinetics and dissociation equilibrium constants for the studied complexes.
• Validated the utility of SPR for analyzing RNA-mediated molecular recognition.

Conclusions:

• SPR is a powerful and versatile tool for studying molecular interactions involving RNA.
• The described methods are adaptable for various RNA-containing complexes and different SPR platforms.
• SPR facilitates a deeper understanding of molecular recognition mechanisms in biological systems involving RNA.