In vitro selected RNA molecules that bind to elongation factor Tu

Area of Science:

• Molecular Biology
• Biochemistry
• RNA Biology

Background:

• Elongation factor Tu (EF-Tu) is crucial for bacterial protein synthesis, facilitating the binding of aminoacyl-tRNA to the ribosome.
• Understanding EF-Tu's interactions is key to deciphering translational regulation and developing novel antibiotics.
• RNA aptamers are powerful tools for studying protein-RNA interactions due to their specific binding capabilities.

Purpose of the Study:

• To isolate and characterize novel RNA molecules (aptamers) that bind to elongation factor Tu (EF-Tu) from *T. thermophilus*.
• To determine the binding characteristics and specificity of these RNA aptamers with EF-Tu.
• To identify the binding site and structural requirements for RNA-EF-Tu interaction.

Main Methods:

• Selection of RNA aptamers from a randomized pool by affinity to EF-Tu.
• Characterization of RNA binding to different forms of EF-Tu (GTP and GDP bound).
• Competition assays to identify binding sites and specificity, including probing with chemical methods and deletion analysis.

Main Results:

• Novel RNA aptamers that bind to *T. thermophilus* EF-Tu were successfully isolated.
• These aptamers interact with EF-Tu in both GTP and GDP-bound states, with a slight preference for the GTP form.
• A conserved consensus sequence (5'-ACCGAAG-3') within the aptamers was identified as essential for EF-Tu binding, located on domain II and distinct from other known binding sites.

Conclusions:

• Specific RNA aptamers can effectively bind to EF-Tu, providing valuable tools for studying its function.
• The identified consensus sequence and its hairpin structure are critical for the interaction with EF-Tu.
• These findings contribute to understanding the complex regulatory mechanisms of translation and potential therapeutic targets.