Global Identification of RNA Helicase Substrates from Large Nucleic Acid Sequence Libraries Using Helicase-SELEX.

In many instances, the RNA sequences or motifs that constitute optimal or physiological substrates for a given RNA helicase are unknown or difficult to identify. In this chapter, we describe a recent methodology, Helicase-induced Selection of Ligands by Exponential enrichment (Helicase-SELEX), which allows the global identification of catalytically productive substrates for a RNA helicase from a large library of nucleic acid sequences. We explain how to use the methodology to identify Rut (Rho utilization) sequences in bacterial genomes, which likely encode the physiological RNA targets used by the transcription termination factor Rho helicase. We discuss the advantages and limitations of the Helicase-SELEX methodology, including which categories of helicases are, in principle, the most amenable to Helicase-SELEX analysis.