Study of RNA-protein recognition by in vitro selection

Abstract A major focus of biochemistry and genetics has been to deduce the determinants of molecular recognition and catalysis. In vitro selection of nucleic acids is a method that represents a synthesis of these two disciplines - a method that retains both the control of in vitro biochemical manipulation and the power of genetic selection. This new tool has been used successfully in many laboratories for applications ranging from defining DNA-binding sites of transcription factors to isolating new ribozymes. The basic features and applications of in vitro selection of nucleic acids have been reviewed extensively (1-6). After a brief overview of these features and applications, this chapter focuses on practical considerations for designing, implementing, and interpreting in vitro selection schemes for the characterization of RNA-protein interactions.