ABSTRACT
This chapter describes a microarray-based method that is used to identify RNA motifs that bind to small molecules. This method, termed two-dimensional combinatorial screening (2DCS), screens chemical and RNA secondary structure spaces simultaneously. A key feature of the approach is the statistical analysis of the selected RNA sequences. By analyzing all statistically signi•cant trends displayed by a singular RNA sequence/structure, we can qualitatively predict both the selectivity and the af•nity of RNA motif-ligand interactions (structure-activity relationships
9.1 Introduction .................................................................................................. 198 9.2 Basics of the Technique ................................................................................ 201
9.2.1 Microarray Construction .................................................................. 201 9.2.2 Design of the RNA Library ..............................................................202 9.2.3 Hybridization of the RNA Library with the Chemical Microarray ........................................................................................203 9.2.4 Identi•cation of the RNAs that Bind Each Ligand ...........................203 9.2.5 Identi•cation of Trends in the Selected RNAs Using Statistical
Analysis ............................................................................................205 9.2.6 Af•nity of RNA-Ligand Interactions ..............................................207 9.2.7 A Database of RNA Motif-Ligand Interactions ..............................208
