Can the Ph.D. libraries be used interchangably with cDNA libraries?
The choice of library depends on whether your goal is to identify a sequence, natural or synthetic, which binds to your target tightly, or solely to identify the natural in vivo ligand for your target. Bear in mind that the Ph.D. kits are based on fully randomized peptide libraries, while cDNA expression libraries are limited to naturally occuring proteins. As a result, the Ph.D. libraries are most suitable for identifying novel ligands (e.g. receptor agonists) or mapping the interactions between two known proteins (e.g. antibody epitope mapping). Since the biopanning is carried out in vitro, the selected sequence may bear little resemblance to any native ligands for your target. For routine identification of the native ligand for a protein, the yeast two-hybrid system, lambda gt11, or other cDNA libraries may be more appropriate.
