Automated Selection of Transcription Factor Binding Sites

Abstract

Double-stranded DNA binding sites that bound with high affinity to the nuclear factor kappa B (NFκB) p50 homodimer were selected using a Tecan Genesis workstation. The adaptation of the Tecan to automated selection required the integration of multiple devices and modifications to standard selection protocols, and resulted in a significant increase in throughput. The sequences obtained by automated selection strongly correlated with the well-known family of natural NFκB double-stranded DNA binding sites and with previous manual selection experiments. In addition, the selection experiments better defined the contributions of residues outside of the well-known, decameric core binding site for NFκB.