An In Vivo UV Crosslinking Assay That Detects DNA Binding by Sequence-Specific Transcription Factors

In vivo UV crosslinking permits direct analysis of protein-DNA interactions in intact cells. This technique has been used to study DNA binding by a wide variety of proteins including RNA Polymerase II, Topoisomerase I, and sequence specific transcription factors such as Even-Skipped, Zeste, and GAGA (1 –4 ). For many of these proteins, the pattern of DNA binding discovered by UV crosslinking differs dramatically from that predicted by earlier indirect approaches. This has led to fundamental reassessments of how these proteins act and illustrates the importance of examining protein-DNA interactions in vivo.