Immunoprinting: A technique used to study dynamic protein-nucleic acid interactions within transcription elongation complex

Abstract

This chapter discusses the immunoprinting technique to study dynamic protein-nucleic acid interactions within transcription elongation complex. Immunoprinting is used to locate the sites within the phage λ genome where the phage N gene product specifically captures Escherichia coli RNA polymerase (RNAP). It provided evidence that an antiterminator such as N can become an integral subunit of the transcription machinery once it captures RNAP at a genetically defined site. The chapter describes the basic strategies of the immunoprinting method, its application to the N system, and the implication of the findings on the mechanism of N action. The N antiterminator suppresses both Rho-dependent and Rho-independent terminators on the λ genome that are located within the two early operons at many intergenic sites. Two simple models can explain how the nut site acts at a distance to mediate N antitermination. Both models invoke an interaction between N and nut, as well as an interaction between N and polymerase.