Although much is known about which DNA sequences are involved in cellular regulation, much less is known about how such regulation occurs. Central to genomic expression, an RNA polymerase must initiate RNA synthesis at a unique site in the DNA, release the promoter and transcribe faithfully and stably, and then terminate transcription at specific signals in the DNA. Regulation of gene expression can (and does) occur at each of these steps. Our group aims to tie an understanding of structure-function relationships to the detailed mechanism of transcription. The family of RNA polymerases encoded by the bacteriophages T7, T3, and SP6 presents an ideal model system in which to study fundamental aspects of transcription. T7 RNA polymerase is the only RNA polymerase for which high resolution crystal structures are available not only for the enzyme in isolation, but also bound to promoter DNA and in the process of initial transcription. Through a variety of approaches merging biophysical and enzymological tools with approaches from molecular biology, we have made substantial advances in our understanding of structure and function in this system. In particular, we have shown via mutation of both the protein and the DNA that the crystal structures, while extremely valuable in guiding experiment, can be misleading in terms of energetics and mechanism. Fluorescence probes have shed light on both the initial transcription complex and on a complex paused away from the promoter (for which no x-ray data exists). Biochemical assays have allowed us to propose specific mechanisms for various stages in transcription. Major challenges remain, however, including a mechanistic understanding of how the enzyme translocates away from the promoter and converts into a stably elongating complex.