Curvature of dinucleotide poised for formation of trinucleotide in transcription with Escherichia coli RNA polymerase.

A frequently used schematic model of transcriptional elongation shows an RNA polymerase molecule moving along a linear DNA. This model is of course highly idealized and not compatible with promoter sequences [Gralla, J. D. (1991) Cell 66, 415−418; Schleif, R. (1992) Annu. Rev. Biochem. 61, 199−223] and regulatory proteins [Koleske, A. J., and Young, R. A. (1995) Trends Biochem. Sci. 20, 113−116; Dunaway, M., and Droge, P. (1989) Nature 341, 657−659; Muller, H. P., Sogo, J. M., and Schaffner, W. (1989) Cell 58, 767−777] located some distance away from the point of transcription initiation [Karsten, R., von Hippel, P. H., and Langowski, J. (1995) Trends Biochem. Sci. 20, 500−506]. These circumstances lead to the expectation of curvature along the DNA strand and require looping between sometimes distant points. We have now shown curvature in a dinucleotide formed at the very onset of transcription when it is poised for reaction with a mononucleotide to form a trinucleotide. The curvature became evident from ...