Amino acid residues in region 2 of 70 have been shown to play an important role in the strand separation step that is necessary for formation of the functional or open RNA polymerase-promoter complex. Here we present a comparison of the roles of basic and aromatic amino acids in the accomplishment of this process, using RNA polymerase bearing alanine substitutions for both types of amino acids in region 2. We determined the effects of the substitutions on the kinetics of open complex formation, as well as on the ability of the RNA polymerase to form complexes with singlestranded DNA, and with forked DNA duplexes carrying a single-stranded overhang consisting of bases in the ؊10 region. We concluded that two basic amino acids (Lys 414 and Lys 418 ) are important for promoter binding and demonstrated distinct roles, at a subsequent step, for two aromatic amino acids (Tyr 430 and Trp 433 ). It is likely that these four amino acids, which are close to each other in the structure of 70 , together are involved in the nucleation of the strand separation process.RNA synthesis in prokaryotes is carried out by a multisubunit RNA polymerase commonly referred to as the core enzyme (E).1 For promoter recognition, a sigma (initiation) factor is required; it interacts with the core polymerase to yield the holoenzyme (E), which is able to form an initiation-competent complex at promoter sequences in a multistep process involving conformational changes in both the protein and the DNA (1-3). A striking feature of such a complex is a region of strand separation that spans about 14 base pairs from the upstream edge of the conserved Ϫ10 promoter element to just beyond the start site of transcription initiation (4). It is thought that, kinetically, strand separation initiates in the Ϫ10 region and proceeds in a downstream direction. Measurement of the size and location of the region of strand separation as a function of temperature shows that at low temperatures a small single-stranded region can be detected that, as the temperature is increased, expands toward the start site (3, 5-7). In addition, the introduction of nicks and mismatches in the Ϫ10 region is more effective in the acceleration of open complex formation than if such distortions are introduced at a more downstream position (8, 9).The predominant sigma factor in Escherichia coli, which enables recognition of promoters of housekeeping genes, is referred to as 70 . Sequence comparison has shown that a large group of sigma factors shows significant homology to 70 . Four regions of sequence conservation have been identified, of which some have been subdivided to reflect the most extensive sequence conservation (10). A large body of data has implicated region 2.3 of the main sigma factors of E. coli, Bacillus subtilis, and other prokaryotes in the nucleation of the strand separation. This process eventually results in the formation of the active or open complex, possibly by facilitating base flipping of the highly conserved A at Ϫ11 of the nontemplate strand. The support...