DNA binding factors assemble in a sequence-specific manner on the maize mitochondrial atpA promoter

The maize mitochondrial atpA promoter has been well-characterized using in vitro transcription. The functional elements of this promoter comprise a ce ntral domain extending from -7 to +5 relative to the transcription start si te, and an upstream domain of 1-3 bp that is purine-rich and centered aroun d positions -11 to -12. As a first step in characterizing the transcription al machinery, exonuclease-III mapping (toeprinting) was used to map the bor ders of DNA-protein interactions using either a 107-bp wild-type template o r transcriptionally-inactive templates containing linker-scanning mutations . These experiments revealed that, with a wild-type promoter, protein facto rs occupy as much as 36 bp, from positions -20 to +16 relative to the trans cription initiation site. Protein-binding patterns were altered when the li nker-scanning mutants were used, suggesting that either the number or confo rmation of DNA-binding proteins could account for their inability to promot e transcription initiation.