Changes in DNA binding by purified simian RNA polymerase II under transcribing and nontranscribing conditions

The interaction of RNA polymerase II from African Green Monkey liver tissue with SV40 DNA was examined by a DNAase protection technique. In the absence of nucleoside triphosphates, simian polymerase binds to nicked, linear SV40 DNA and protects 30 bp of binary complex DNA from DNAase I digestion. With the addition of nucleoside triphosphates to initiate transcription, polymerase protects 40 bp of the ternary complex DNA from DNAase I. Thus, a conformational change in either the polymerase, the DNA, or both occurs during the transition from binary to ternary complex, and this altered conformation allows a larger protection of template DNA. Similar results were seen with Escherichia coli RNA polymerase holoenzyme on SV40 DNA.