Dinucleotide priming of RNA synthesis

Initiation of RNA synthesis with preformed dinucleotides as primers and either a bacterial or a eukaryotic DNA-dependent RNA polymerase was used to probe sequences on DNA or chromatin that are available for transcription. Using saturating levels of Escherichia coli RNA polymerase or wheat germ RNA polymerase II to transcribe free DNA, a preference was noted for the dinucleotides GpA, GpG, ApG, and UpG for initiation of RNA synthesis. When saturating levels of E. coli RNA polymerase were used to transcribe chromatin, a little preference was noted for UpA and UpC; wheat germ RNA polymerase II, on the other hand, utilized the dinucleotides GpA, ApG, ApA, and UpG more efficiently. Under conditions of limiting amounts of enzyme to transcribe chromatin, wheat germ RNA polymerase preferred to initiate RNA synthesis with the dinucleotide primers GpA, ApA, ApC, and UpG; E. coli RNA polymerase preferred GpA and GpG. These results emphasize both the role of the configuration of the template and the role of the enzyme in sequence selection for initiation of transcription.