Determination of secondary structure in the initiation region of ovalbumin mRNA

We have analyzed the secondary structure in the region surrounding the initiation codons of both cellular and synthetic versions of ovalbumin mRNA. RNase V1 cleavage sites and structure-dependent, chemically modified bases in cellular ovalbumin mRNA were determined by reverse transcription of hen poly A(+) RNA using ovalbumin-specific, synthetic DNA primers. These results indicate an extensive region of unpaired nucleotides preceding the initiation codon and a region of base-paired nucleotides including and following the initiation codon. A synthetic ovalbumin mRNA (SP65.OV) was prepared by run-off transcription of a cloned ovalbumin cDNA (pSP65.OV). Identical regions of hen ovalbumin and SP65.OV mRNAs gave identical patterns of structure-dependent base modifications. A computer program for determining RNA secondary structure was used to find a 5'-region structure for ovalbumin mRNA that is consistent with our data.