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 nucleotldes including and following the initiation codon. A synthetic ovalbumln mRWA (SP65.OV) was prepared by run-off transcription of a cloned ovalbumin cDNA (pSP65.0V). 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.
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