Sequence analysis of protamine mRNA from the rainbow trout. Depurination and nearest neighbor analysis of protamine...

Protamine cDNA, which was a full length copy of protamine mRNA was labeled during its synthesis by using deoxynucleoside [alpha-32P]triphosphates. Depurination analysis showed that there were 19 different pyrimidine oligonucleotides in protamine cDNA, some of which contained isomeric sequences. The stoichiometry of the pyrimidine oligonucleotides indicated that, while some sequences probably occur in each of the protamine mRNA components, other sequences are clearly absent from one or more of the components. Several of the pyrimidine oligonucleotides had sequences consistent with the amino acid sequences of the rainbow trout protamines. The longest oligopyrimidine tract, C7T4, had a complementary RNA sequence of AGGAGAGGAGG, a stoichiometry of close to 1, and fitted the amino acid sequence Arg-Arg-Gly-Gly which occurs near the COOH terminus of each of three major protamine components. Other pyrimidine oligonucleotides analyzed were complementary to RNA sequences from the noncoding region of protamine mRNA. There appears to be no preferential use of one particular arginine codon or set of codons. Of the 21 to 22 arginine codons in protamine mRNA no less than 7 and no more than 12 are of the CGX series. The other two codons, AGA and AGG, both occur but not in a series of more than two together. This indicates that the RNA sequences coding for the arginine tracts tend to contain a mixture of arginine codons. Nearest neighbor frequency analysis of protamine cDNA gives a low value for the frequency of the CpG doublet, despite its occurrence in four out of the six arginine codons. This is in accordance with the observation that the sequence CpG is surprisingly rare in vertebrate DNA and in the RNA transcribed from it.