JBC, Vol. 252, Issue 4, 1386-1393, Feb, 1977
Sequence analysis of protamine mRNA from the rainbow trout. Depurination and nearest neighbor analysis of protamine cDNA
P. L. Davies, L. N. Ferrier and G. H. Dixon
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.
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