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Mapping of mRNA isoforms with an oligonucleotide probe: exonuclease VII compared with endonucleases.

Cardiac muscle expresses two isoforms of the myosin heavy chain, a- and f-MHC, whose differential expression can directly influence the velocity of cardiac contraction. A precise knowledge of their relative expressions under physiological and pathological conditions is therefore useful to better understand the molecular basis of cardiac contractility. A 'S 1 nuclease mapping' technique using a 62 base labelled oligonucleotide, complementary to a 40 nucleotide common coding sequence towards the 3' end of both the a- and 3-MHC iso-mRNA and to an additional 15 nucleotides in the coding sequence of the fl-MHC iso-mRNA, was recently described for this purpose (1), but it yielded multiple bands that were not specific for either a- or 3-MHC. In an attempt to eliminate these extra bands, we followed the same protocol except that Mung Bean Nuclease (Biolabs-40 units), an enzyme that is somewhat more precise in its action than SI Nuclease, was used to analyze control RNA obtained from rat liver (negative control), soleus muscle (3-MHC only), 23 day old rat ventricular muscle (a-MHC only), and neonatal rat ventricular muscle (a- and 3-MHC (2)); however, this also yielded non specific bands between a- and f-MHC mRNA (Figure A). We then hypothetized that the use of an exonuclease might yield more clearcut results than those achieved with an endonuclease. The same 62 base oligonucleotide plus a five-nucleotide non-complementary extension of its 5' end (5'-TTGTT-3') was prepared and purified by Eurogentec S.A. (Liege, Belgium). After a 3' end-labelling with (a- 32P