Antisense sequences of antigenic peptides are found in MHC class II molecules

The sequence of the well known antigenic peptide OVA 323-339 as well as other peptides containing reiterative motifs of the core region essential for binding to Class II MHC molecules was compared for homology with the DNA derived antisense peptide sequences corresponding to the alpha chain of the mouse IAd molecule. Homology was obtained within the sequence found in the transmembrane region of the molecule. Increased binding of the peptides containing the reiterative motifs based on the OVA 323-339 sequence may be due to the increased number of contact sites on IAd molecules which were identified as being complementary in a sense-antisense manner.