MONOCLONAL-ANTIBODIES WITH SEQUENCE SPECIFIC AFFINITY FOR A STEM-LOOP STRUCTURE IN DNA

Monoclonal antibodies have been raised against an oligonucleotide with a stem-loop structure (1). Antibody 41H7 binds the oligonucleotide hapten with a dissociation constant of 2.0 x 10(-6) M. The antibody shows sequence specificity in its binding, as it shows no detectable binding to a sequence (12) which differed from the hapten by only three bases in the loop. Additionally, a change of ten base pairs in the stem portion of the sequence (13) led to a four-fold reduction in the antibody affinity. These results indicate that antibody 41H7 mainly recognizes the single stranded region of hapten 1, and that antibody recognition of the double stranded stem occurs to a lesser extent.