Conformations of oligonucleotides in solution as determined by sequence-specific antibodies

The conformations of some related oligoribonucleotides in solution were investigated immunochemically with antisera specific for two synthetic oligonucleotide sequences, A-A-U and A-A-U-U. Radioimmunoassay showed differences of as much as three or more orders of magnitude in binding among oligonucleotides with commonly shared sequences. These large differences, which reflect the loss of many points of contact with antibody because of changes in overall conformation, allow the following conclusions: (1) A-A-U and A-A-U-U have conformations distinct from any present in the Un family of oligomers. (2) Conformations of A-A-U and A-A-U-U differ markedly from those of oligomers of A. The dinucleotide A-A, in particular, bears little resemblance in conformation to the A-A sequence in A-A-U and A-A-U-U. (3) The recognizable conformational unit appears to be the triplet A-A-U, which binds as well as A-A-U-U and far better than its component dimers. Interactions between non-adjacent bases may be a factor here, as well as in codon recognition. The immunological data support the conclusion that, in oligonucleotides, as in polypeptides, primary sequence can determine conformation in solution.