SLIPPED LOOP STRUCTURE OF DNA - A SPECIFIC NUCLEOTIDE-SEQUENCE FORMS ONLY ONE UNIQUE CONFORMER

Earlier with some DNA sequences we were able to prove the existence of a new polynucleotide chain folding named slipped loop structure, or S LS [1,2]. However, the possibility of the presence of two SLS isomers in equilibrium was not excluded in the experiments. Here we are dealin g with a specially designed structure formed by two short oligonucleot ides intended for avoiding such a situation. To minimize the possibili ty of alternative structure formation and stabilize the conformation u nder investigation, the oligonucleotide sequences mere designed in suc h a way that the bimolecular structure SLS31 would have two binding si tes for antibiotic distamycin A. The sample was exposed to chemical pr obing both in the presence of distamycin A and without the ligand and the accessible nucleotides were mapped. The results do not suggest the presence in the solution of two isomers with different types of loop slippage without interloop interactions and strongly support the forma tion of a unique slipped loop conformation stabilized by an additional interloop helix, or slipped loop structure. (C) 1998 Federation of Eu ropean Biochemical Societies.