Slipped loop structure of DNA: a specific nucleotide sequence forms only one unique conformer

AbstractEarlier with some DNA sequences we were able to prove the existence of a new polynucleotide chain folding named slipped loop structure, or SLS [1, 2]. However, the possibility of the presence of two SLS isomers in equilibrium was not excluded in the experiments. Here we are dealing with a specially designed structure formed by two short oligonucleotides intended for avoiding such a situation. To minimize the possibility of alternative structure formation and stabilize the conformation under investigation, the oligonucleotide sequences were designed in such a way that the bimolecular structure SLS31 would have two binding sites for antibiotic distamycin A. The sample was exposed to chemical probing 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 formation of a unique slipped loop conformation stabilized by an additional interloop helix, or slipped loop structure