Noncanonical conformation of nucleic acids: the slipped-loop structure in DNA oligonucleotides

The paper deals with a new type of polynucleotide chain packing in the slip ped-loop structure (SLS) proposed by us earlier. A number of sequences able to form such a structure were studied. However, many sequences, especially long ones, are able to form alternative structures. To lessen the possibil ity of their formation, we designed and studied several short oligodeoxynuc leotides. SLS-25 is a symmetrical structure formed by two identical strands . SLS-31 is formed upon interaction of two different strands carrying at th eir ends specific sites for distamycin A binding; the latter could not only stabilize the arising SL structure but also provide direct proof of the ex istence of corresponding paired SLS sites. Application of chemical modifica tions of bases allows us to say that SLS really arises in the oligodeoxynuc leotides studied.