Intramolecular Folding of Pyrimidine Oligodeoxynucleotides into an i-DNA Motif

At slightly acidic or even neutral pH, oligodeoxynucleotides which include a stretch of cytidines form a tetrameric structure in which two parallel-stranded duplexes have their hemiprotonated C.C+ base pairs face to face and fully intercalated, in a so-called i-motif, first observed for d-TCCCCC. Cytosine-rich pyrimidine oligodeoxynucleotides, 14-30 bases long, can form an intramolecular "i-motif", in a manner similar to that observed in strands of telomeric repeat sequences. This intramolecular i-motif can accommodate as few as eight cytosines (four intercalated C.C+ base pairs). Evidence for intramolecular pairing was provided by thermal denaturation, nondenaturing gel electrophoresis, and gel filtration experiments and was characterized by specific NMR cross-peaks. The stability of a C.C super(+) base pair is very high at pH 5 and still detectable at neutral pH. Formation of the i-motif, whether intramolecular or intermolecular, should be taken into account as a competing structure in the design of triplex-forming oligodeoxynucleotides.