Fluorescence energy transfer as a probe for tetraplex formation: The i- motif

The secondary structure of cytosine-rich oligodeoxynucleotides has been investigated with fluorescent probes. Intramolecular folding of an oligonucleotide into an i-DNA motif led to fluorescence excitation energy transfer between a donor (fluorescein) and an acceptor (tetramethylrhodamine) covalently attached to the 5' and 3' ends of the DNA, respectively, provided that a suitable linker was chosen. The conjugation of the dyes to the oligonucleotide had an influence on the thermodynamics of i-motif formation as well as on the kinetics of folding. Intramolecular folding was demonstrated from the concentration independence of FRET over a wide concentration range. Folding of the oligonucleotide was confirmed by UV absorption melting experiments. The folding of the i-motif could be followed at concentrations as low as 50 pM. Fluorescence energy transfer can thus be used to reveal the formation of multistranded DNA structures.