Synthesis and Hybridization Properties of Oligodeoxynucleotides with Long-Chain Linkers

New oligonucleotides with a long-chain linker (6,9-dioxa-3,12-diazatetradecane-1,14-diyl) in their backbone were synthesized, and their hybridization properties were studied by measurement of their Tm curves and fluorescence spectra. The Tm analyses revealed that these oligonucleotides could bind to their complementary strands despite the presence of the long-chain linker. We also demonstrated interesting fluorescence properties of oligodeoxynucleotides with an anthracen-9-ylmethyl group on one of the two N-atoms in the long-chain linker. The fluorescence intensity of these oligonucleotides increased upon their hybridization to the complementary strands and was sensitive to the presence of the mismatch base pairs at a specific position.