Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides

Base stacking is important for the base pair interaction of a DNA duplex, DNA replication by polymerases, and single-stranded nucleotide overhangs. To study the mechanisms responsible for DNA stacking interactions, we measured the thermal stability of DNA duplexes containing a non-natural nucleotide tethered to a simple aromatic hydrocarbon group devoid of dipole moments and hydrogen bonding sites. The duplexes containing tetrahydrofuran were paired with a deoxyadenosine derivative (A/T base pair analog) or a deoxycytidine derivative (C/G base pair analog) and showed a lower stability than Watson-Crick base pairing, partly due to the loss of interbase hydrogen bonds. Conversely, non-natural nucleotides present at a dangling end yielded an interaction energy as high as that observed with base pairing. Importantly, the non-natural nucleotides yielded an interaction energy with a linear correlation similar to that of the analogous Watson-Crick base pairs both in the middle and at the end of a DNA duplex, although a different stacking mechanism between the middle and the end was suggested. Moreover, a positive cooperativity was observed in dangling end stacking of the nucleotide base moiety and aromatic hydrocarbon group. These observations are useful to understand nucleic acid interactions and to design new non-natural nucleotides.