Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

The stable T-Hg-T base pair in nucleic acids has been widely applied for Hg2+ biosensors. Based on the N-Hg binding mechanism for a mercury ion to nucleobases, the N-Hg-N bond was studied in other base pairs (T-T, T-G, G-G, C+-C+) with two imino groups within the base pairing face, in the context of parallel DNA duplexes. In the six C+-C+ pairs - defined parallel DNA duplexes at pH 5.0, the parallel T-Hg-T was suggested to be a very weak base pair, as it was not stable enough to support a long T-Hg-T stem, unlike the anti-parallel T-Hg-T base pair. No interactions between Hg2+ and the parallel T-G, G-G, and C+-C+ pairs were observed. In the anti-parallel dsDNA, the stabilizing effect of T-Hg-T was significant, but with position and sequence dependence, it was mostly less stable than the natural A-T base pair. An anti-parallel T-Hg-T stem is preferred over a parallel stem in the functional nucleic acids for the design of Hg2+ biosensors. It seems that the N-Hg-N bond is only accommodated in the T-T pair within the DNA duplex, different from the free bonding mode between individual nucleobases, nucleosides, or nucleotides. These results are helpful for the design of the T-Hg-T stem in Hg2+ biosensors based on functional nucleic acids.