Pyridine: a Denaturant or Stabilizer of Spherical Nucleic Acids?

Abstract

The spotlighted dual functions of pyridine as a denaturant and as a stabilizer for duplex DNA are thoroughly investigated using spherical nucleic acids (SNAs). At neutral pH, pyridine destabilizes the duplex interconnects of assembled SNAs, resulting in a gradual decrease in their melting temperature (T-m) as a function of the pyridine concentration. This result is in good agreement with the conventional role of pyridine as a powerful denaturant for free duplex DNA. On the contrary, the addition of pyridine dramatically increases the T-m of hybridized SNAs under acidic conditions, which could be a striking result of pyridine's stabilizing effect for DNA duplex as previously suggested on the basis of the pyridine nucleobase interactions. After comprehensive and quantitative investigation based on the analysis of the sharp melting transitions of SNAs, however, we report that, in fact, the pH increase induced by pyridine is also an essential parameter accounting for pyridine's DNA-stabilizing effects under acidic conditions. Importantly, we prove that pyridine, particularly at a low concentration, does not increase the T-m of hybridized SNAs evert under acidic conditions, if the pH increase by pyridine is corrected to maintain the same initial pH.