Molecular crowding effect on specific binding of Hg2+ to T–T mismatched base pair in duplex DNA

Abstract

Many biomolecules are crowded in vivo environments. Metal ion–nucleic acid interactions are important in vivo molecular crowding conditions for structure formation and biological activity of nucleic acids. Although metal ion–nucleic acid interactions have been investigated in detail under diluted conditions, studies examining the molecular crowding effect on metal ion–nucleic acid interactions are limited. Hg²⁺ specifically binds to T–T mismatched duplex DNA to form T–Hg–T base pair under diluted conditions. Here, we examined the binding under molecular crowding conditions. To the best of our knowledge, no previous studies reported the metal-mediated base-pair formation under molecular crowding conditions. UV melting showed that the specific stabilization of only the T–T mismatched duplex by Hg²⁺ addition was maintained under molecular crowding conditions. CD spectra showed that no significant structural change of the T–T mismatched duplex by Hg²⁺ addition was preserved under molecular crowding conditions. Isothermal titration calorimetric analyses showed that the 1:1 M ratio for the specific binding of Hg²⁺ to T–T was maintained under molecular crowding conditions. However, the magnitudes of the negative ∆H and the positive ∆S were significantly larger and smaller, respectively, than those under diluted conditions, which may lead to the smaller magnitudes of K_a and ∆G. Smaller number of released water molecules upon the binding under molecular crowding conditions may result in these results. The present findings may be useful for developing efficient metal-mediated base-pair formation, leading to progress in their efficient applications in various fields including nanotechnology.