Silver-Mediated Double Helix: Structural Parameters for a Robust DNA Building Block

The
DNA double helix is a versatile building block used in DNA
nanotechnology. To potentiate the discovery of new DNA nanoscale assemblies,
recently, silver cations have been introduced to pair DNA strands
by base–Ag+–base bonding rather than by Watson–Crick
pairing. In this work, we study the classical dynamics of a parallel
silver-mediated homobase double helix and compare it to the dynamics
of the antiparallel double helix. Our classical simulations show that
only the parallel double helix is highly stable through the 100 ns
simulation time. A new type of H-bond previously proposed by our collaboration
and recently observed in crystal-determined helices drives the physicochemical
stabilization. Compared to the natural B-DNA form, the metal-mediated
helix has a contracted axial base pair rise and smaller numbers of
base pairs per turn. These results open the path for the inclusion
of this robust metal-mediated building block into new nanoscale DNA
assemblies.