Silver-Stabilized Guanine Duplex: Structural and Optical Properties

Recent
experimental duplexes of DNA stabilized by Ag cations, pairing
homostrands of guanine–guanine, cytosine–cytosine, adenine–thymine,
and thymine–thymine, display much higher stability than the
Watson–Crick paired DNA duplexes; these broaden the range of
applications for DNA nanotechnology. Here we focus on silver-stabilized
guanine duplexes in water. Using hybrid quantum mechanics/molecular
mechanics simulations, we propose an atomic structure for the Ag+-mediated guanine duplex with two nucleobases per strand,
G2–Ag2+–G2. We then compare experimental
and time-dependent density functional theory-simulated electronic
circular dichroism (ECD) spectra to validate our results. Both experimental
and simulated ECD share two negative peaks around 220 and 280 nm,
with no positive signal in the measured wavelength range. We found
that the left- or right-handed disposition of bases in the structure
has a decisive effect on the signs of the ECD. We conclude that G2–Ag2+–G2 is left-hand-oriented, and extrapolation
of this orientation to longer strands gives rise to a left-hand-oriented
parallel helix stabilized by interplanar H bonds.