Formation and Nanomechanical Properties of Silver-Mediated Guanine DNA Duplexes in Aqueous Solution
Eshana Bethur, Rweetuparna Guha, Ziqian Zhao, Benjamin B. Katz, Paul D. Ashby, Hongbo Zeng, Stacy M. Copp
Abstract
High Resolution Image Download MS PowerPoint Slide Silver cations can mediate base pairing of guanine (G) DNA oligomers, yielding linear parallel G–Ag + –G duplexes with enhanced stabilities compared to those of canonical DNA duplexes. To enable their use in programmable DNA nanotechnologies, it is critical to understand solution-state formation and the nanomechanical stiffness of G–Ag + –G duplexes. Using temperature-controlled circular dichroism (CD) spectroscopy, we find that heating mixtures of G oligomers and silver salt above 50 °C fully destabilizes G-quadruplex structures and converts oligomers to G–Ag + –G duplexes. Electrospray ionization mass spectrometry supports that G–Ag + –G duplexes form at stoichiometries of 1 Ag + per base pair, and CD spectroscopy suggests that as the Ag + /base stoichiometry increases further, G–Ag + –G duplexes undergo additional morphological changes. Using liquid-phase atomic force microscopy, we find that this excess Ag + enables assembly of long fiberlike structures with ∼2.5 nm heights equivalent to a single DNA duplex but with lengths that far exceed a single duplex. Finally, using the conditions established to form single G–Ag + –G duplexes, we use a surface forces apparatus (SFA) to compare the solution-phase stiffness of single G–Ag + –G duplexes with dG-dC Watson–Crick–Franklin duplexes. SFA shows that G–Ag + –G duplexes are 1.3 times stiffer than dG-dC duplexes, confirming gas-phase ion mobility spectrometry measurements and computational predictions. These findings may guide the development of structural DNA nanotechnologies that rely on silver-mediated base pairing.