Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation

Abstract

We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.

Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets

“…The above observations allow us to set a separation distance D 0 at any position in the plateau 1.2 > D > 0.9 nm to define an adsorbed state (a) for distances shorter than D 0 and a solution state (s) for larger distances than D 0 . Thus, the average probability of finding the peptide in the adsorbed and solution states is proportional to ρ a and ρ s , which can be calculated by [38][39][40]…”

The Controversial Orientation of Adenine on Gold and Silver

“…Conversely, the computational studies discussed in Sections 2.2 and 2.4 have reported significantly different conclusions from each other . These discrepancies, at least for this field, highlight the importance of using computational tools to help interpret experimental measurements of physical phenomena, rather than relying on them exclusively.…”

“…Nevertheless, N7/N10 adsorption was recently reported on gold in a study combining EC‐STM and DFT calculations . Another study that used atomic force microscopy (AFM)‐based single molecule force spectroscopy (SMFS) and theoretical calculations reported N1/N10 adsorption on gold . The IR‐based (ATR‐SEIRAS and subtractively normalized interfacial Fourier transform infrared spectroscopy, SNIFTIRS) studies discussed in Sections 2.3 and 2.4 have proposed adsorption via the N1/N10 or N7/N10 sites, [209 , 231, 232] with a recent comprehensive study favoring the former .…”

Single-molecule force spectroscopy: A facile technique for studying the interactions between biomolecules and materials interfaces

“…In addition, other kind of materials interfaces, such as silica wafer [32], single-crystalized fused silica [23], graphite [22,43], and single-crystalized Au(111) [44] surface have also been prepared for studying the interactions between materials interfaces and protein, peptide, as well as ssDNA molecules.…”