Open AccessAdsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation
Author(s) -
Zak E. Hughes,
Gang Wei,
Kurt L.M. Drew,
Lucio Colombi Ciacchi,
Tiffany R. Walsh
Publication year - 2017
Publication title -
langmuir
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.042
H-Index - 333
eISSN - 1520-5827
pISSN - 0743-7463
DOI - 10.1021/acs.langmuir.7b02480
Subject(s) - metadynamics , adsorption , guanine , chemistry , aqueous solution , nucleobase , graphite , nucleic acid , molecule , dna , chemical physics , nucleotide , computational chemistry , molecular dynamics , organic chemistry , biochemistry , gene
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.