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Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation
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posted on 2022-10-26, 04:31 authored by Z E Hughes, G Wei, K L M Drew, L Colombi Ciacchi, Tiffany WalshTiffany WalshWe 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.
History
Journal
LangmuirVolume
33Pagination
10193 - 10204Publisher DOI
ISSN
0743-7463eISSN
1520-5827Copyright notice
2017, American Chemical SocietyUsage metrics
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No categories selectedKeywords
Science & TechnologyPhysical SciencesTechnologyChemistry, MultidisciplinaryChemistry, PhysicalMaterials Science, MultidisciplinaryChemistryMaterials ScienceMOLECULAR-DYNAMICS SIMULATIONSINGLE-STRANDED-DNAFREE-ENERGYFORCE SPECTROSCOPYCARBON-NANOTUBESURFACEGOLDPEPTIDEINTERFACEEFFICIENTDNAAdsorptionAqueous GraphiteAu(111)aqueous graphite C(0001)
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