Conformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold

Abstract

Cryo-electron microscopy can determine the structure of biological matter in vitrified liquids. However, structure alone is insufficient to understand the function of native and engineered biomolecules. So far, their mechanical properties have mainly been probed at room temperature using tens of pico-newton forces with a resolution limited by thermal fluctuations. Here we combine force spectroscopy and computer simulations in cryogenic conditions to quantify adhesion and intra-molecular properties of spray-deposited single-strand DNA oligomers on Au(111). Sub-nanometer resolution images reveal folding conformations confirmed by simulations. Lifting shows a decay of the measured stiffness with sharp dips every 0.2–0.3 nm associated with the sequential peeling and detachment of single nucleotides. A stiffness of 30–35 N m−1 per stretched repeat unit is deduced in the nano-newton range. This combined study suggests how to better control cryo-force spectroscopy of adsorbed heterogeneous (bio)polymer and to potentially enable single-base recognition in DNA strands only few nanometers long.

Giant thermal expansion of a two-dimensional supramolecular network triggered by alkyl chain motion

“…To safely deposit the SW precursors onto Au(111), we used an electrospray deposition (ESD) device attached to the UHV setup 24,[27][28][29][30][31][32][33] . The spray-deposition was always performed on the Au(111) substrates kept at room temperature and followed by an annealing step at 450 K. As shown in large-scale STM measurements ( Supplementary Fig.…”

“…Van der Waals interactions were truncated at the real space cutoff, and Lorentz-Berthelot mixing rules were used to determine the interaction parameters between different atoms. All simulations are preformed in vacuum conditions and the volume of the system was kept fixed and the temperature was adjusted by means of a Langevin thermostat 41 with a damping rate of 1 ps −1 which ensures fast thermalization with a minimal effect on the dynamics 33 of the arms and slip dynamics governing the diffusion of the SW core. The SHAKE algorithm 42 was used to constrain bonds containing hydrogen, thus allowing the use of an integration time step of 1 fs.…”

“…This force field has been extensively tested by studying the adsorption of small organic molecules (charged and uncharged and within the same chemical space as SW) against both density-functional-theory simulations as well as available experimental results [51][52][53] . Moreover, its suitability to describe the interaction with small organic molecules and their surface mobility has been recently validated through single molecule manipulation experiments 33,54 .…”

“…In UHV conditions, the electrospray deposition (ESD) technique allows the introduction of large molecules. Therefore, it is possible to study in UHV conditions the adsorption properties of molecules and their assemblies that mimic established assemblies at the liquid-solid interface 24,[27][28][29][30][31][32][33] . In this context, temperature-dependent STM/AFM investigations of supramolecular systems might enable the analysis of their thermoresponse down to the atomic scale.…”

Direct Visualization of Individual Aromatic Compound Structures in Low Molecular Weight Marine Dissolved Organic Carbon

“…Recently, atomic force microscopy (AFM) with CO-functionalized tips demonstrated the real-space visualization of the chemical structure of molecules (Gross et al, 2009). The methodology has since been applied to different molecular systems, ranging from on-surface chemical reactions (de Oteyza et al, 2013;Kawai et al, 2016;Pawlak et al, 2017;Riss et al, 2016;Schuler et al, 2016;Schulz et al, 2017;van der Lit et al, 2013) to natural products (Gross et al, 2010;Hanssen et al, 2012;Hinaut et al, 2018;Schuler et al, 2015;. A fraction of DOC has been previously characterized by AFM (Maurice & Namjesnik-Dejanovic, 1999;Pan et al, 2008).…”