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Determination of Average Internucleotide Distance in Variable Density ssDNA Nanobrushes in the Presence of Different Cations Species

Nkoua Ngavouka, Maryse D., Bosco, Alessandro, Casalis, Loredana, Parisse, Pietro
Macromolecules 2014 v.47 no.24 pp. 8748-8753
atomic force microscopy, binding capacity, biosensors, brushes, calcium chloride, cations, ionic strength, liquids, magnesium chloride, mechanical properties, models, potassium chloride, salt concentration, screening, single-stranded DNA, sodium chloride, topography
Controlling conformational and mechanical properties of single-stranded DNA (ssDNA) nanobrushes is crucial for the design of new, miniaturized DNA-based functional biosensors. In particular, counterions diffusion and binding affinity to DNA impact on ssDNAs curvature and flexibility and modify their binding properties. In order to highlight the role of cation electrostatic screening and molecular crowding on the conformational stability of DNA brushes, we propose here to use atomic force microscopy (AFM) and AFM-based lithography to create ssDNA assemblies of variable density and to analyze their collective response to changes of ionic strength. We confined ssDNA brushes with controlled surface densities within a biorepellent self-assembled monolayer. We then monitored the topographic brush height variation upon changing salt type (NaCl, KCl, CaCl₂, and MgCl₂) and concentration inside the liquid cell. We show that the measured height is related to scaling law of salt concentration, in agreement with the theory of polyelectrolyte brush. We find the same scaling exponent α = −1/6 for the different density regimes exploited. Using this scaling model to fit our experimental data, we quantified structural parameters such as the average internucleotide distance (d) for ssDNA brushes of different and estimated surface density (σ), featuring a strong dependence of d on different salts species.