Table 3.

Comparison of actual ssDNA conditions experienced at array surfaces versus those typically reported in ssDNA physicochemical models and simulations.

ssDNA properties at surfaces	ssDNA tethered in microarrays	ssDNA brush modeling
ssDNA grafting density	Uncontrolled grafting density, spanning sparse, mushroom and brush in the same surface locale	Controlled, uniform grafting density of mushroom or brush across an impenetrable surface
Tethered ssDNA chain orientations	Uncontrolled immobilized chain orientations and conformations	Uniform controlled brush heights and chain orientations
ssDNA chain lengths	20–200 bases (short) probes	>1000 bases (long) brushes
ssDNA chain flexibility	ssDNA is short, rigid, rod-like	ssDNA is longer, flexlble
ssDNA solvent/media exposure	High ionic strength but complex mixed salt solutions, surfactants and other solutes in drying cycles	Wide range of salt concentrations (monovalent)
Interactive conditions at the surface	Repeated surface solvation/drying steps in assay that modulate ionic strength and solvation dramatically	Equilibrium models or constrained simulations, with little dynamic interactive changes in polymer/solvent/surface conditions
ssDNA chain dynamics under a given analysis	Persistence lengths, radius of gyration, brush heights and chain condensation vary widely	Persistence lengths, radius of gyration, brush heights and chain condensation vary little