Optically characterized DNA multilayered assemblies and phenomenological modeling of layer-by-layer hybridization

Layer-by-layer assemblies based on deoxyribonucleic acid (DNA) hybridization have potential for various bio- and nanotechnology applications because of their programmability, biodegradability, and ability to control the structure of the assemblies on the nanometer scale. Herein, we investigate the growth and salt stability of DNA films by the optical technique dual polarization interferometry and numerically model the film buildup. The DNA films were assembled by sequentially depositing pairs of oligonucleotides comprised of two different block sequences onto the surface. The oligonucleotides used in the assembly of the different films were as follows: a homopolymeric diblock pair of A_xG_x/T_xC _x (x = 15, 20, or 30), a homopolymeric diblock pair of A ₁₅G₁₅/C₁₅T₁₅ in which the orientation of the T₁₅C₁₅ diblock was reversed (C ₁₅T₁₅), and a random diblock pair of X₁₅Y ₁₅/X'₁₅Y'₁₅. The characteristics of the layer growth were highly dependent on the type of the oligonucleotide pair used: the mass of DNA deposited followed a linear, stepwise, or saturated growth with increasing layer deposition. The layer growth of each film was numerically modeled by taking into account the effective hybridization rate and the effective dissociation rate of the oligonucleotides. The proposed modeling offers a framework for molecularly designing oligonucleotide pairs to obtain DNA multilayer films with desired physicochemical properties (thickness, density, stability).