Confinement effects on DNA hybridization in electrokinetic micro‐ and nanofluidic systems

Abstract

Spatial confinement, within cells or micro‐ and nanofabricated devices, impacts the conformation and binding kinetics of biomolecules. Understanding the role of spatial confinement on molecular behavior is important for comprehending diverse biological phenomena, as well as for designing biosensors. Specifically, the behavior of molecular binding under an applied electric field is of importance in the development of electrokinetic biosensors. Here, we investigate whether confinement of DNA oligomers in capillary electrophoresis impacts the binding kinetics of the DNA. To infer the role of confinement on hybridization dynamics, we perform capillary electrophoresis measurements on DNA oligomers within micro‐ and nanochannels, then apply first‐order reaction dynamics theory to extract kinetic parameters from electropherogram data. We find that the apparent dissociation constants at the nanoscale (i.e., within a 100 nm channel) are lower than at the microscale (i.e., within a 1 μm channel), indicating stronger binding with increased confinement. This confirms, for the first time, that confinement‐based enhancement of DNA hybridization persists under application of an electric field.

Statistical mechanics of dimerizations and its consequences for small systems

“…Yet with recent advancements of technology experimental studies, able to conduct and monitor associations of the type shown in Eq. 1 in systems with small numbers of reactants, reported that bound products are observed at higher concentrations than predicted by the expression of K mentioned above [4][5][6][7][8][9][10][11] . Different explanations were put forward that include conformational changes of the unbound molecule(s), non-fluorescent bindings, and missed events due to transient interactions 12 .…”

“…We now evaluate the ratio of the partition functions in eqn (11). Due to translational degrees of freedom, q + A 2 and q +…”

“…Yet with recent advancements of technology, experimental studies, able to conduct and monitor associations of the type shown in eqn (1) in systems with small numbers of reactants, reported that bound products are observed at higher concentrations than predicted by the expression of K mentioned above. [4][5][6][7][8][9][10][11][12] Different explanations were put forward that include conformational changes of the unbound molecule(s), non-fluorescent bindings, and missed events due to transient interactions. 13,14 Several theoretical studies proposed that small systems, attributed to be stochastic in nature, are characterized by equilibrium constants different than that observed for a macroscopic system, which attributed to be deterministic.…”

Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array

“…The DNA hybridization reaction is an interchain reaction of macromolecules, which can be regarded as an association reaction involving diffusion in three-dimensional finite domains . The hybridization reaction of two complementary ssDNA might be symbolized as the following: , where SS 1 and SS 2 refer to the two complementary single strands, k on and k off represent the formation and dissociation rates constant of SS 1 ·SS 2 , respectively, k r is the formation rates constant of double-stranded DNA (P), using the following rate equation: …”

Modulation of DNA conformation in electrolytic nanodroplets

“…18–20 The effects of confinement on polymers have been extensively studied by theoretical predictions, 21,22 numerical simulations, 8,21–33 and experimental investigations. 34–39 A variety of micro- or nano-circumstances has been considered in previous literature, such as the extension of a polymer chain in nanochannels with different geometry, 25,30,31,33–35,39 packaging of a DNA chain in spherical cavities 22,27,38 and knotting in nanoslits. 8,32…”