The stability and characteristics of a DNA Holliday junction switch

Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures

Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions.

Tuning phase and aging of DNA hydrogels through molecular design

The programmable, sequence-dependent hybridization of DNA has spurred the development of DNA hydrogels, polymer networks that swell in water and are comprised either entirely or partially of DNA. Specific applications require hydrogels of particular structure for optimal functionality. Here, we use self-assembling, multi-valent DNA nanostars to examine how hydrogel structure is influenced by the non-equilibrium dynamics of its interacting components. We show that hydrogel aging kinetics - from an arrested, solid-like percolated network to an equilibrium, phase-separated liquid analogous to coacervates - are modulated by DNA hybridization strength and ion-specific nanostar internal flexibility. Together, our results demonstrate strategies to control hydrogel kinetic phenomena, and thus the hydrogel structure, through the rational design of gel-forming elements and solvent conditions.

An on-demand four-way junction DNAzyme nanoswitch driven by inosine-based partial strand displacement

A DNA four-way junction device capable of junction expansion and contraction cycles using an inosine-based partial strand displacement scheme is reported. These nanoscale positioning capabilities are used to provide on-demand activation and deactivation of a pair of split E6 DNAzymes on the device. The device also demonstrates a combined catalytic rate significantly higher than the original E6 DNAzyme under similar operational conditions. This approach can provide structural organization and spatially control other multicomponent molecular complexes.

Bio-switchable optofluidic lasers based on DNA Holliday junctions

Bio-switchable optofluidic lasers based on DNA Holliday junctions were demonstrated. Nearly 100% wavelength switching was achieved through reversible conformational change of the Holliday junction controlled by magnesium ionic strength.

Acoustic characterization of nanoswitch structures: application to the DNA Holliday Junction

A novel biophysical approach in combination with an acoustic device is demonstrated as a sensitive, rapid, and label-free technique for characterizing various structures of the DNA Holliday Junction (J1) nanoswitch. We were successful in discriminating the "closed" from the "open" state, as well as confirming that the digestion of the J1 junction resulted in the two, anticipated, rod-shaped, 20 bp long fragments. Furthermore, we propose a possible structure for the ∼10 nm long (DNA58) component participating in the J1 assembly. This work reveals the potential of acoustic devices as a powerful tool for molecular conformation studies.

Time-Resolved FRET and FLIM of Four-way DNA Junctions

Conformational transitions in a 4-way DNA junction when titrated with ionic solutions are studied using time-resolved fluorescence resonance energy transfer. Parameters characterising the transition in terms of critical ion concentration (c1/2) and the Hill coefficient for ion binding are obtained by fitting a simple two-state model using steady-state spectra. Data obtained from a fluorescence lifetime plate reader and analysed by fitting a single exponential to donor fluorescence lifetime decays are shown to be in good agreement with the parameters obtained from steady-state measurements. Fluorescence lifetimes, however, offer advantages, particularly in being independent of fluorophore concentration, output intensity, inhomogeneity in the excitation source and output wavelength. We demonstrate preliminary FRET-FLIM images of DNA junction solutions obtained using a picosecond gated CCD which are in agreement with results from a fluorescence lifetime plate reader. The results suggest that time-resolved FRET-FLIM is sensitive to subtle structural changes and may be useful in assays based on 4-way DNA junctions.