Analysis of DNA Origami Nanostructures Using Capillary Electrophoresis

Resolution of complex mixtures of duplex and antiparallel triplex DNA structures by capillary electrophoresis and multivariate analysis

Triplex DNA structures, which are formed by the addition of an extra strand to a target B-DNA duplex, have attracted increasing interest due to their analytical and therapeutic applications. These structures are classified into parallel and antiparallel, depending on the orientation of the Triplex-Forming Oligonucleotide (TFO) relative to the B-DNA duplex. Whereas the formation of parallel triplexes is easily detected by monitoring spectral changes in the UV region, the formation of antiparallel triplexes produces small or even no spectral variations, which makes their detection difficult and uncertain. In this study, we propose the use of capillary electrophoresis with ultraviolet absorption spectrophotometric (CE-UV) detection combined with the multivariate curve resolution-alternating least squares (MCR-ALS) chemometric method to analyse mixtures of DNA sequences capable of forming mixtures of B-DNA duplex and triplex antiparallel structures. Rapid and reproducible CE-UV analysis in hydroxypropylcellulose (HPC)-coated capillaries are done in a pH 7.4 buffer containing Mg(II) for the stabilization of the intermolecular species. Spectra measured from 220 to 300 nm along the CE-UV analysis of individual DNA strands and of their mixtures at different ratios are merged into an augmented data matrix. This is later analyzed with MCR-ALS to deconvolute characteristic pure spectra and electropherograms for each one of the CE-UV analysis considered. This procedure has allowed the resolution and detection of DNA species present in mixtures of DNA strands capable of forming duplexes, as well as antiparallel triplex structures.

Microfluidic-based electrically driven particle manipulation techniques for biomedical applications

Microfluidic chips exhibit unique advantages in both economy and rapidity, particularly for the separation and detection of biomolecules. In this review, we first introduced the mechanisms of several electrically driven methods, such as electrophoresis, dielectrophoresis, electro-wetting and electro-rotation. We then discussed in detail the application of these methods in nucleic acid analysis, protein manipulation and cell treatment. In addition, we outlined the considerations for material selection, manufacturing processes and structural design of microfluidic chips based on electrically driven mechanisms.

Deep eutectic solvents as a green alternative to organic solvents for β-cyclodextrin pseudo-stationary phase in capillary electrophoresis

β-cyclodextrin (β-CD), as an important pseudo-stationary phase (PSP) in capillary electrophoresis (CE), frequently confronts challenges stemming from its limited water solubility, particularly when high concentrations are required for resolving complex analytes. Traditionally, researchers often resort to the use of (toxic) organic solvents to enhance the solubility of β-CD, establishing non-aqueous capillary electrophoresis (NACE) for specific separations. However, such practices are hazardous to health and run counter to the principles of green analytical chemistry. In this study, we demonstrate a deep eutectic solvent (DES), Proline:Urea (PU), as a promising alternative to conventional organic solvents for β-CD-based CE separations. The DES exhibits a solubility of up to 30% for β-CD, a significant improvement compared to the 1.8% solubility in the aqueous phase. Utilizing this DES-type separation medium, we achieved simultaneous baseline separation of a complex analyte composed of eight structurally similar naphthoic acid derivatives. Furthermore, we conducted a systematic comparison of β-CD's performance in aqueous CE buffers, organic solvents, and DESs, highlighting the superiority of this novel and environmentally friendly CE separation medium.

Dominant Analytical Techniques in DNA Nanotechnology for Various Applications

DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.