Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics

Abstract

Detection of conformational changes in biomolecular assemblies provides critical information into biological and self-assembly processes. State-of-the-art in situ biomolecular conformation detection techniques rely on fluorescent labels or protein-specific binding agents to signal conformational changes. Here, we present an on-chip, label-free technique to detect conformational changes in a DNA nanomechanical tweezer structure with microwave microfluidics. We measure the electromagnetic properties of suspended DNA tweezer solutions from 50 kHz to 110 GHz and directly detect two distinct conformations of the structures. We develop a physical model to describe the electrical properties of the tweezers, and correlate model parameters to conformational changes. The strongest indicator for conformational changes in DNA tweezers are the ionic conductivity, while shifts in the magnitude of the cooperative water relaxation indicate the addition of fuel strands used to open the tweezer. Microwave microfluidic detection of conformational changes is a generalizable, non-destructive technique, making it attractive for high-throughput measurements.

A DNA nanopillar as a scaffold to regulate the ratio and distance of mimic enzymes for an efficient cascade catalytic platform

“…To date, DNA nanostructures, such as origami, 20,21 tetrahedra 22 and nanotweezers, 23 have emerged as promising scaffolds to tether cascade enzymes with an equivalent ratio and regulate enzyme spacing at nanoscale on account of their structural programmability and accurate addressability. Despite these successes, the uncontrolled stoichiometric ratio of cascade enzymes does not favor better cooperation of the rst and second enzymatic reactions, and thus ineffective diffusion of intermediates in enzyme cascade processes limited catalytic efficiency.…”

Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures

“…Often the chip consists of two parts: the first part is glass or silicone with golden electrodes sputtered on top of it, and the second part is bonded on top of a molded or hot-embossed polymer microfluidic structure. Several groups achieved good results with this approach using microfluidics [ 99 , 386 , 387 , 388 ]. By using two glass layers with electrodes on the top and bottom, with a microfluidic channel cut through an additional sandwich layer in between, it is possible to fabricate sensor electrodes placed on two opposite sides ( Figure 14 ).…”

Going beyond the Debye Length: Overcoming Charge Screening Limitations in Next-Generation Bioelectronic Sensors

“…This approach, known as dielectric spectroscopy, 46 , 47 can be very sensitive and has been used to differentiate open and closed DNA-based molecular tweezers in buffer. 48 It is challenging to use this technique for specific biomolecular detection in biological samples, however, because any molecular changes in the complex sample can alter signals. However, dielectric spectroscopy has proven to be suitable for other biomedical applications.…”