Supramolecular Interactions Modulate RNA:DNA Folding Observed via Nanopore Sensing

Area of Science:

• Biotechnology
• Nanotechnology
• Supramolecular Chemistry

Background:

• DNA and RNA nanotechnology allow precise molecular assembly for bioengineering and sensing.
• Material properties of biopolymers are tunable via covalent or non-covalent interactions.
• Small molecules offer a simple method for modulating biopolymer properties.

Purpose of the Study:

• To investigate the use of urea as a small molecule to modulate the stiffness of RNA:DNA hybrid nanostructures.
• To assess the impact of urea on the structural properties and sensing applications of these nanostructures.

Main Methods:

• Solid-state nanopore measurements to assess structural changes and translocation events.
• Atomic force microscopy (AFM) to provide evidence of structural rigidification.
• Preparation of topologically-barcoded RNA:DNA hybrids in the presence of urea.

Main Results:

• Urea non-covalently interacts with the A-form-like helix of RNA:DNA hybrids, leading to rigidification.
• Solid-state nanopore and AFM measurements confirmed the stiffening effect of urea.
• Preparation in urea reduced folded translocation events by 50% in nanopore sensing experiments.

Conclusions:

• Urea effectively modulates the stiffness of RNA:DNA hybrid nanostructures through supramolecular interactions.
• The reduction in folded events enhances data quality for single-molecule detection.
• This approach facilitates robust detection of low-abundance RNA analytes.