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Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Label-Free Microfluidic Modulation Spectroscopy Monitors RNA Origami Structure and Stability.

Phoebe S Tsoi1, Lathan Lucas1, Allan Chris M Ferreon1

  • 1Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA.

Biosensors
|March 27, 2026
PubMed
Summary
This summary is machine-generated.

Microfluidic Modulation Spectroscopy (MMS) offers a new way to analyze RNA origami nanostructures in solution. This label-free method efficiently tracks RNA folding, maturation, and stability, aiding biosensor development.

Keywords:
RNA foldingRNA origamiinfrared spectroscopykinetic trapmicrofluidic modulation spectroscopy

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Area of Science:

  • Biotechnology
  • Nanotechnology
  • Structural Biology

Background:

  • RNA origami allows for self-assembling RNA nanostructures for applications in biosensing, synthetic biology, and nanomedicine.
  • A key challenge is assessing the structural integrity and folding dynamics of these RNA scaffolds in solution.
  • Existing methods for structural readout can be limited in scalability and require specific labeling.

Purpose of the Study:

  • To adapt microfluidic modulation spectroscopy (MMS) as a label-free technique for analyzing RNA folding and structure.
  • To establish a workflow for quantifying RNA base-pairing states and monitoring structural maturation.
  • To demonstrate the utility of MMS for studying RNA origami nanostructures under native conditions.

Main Methods:

  • Microfluidic Modulation Spectroscopy (MMS) was employed, utilizing the vibrational fingerprints of RNA bases and base pairs (1760-1600 cm⁻¹).
  • A microfluidic transmission cell was used for automated background subtraction, enabling measurements from small sample volumes.
  • An analysis workflow involving baselined second derivative and constrained deconvolution was developed to quantify paired and unpaired RNA populations.

Main Results:

  • MMS successfully measured RNA folding and structural states in microliter volumes under native solution conditions.
  • Thermal ramping experiments revealed distinct unfolding barcodes for different RNA conformational states, distinguishing young and mature ensembles.
  • The study tracked the post-transcriptional maturation of RNA origami from a kinetically trapped state to a more compact, base-paired structure.

Conclusions:

  • MMS serves as a rapid, automated, and scalable method for structural analysis of RNA origami.
  • This technique complements high-resolution methods like cryo-EM and SAXS for engineering dynamic RNA nanostructures.
  • MMS facilitates the characterization of RNA folding dynamics, crucial for the development of advanced RNA-based biosensors and nanomedicines.