Single-Molecule Monitoring of Nucleic Acid Dynamics Using Raman Correlation Spectroscopy in Plasmonic Nanowells

Area of Science:

• Plasmonics
• Spectroscopy
• Nanotechnology

Background:

• Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) enables tracking molecular dynamics but faces challenges like unstable hot spots and citrate interference.
• Existing methods struggle with data analysis and limit biomedical applications due to these limitations.

Purpose of the Study:

• To develop a novel SM-SERS method for stable, continuous single-molecule readout and long-term monitoring of DNA diffusion.
• To overcome limitations of previous SM-SERS techniques, including plasmonic instability and molecule movement.

Main Methods:

• A fixed plasmonic gap-mode hot spot was created by immobilizing a gold nanoparticle in a gold nanowell.
• This setup allowed for continuous single-molecule readout and long-term monitoring of DNA diffusion.
• Raman correlation spectroscopy was employed to analyze diffusion dynamics.

Main Results:

• The new method achieved unlimited resident time for DNA in the hot spot, revealing sequence-dependent diffusion patterns at single-base resolution.
• The hot spot's spatial resolution covered neighboring nucleobases, the DNA backbone, and citrate molecules.
• Diffusion times for DNA nucleobases (5-22 s) and citrate (0.1-7 s) were determined.

Conclusions:

• The developed SM-SERS method provides a stable platform for biomolecular dynamics monitoring with high resolution.
• This technique shows promise for investigating oligonucleotide hybridization kinetics and could form the basis for SM-SERS sequencing technologies.