Classification and recognition of noncanonical DNA secondary structures by surface-enhanced Raman spectroscopy and...

Area of Science:

• Biophysical Chemistry
• Molecular Biology
• Analytical Chemistry

Background:

• Understanding DNA secondary structures is crucial for nucleic acid function and regulation.
• Existing methods for analyzing DNA secondary structure diversity lack high-throughput and label-free capabilities.

Purpose of the Study:

• To develop an optimized surface-enhanced Raman spectroscopy (SERS) substrate for high-throughput, label-free classification of diverse DNA secondary structures.
• To utilize principal component analysis (PCA) for substrate optimization and accurate recognition of noncanonical DNA structures.

Main Methods:

• Optimization of SERS substrates by modifying silver nanoparticles (AgNPs) and gold nanoparticles (AuNPs) with various anions (Cl-, Br-, I-) and cations as aggregation agents.
• Selection of optimal substrates: I- ions modified AgNPs with Ba2+ (Ag IMNPs-Ba2+) and Br- ions modified AuNPs with Ba2+ (Au BrMNPs-Ba2+).
• Classification of various DNA secondary structures, including parallel, hybrid, and antiparallel G4 structures, i-motifs (iM), and double-strand DNA (dsDNA) using the optimized SERS substrates.

Main Results:

• Identified optimal SERS substrates (Ag IMNPs-Ba2+ and Au BrMNPs-Ba2+) capable of distinguishing DNA secondary structures based on characteristic Raman peaks.
• Successfully classified parallel, hybrid, and antiparallel G4 structures, iM with varying C:CH+ base pairs, and different dsDNA forms.
• Accurately identified complex DNA secondary structures within mixed solutions.

Conclusions:

• The developed PCA-optimized SERS platform provides a universal and efficient method for analyzing DNA secondary structure diversity.
• This approach enables unambiguous classification and identification of various DNA secondary structures, including noncanonical forms.
• The study offers a foundation for large-scale screening of SERS substrates for advanced DNA analysis.