Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective

Area of Science:

• Nanotechnology
• Biotechnology
• Molecular Biology

Background:

• DNA-modified gold nanoparticles (AuNPs) are essential in bio-nanotechnology for applications like bio-sensing, bio-imaging, and drug delivery.
• Current synthesis methods optimize DNA receptor density on AuNPs, but the kinetics of DNA hybridization and its particle-to-particle variability remain poorly understood.

Purpose of the Study:

• To investigate the molecular mechanisms governing DNA hybridization kinetics on densely coated AuNPs.
• To quantify the impact of DNA density and spacer strands on hybridization association and dissociation rates.
• To analyze the heterogeneity of hybridization kinetics at both single-molecule and particle levels.

Main Methods:

• Utilized single-molecule microscopy to observe and quantify DNA hybridization events on individual AuNPs.
• Employed coarse-grained molecular dynamics simulations to model DNA behavior and hybridization on nanoparticle surfaces.
• Integrated experimental and simulation data to determine molecular rate constants and understand underlying mechanisms.

Main Results:

• DNA receptor density and spacer strand length significantly influence DNA association kinetics, with short spacers increasing rates up to approximately 15-fold.
• Dissociation kinetics were found to be relatively insensitive to DNA receptor density within the investigated range.
• Single-particle analysis revealed significant intra- and inter-particle heterogeneity in hybridization kinetics.
• Coarse-grained DNA modeling corroborated experimental findings and highlighted the role of transient base pairing in kinetics.

Conclusions:

• The study provides a quantitative understanding of DNA hybridization kinetics on densely functionalized AuNPs, emphasizing the importance of receptor density and spacers.
• Variability in hybridization kinetics is an inherent feature of these systems, requiring consideration in sensor design.
• The combined approach of single-molecule experiments and molecular dynamics simulations offers valuable insights into nanoparticle surface dynamics.
• Findings guide the rational design of DNA-functionalized nanoparticles for enhanced performance in sensor applications.