Choice of fluorophore affects dynamic DNA nanostructures

Area of Science:

• Nanotechnology
• Biochemistry
• Molecular Biology

Background:

• Dynamic DNA nanostructures are crucial for nanotechnology.
• Fluorophores are commonly used to monitor DNA nanodevice dynamics.
• Fluorophore selection can inadvertently affect DNA nanostructure behavior.

Purpose of the Study:

• To investigate how fluorophore choice influences the reconfiguration of DNA nanostructures.
• To demonstrate a method for tuning the energy landscape of dynamic DNA nanodevices.
• To highlight the importance of considering fluorophore side effects in DNA nanotechnology.

Main Methods:

• Encapsulating triple-stranded DNA (tsDNA) in water-in-oil compartments.
• Functionalizing tsDNA with single-stranded DNA (ssDNA) handles for binding and unbinding.
• Utilizing experiments, molecular dynamics (MD) simulations, and reaction-diffusion modeling.
• Testing 12 different fluorophore combinations.

Main Results:

• Fluorophore selection significantly alters or inhibits DNA nanostructure formation.
• The DNA sequence remained unchanged, indicating fluorophore-specific effects.
• Demonstrated control over DNA nanostructure reconfiguration through fluorophore choice.
• Identified a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.

Conclusions:

• Fluorophore choice is a critical parameter in designing and validating dynamic DNA nanostructures.
• Understanding fluorophore-induced effects enables precise control over DNA nanodevice behavior.
• This work provides a strategy for optimizing dynamic DNA nanodevices and pH-responsive switches.