Failure Mechanisms in DNA Self-Assembly: Barriers to Single-Fold Yield

Area of Science:

• Nanotechnology
• Biochemistry
• Molecular Biology

Background:

• DNA origami is a nanotechnology that uses DNA strands to create nanoscale structures.
• Origami assembly involves hundreds of simultaneous hybridization events between scaffold and staple strands.
• Understanding the folding process is crucial for advancing nucleic acid nanofabrication.

Purpose of the Study:

• To develop a real-time method for observing individual DNA origami folding events.
• To investigate how fold distance and staple/scaffold ratio affect single fold dynamics.
• To identify factors limiting the efficiency of DNA origami assembly.

Main Methods:

• Developed a real-time probe to monitor single hybridization events (folds) in DNA origami.
• Analyzed the folding process as a function of varying fold distances and staple/scaffold ratios.
• Investigated the dynamics of individual folding operations across the DNA scaffold.

Main Results:

• Successfully monitored individual folding events in real-time.
• Identified a predicted but previously unobserved blocked state during single fold operations.
• Demonstrated that this blocked state limits the yield of individual folds.

Conclusions:

• The study provides a new method to probe unit operations in DNA origami assembly.
• A blocked state acting as a yield-limiting barrier for single folds was elucidated.
• Findings offer insights into optimizing whole origami assembly processes.