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

Jacob M Majikes1, Paul N Patrone1, Anthony J Kearsley1

  • 1National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States.

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|February 10, 2021
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Summary

This study probes single DNA origami folds in real-time. A previously unobserved blocked state limits the yield of individual folds, impacting overall DNA origami assembly.

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DNA origamihybridizationmeltingnanostructuresself-assembly yieldthermodynamic modeling

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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.