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Related Experiment Video

Updated: May 28, 2026

Folding and Characterization of a Bio-responsive Robot from DNA Origami
07:59

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Published on: December 3, 2015

Optimising DNA origami assembly by reducing off-target interactions.

Ben Shirt-Ediss1, Emanuela Torelli1,2, Silvia Adriana Navarro1

  • 1Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, UK.

Nature Communications
|May 26, 2026
PubMed
Summary

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This summary is machine-generated.

Scaffold sequence significantly impacts DNA origami folding reliability by influencing off-target interactions. A new computational tool helps select sequences that minimize these effects, improving assembly yield and structural uniformity.

Area of Science:

  • Nanotechnology
  • Molecular Biology
  • Biophysics

Background:

  • DNA origami allows programmable self-assembly of nucleic acids into nanostructures.
  • The role of primary base sequence in DNA origami folding reliability is not fully understood.
  • Off-target interactions can lead to kinetic traps and reduced assembly yield.

Purpose of the Study:

  • To investigate how scaffold sequence affects DNA origami assembly reliability.
  • To develop a computational framework for predicting and minimizing off-target interactions.
  • To experimentally validate the impact of scaffold sequence on folding yield and structural uniformity.

Main Methods:

  • Developed a multi-objective computational framework to score scaffold sequences based on off-target interactions.

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Designing a Bio-responsive Robot from DNA Origami

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Related Experiment Videos

Last Updated: May 28, 2026

Folding and Characterization of a Bio-responsive Robot from DNA Origami
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Folding and Characterization of a Bio-responsive Robot from DNA Origami

Published on: December 3, 2015

DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications
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DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications

Published on: September 27, 2019

Designing a Bio-responsive Robot from DNA Origami
13:32

Designing a Bio-responsive Robot from DNA Origami

Published on: July 8, 2013

  • Identified favorable and unfavorable scaffold regions from biological and synthetic sequences.
  • Experimentally tested selected scaffold sequences using atomic force microscopy and single-molecule optical tweezers.

    • Main Results:

    • Scaffold sequences predicted to have fewer off-target interactions consistently yielded higher DNA origami assembly.
    • Off-target-prone scaffolds resulted in significantly lower assembly yields, even with complementary staple strands.
    • Scaffold variants with reduced off-target interactions produced more mechanically uniform origami structures.

    Conclusions:

    • Off-target sequence effects are a major determinant of DNA origami folding reliability.
    • The developed computational tool can guide the selection of optimal scaffold sequences for any DNA origami design.
    • Minimizing off-target interactions enhances both the yield and mechanical uniformity of DNA origami nanostructures.