ArticleNucleic acids research2023
Toehold clipping: A mechanism for remote control of DNA strand displacement.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Recent Advances in Conjugation Chemistry Expanding the Applications of the DNA Tetrahedron.Chemical biology & drug design · 2026Review
- DNA-Based Boolean Logic Gates for Molecular Computation and Biosensing: A Critical Review.Molecular biotechnology · 2026Review
- Light-responsive DNA nanostructures.Nature reviews. Chemistry · 2026Review
- crRNA scaffold remodeling controls CRISPR-Cas12a activity for enhanced performance.Nucleic acids research · 2026Article
- Functions and applications of enzymes in nucleic acid nanotechnology.Journal of nanobiotechnology · 2025Review
- Mismatch-Induced Toehold-Free Strand Displacement Used to Control a DNA Nanodevice.ACS synthetic biology · 2025Article
- GelGenie: an AI-powered framework for gel electrophoresis image analysis.Nature communications · 2025Article
- DNA Nanotechnology in the Undergraduate Laboratory: Toehold-Less Strand Displacement in Switchback DNA.JACS Au · 2025Article
- Fluorescence-Based Multimodal DNA Logic Gates.Nanomaterials (Basel, Switzerland) · 2024Article
- A DNA rotary nanodevice operated by enzyme-initiated strand resetting.Chemical communications (Cambridge, England) · 2024Article
- Light-controlled growth of DNA organelles in synthetic cells.Interface focus · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The ability to create stimuli-responsive DNA nanostructures has played a prominent role in dynamic DNA nanotechnology. Primary among these is the process of toehold-based strand displacement, where a nucleic acid molecule can act as a trigger to cause conformational changes in custom-designed DNA nanostructures. Here, we add another layer of control to strand displacement reactions through a 'toehold clipping' process. By designing DNA complexes with a photocleavable linker-containing toehold or an RNA toehold, we show that we can use light (UV) or enzyme (ribonuclease) to eliminate the toehold, thus preventing strand displacement reactions. We use molecular dynamics simulations to analyze the structural effects of incorporating a photocleavable linker in DNA complexes. Beyond simple DNA duplexes, we also demonstrate the toehold clipping process in a model DNA nanostructure, by designing a toehold containing double-bundle DNA tetrahedron that disassembles when an invading strand is added, but stays intact after the toehold clipping process even in the presence of the invading strand. This work is an example of combining multiple physical or molecular stimuli to provide additional remote control over DNA nanostructure reconfiguration, advances that hold potential use in biosensing, drug delivery or molecular computation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.