ArticleNucleic acids research2017
Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves.
Article in Nucleic acids research, 2017. 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, 37 citations in OpenAlex.
- Isothermal assembly of DNA nanostructures.Chemical communications (Cambridge, England) · 2025Review
- Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing.Advances in biochemical engineering/biotechnology · 2024Review
- Functional advantages of building nanosystems using multiple molecular components.Nature chemistry · 2023Article
- Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes.Analytical chemistry · 2022Article
- DNA mechanical flexibility controls DNA potential to activate cGAS-mediated immune surveillance.Nature communications · 2022Article
- Temperature-dependent elastic properties of DNA.Biophysical reports · 2022Article
- Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters.Nucleic acids research · 2022Article
- Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies.Langmuir : the ACS journal of surfaces and colloids · 2022Article
- Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study.Analytical and bioanalytical chemistry · 2021Article
- Reprogrammable Gel Electrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization Chain Reaction.Analytical chemistry · 2021Article
- Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.Nucleic acids research · 2017Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson-Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers.
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