Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness
| Autor: | Stavros Gaitanaros, Enze Chen, Remi Veneziano, Wei-Hung Jung, Yun Chen |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Polynucleotide 5'-Hydroxyl-Kinase
AcademicSubjects/SCI00010 DNA Single-Stranded 02 engineering and technology Biology Molecular physics 03 medical and health sciences chemistry.chemical_compound Genetics Holliday junction Fluid dynamics medicine DNA origami Elasticity (economics) 030304 developmental biology 0303 health sciences DNA Cruciform Stiffness 021001 nanoscience & nanotechnology Elasticity Biomechanical Phenomena Nanostructures chemistry DNA Viral Thermodynamics Elastic rods medicine.symptom 0210 nano-technology Synthetic Biology and Bioengineering Order of magnitude DNA Bacteriophage M13 |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force–displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles. |
| Databáze: | OpenAIRE |
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