Stabilization and structural changes of 2D DNA origami by enzymatic ligation
| Autor: | Takashi Morii, Eiji Nakata, Amulya Giridasappa, Arivazhagan Rajendran, Kirankumar Krishnamurthy |
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| Rok vydání: | 2021 |
| Předmět: |
DNA Ligases
AcademicSubjects/SCI00010 Intercalation (chemistry) 02 engineering and technology Biology Microscopy Atomic Force Nucleic Acid Denaturation 010402 general chemistry 01 natural sciences chemistry.chemical_compound Chemical Biology and Nucleic Acid Chemistry Ethidium DNA nanotechnology Genetics DNA origami Thermal stability Phosphorylation Electrophoresis Agar Gel chemistry.chemical_classification DNA ligase Temperature DNA 021001 nanoscience & nanotechnology Nanostructures 0104 chemical sciences Kinetics chemistry Biophysics Nucleic Acid Conformation Thermodynamics 0210 nano-technology Ligation Ethidium bromide |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In molecular biology, enzymatic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnology, the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed analysis and optimization of the conditions for the enzymatic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temperature, and typically requires much higher concentration of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a maximum ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concentration-dependent manner. |
| Databáze: | OpenAIRE |
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