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Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine.

Tagawa M, Shohda K, Fujimoto K, Sugawara T, Suyama A - Nucleic Acids Res. (2007)

Bottom Line: Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components.DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer.The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences and Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo, Japan.

ABSTRACT
Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components. DNA double-crossover AB-staggered (DXAB) tiles were covalently connected by enzyme-free template-directed photoligation, which enables a specific ligation reaction in an extremely tight space and under buffer conditions where no enzymes work efficiently. DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer. The improvement of the heat tolerance of 2D DNA arrays was confirmed by heating and visualizing the DNA nanostructures. The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology.

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AFM images and section profiles of self-assembled 2D DNA arrays of DXAB tiles with or without heat treatment in buffer solutions. The scan sizes of images are 800 nm × 800 nm for large images and 150 nm × 150 nm for inset images. The section profiles correspond to the white lines in the inset images. (a) Non-UV-exposed DNA arrays without heat treatment. (b) Non-UV-exposed DNA arrays after heating at 40°C in buffer solutions. (c) UV-exposed DNA arrays without heat treatment. UV-exposed DNA arrays after heating at 40°C (d), 45°C (e) and 50°C (f) in buffer solutions.
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Figure 3: AFM images and section profiles of self-assembled 2D DNA arrays of DXAB tiles with or without heat treatment in buffer solutions. The scan sizes of images are 800 nm × 800 nm for large images and 150 nm × 150 nm for inset images. The section profiles correspond to the white lines in the inset images. (a) Non-UV-exposed DNA arrays without heat treatment. (b) Non-UV-exposed DNA arrays after heating at 40°C in buffer solutions. (c) UV-exposed DNA arrays without heat treatment. UV-exposed DNA arrays after heating at 40°C (d), 45°C (e) and 50°C (f) in buffer solutions.

Mentions: The self-assembled DXAB tile arrays before and after photoligation reactions were visualized by atomic force microscopy. The samples corresponding to those analyzed in Lanes L1 and L3 in Figure 2 were deposited for adsorption on atomically flat mica surfaces and then imaged in 1×TAE/Mg2+ buffer. The DXAB arrays before photoligation had the periodic structure grown to a micro-scale (Figure 3a). The average distance of the longitudinal AB period (the long axis period) was about 30 nm, which is in good agreement with the designed parameters. The average distance of the short axis period measured from section profiles was about 6 nm. The difference in elevation of the periodic corrugation was about 0.8 nm, which is shorter than the diameter of a hydrated DNA duplex (2 nm). This is because the tip cannot touch the mica surface through the narrow interspaces between DNA duplexes. No significant conformation changes occurred after UV-ray exposure in buffer solutions (Figure 3c). The photoligated arrays show almost the same periodic structure with the long and short axis periods of about 30 and 6 nm, respectively. The self-assembled DXAB tiles using strand-a1, a4, b1, b3 and b4 without phosphorylation were also examined by atomic force microscopy. The sample corresponding to the one that was analyzed in Lane 2 in Figure 2 had no periodic array structure.Figure 3.


Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine.

Tagawa M, Shohda K, Fujimoto K, Sugawara T, Suyama A - Nucleic Acids Res. (2007)

AFM images and section profiles of self-assembled 2D DNA arrays of DXAB tiles with or without heat treatment in buffer solutions. The scan sizes of images are 800 nm × 800 nm for large images and 150 nm × 150 nm for inset images. The section profiles correspond to the white lines in the inset images. (a) Non-UV-exposed DNA arrays without heat treatment. (b) Non-UV-exposed DNA arrays after heating at 40°C in buffer solutions. (c) UV-exposed DNA arrays without heat treatment. UV-exposed DNA arrays after heating at 40°C (d), 45°C (e) and 50°C (f) in buffer solutions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2175349&req=5

Figure 3: AFM images and section profiles of self-assembled 2D DNA arrays of DXAB tiles with or without heat treatment in buffer solutions. The scan sizes of images are 800 nm × 800 nm for large images and 150 nm × 150 nm for inset images. The section profiles correspond to the white lines in the inset images. (a) Non-UV-exposed DNA arrays without heat treatment. (b) Non-UV-exposed DNA arrays after heating at 40°C in buffer solutions. (c) UV-exposed DNA arrays without heat treatment. UV-exposed DNA arrays after heating at 40°C (d), 45°C (e) and 50°C (f) in buffer solutions.
Mentions: The self-assembled DXAB tile arrays before and after photoligation reactions were visualized by atomic force microscopy. The samples corresponding to those analyzed in Lanes L1 and L3 in Figure 2 were deposited for adsorption on atomically flat mica surfaces and then imaged in 1×TAE/Mg2+ buffer. The DXAB arrays before photoligation had the periodic structure grown to a micro-scale (Figure 3a). The average distance of the longitudinal AB period (the long axis period) was about 30 nm, which is in good agreement with the designed parameters. The average distance of the short axis period measured from section profiles was about 6 nm. The difference in elevation of the periodic corrugation was about 0.8 nm, which is shorter than the diameter of a hydrated DNA duplex (2 nm). This is because the tip cannot touch the mica surface through the narrow interspaces between DNA duplexes. No significant conformation changes occurred after UV-ray exposure in buffer solutions (Figure 3c). The photoligated arrays show almost the same periodic structure with the long and short axis periods of about 30 and 6 nm, respectively. The self-assembled DXAB tiles using strand-a1, a4, b1, b3 and b4 without phosphorylation were also examined by atomic force microscopy. The sample corresponding to the one that was analyzed in Lane 2 in Figure 2 had no periodic array structure.Figure 3.

Bottom Line: Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components.DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer.The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences and Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo, Japan.

ABSTRACT
Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components. DNA double-crossover AB-staggered (DXAB) tiles were covalently connected by enzyme-free template-directed photoligation, which enables a specific ligation reaction in an extremely tight space and under buffer conditions where no enzymes work efficiently. DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer. The improvement of the heat tolerance of 2D DNA arrays was confirmed by heating and visualizing the DNA nanostructures. The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology.

Show MeSH
Related in: MedlinePlus