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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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Design of a DXAB tile and arrangement into a 2D DNA array. (a) Strand structure of the DXAB tile for construction of heat-resistant 2D DNA arrays. Complementary sticky-end pairs are labeled as n and n′ (n = 1, 2, 3). Arrowheads at the ends of strands indicate the 3′-terminals. Black triangles indicate nicks in the strands. The solid circles at the 5′-ends represent CVU bases. (b) The lattice topology of a 2D DNA array produced by the DXAB tiles. The strand color is the same as that used in (a). The reverse side of the tile is designated by a gray rectangle. (c) Template-directed DNA photoligation with CVU. (d) The sequences of the DXAB tile. The solid rhomboids at the 5′-ends represent phosphorylation.
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Figure 1: Design of a DXAB tile and arrangement into a 2D DNA array. (a) Strand structure of the DXAB tile for construction of heat-resistant 2D DNA arrays. Complementary sticky-end pairs are labeled as n and n′ (n = 1, 2, 3). Arrowheads at the ends of strands indicate the 3′-terminals. Black triangles indicate nicks in the strands. The solid circles at the 5′-ends represent CVU bases. (b) The lattice topology of a 2D DNA array produced by the DXAB tiles. The strand color is the same as that used in (a). The reverse side of the tile is designated by a gray rectangle. (c) Template-directed DNA photoligation with CVU. (d) The sequences of the DXAB tile. The solid rhomboids at the 5′-ends represent phosphorylation.

Mentions: The DXAB tile (Figure 1a) used in the construction of 2D DNA arrays by self-assembly consists of two parts, namely A and B, derived from the well-known DX tiles (5). Part A and part B are held together by strand-ab, and their junction point has a certain degree of flexibility due to the nick. The complementary sticky-end pairs labeled as n and n′ (n = 1, 2, 3) can bind to each other, and the DXAB tiles can form the 2D arrays (Figure 1b). The sequences of sticky ends were designed to carry out the photoligation reactions. Both 5′-ends of one double-helix of part A have UV-sensitive 5-carboxyvinyl-2′-deoxyuridine (CVU) (2), which can bind to the thymine or cytosine base at the neighboring 3′-end by 366-nm UV-ray exposure (Figure 1c).Figure 1.


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)

Design of a DXAB tile and arrangement into a 2D DNA array. (a) Strand structure of the DXAB tile for construction of heat-resistant 2D DNA arrays. Complementary sticky-end pairs are labeled as n and n′ (n = 1, 2, 3). Arrowheads at the ends of strands indicate the 3′-terminals. Black triangles indicate nicks in the strands. The solid circles at the 5′-ends represent CVU bases. (b) The lattice topology of a 2D DNA array produced by the DXAB tiles. The strand color is the same as that used in (a). The reverse side of the tile is designated by a gray rectangle. (c) Template-directed DNA photoligation with CVU. (d) The sequences of the DXAB tile. The solid rhomboids at the 5′-ends represent phosphorylation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Design of a DXAB tile and arrangement into a 2D DNA array. (a) Strand structure of the DXAB tile for construction of heat-resistant 2D DNA arrays. Complementary sticky-end pairs are labeled as n and n′ (n = 1, 2, 3). Arrowheads at the ends of strands indicate the 3′-terminals. Black triangles indicate nicks in the strands. The solid circles at the 5′-ends represent CVU bases. (b) The lattice topology of a 2D DNA array produced by the DXAB tiles. The strand color is the same as that used in (a). The reverse side of the tile is designated by a gray rectangle. (c) Template-directed DNA photoligation with CVU. (d) The sequences of the DXAB tile. The solid rhomboids at the 5′-ends represent phosphorylation.
Mentions: The DXAB tile (Figure 1a) used in the construction of 2D DNA arrays by self-assembly consists of two parts, namely A and B, derived from the well-known DX tiles (5). Part A and part B are held together by strand-ab, and their junction point has a certain degree of flexibility due to the nick. The complementary sticky-end pairs labeled as n and n′ (n = 1, 2, 3) can bind to each other, and the DXAB tiles can form the 2D arrays (Figure 1b). The sequences of sticky ends were designed to carry out the photoligation reactions. Both 5′-ends of one double-helix of part A have UV-sensitive 5-carboxyvinyl-2′-deoxyuridine (CVU) (2), which can bind to the thymine or cytosine base at the neighboring 3′-end by 366-nm UV-ray exposure (Figure 1c).Figure 1.

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