Size selective absorption of DNA tetrahedra in ATO nanomaterials

22 Jun 2011

A group of Center for Bio-inspired Solar Fuel Production researchers collaborating on Subtask 2 (Water oxidation catalyst) and Subtask 5 (Functional nanostructured transparent electrode materials) have found that transparent and conducting antimony tin oxide with controlled pore size incorporates DNA nanocages with high affinity and without damage. Results of the study have been published in  the June 2011 issue of ACS Nano. The study has brought the Center scientists a bit closer to a design of a transparent nanostructured electrode with entrapped functional water oxidation catalysts.

The major goal of Subtask 2 is to build an artificial water oxidation catalyst. The design of that complex is bio-inspired by the natural water oxidation complex (a.k.a. oxygen evolving complex) in Photosystem II. The natural water splitting enzyme uses cluster of manganese atoms to split the water. Amino acid residues of the core Photosystem II proteins position the cluster in close proximity to the reaction center, which provides the driving force for the water oxidation. Researchers of Subtask 2 are trying to mimic the protein environment for the inorganic water oxidation catalyst by synthesizing artificial peptides that bind the catalyst. To be a part of the artificial biofuel cell the water oxidation catalyst should be coupled to an electrode. In order for the electrodes to host the functional catalyst Hao Yan, Yan Liu and colleagues are working to introduce the artificial peptide based catalyst to the electrode via a structural DNA framework.

Researchers of Subtask 5 led by Don Seo strive to develop a high surface area electrode that could  bind the water oxidation catalyst while maintaining transparency, high electrical conductivity, specifically-tuned semiconductor properties, chemical inertness, and physical robustness.

 

Fluorescently labeled DNA nanocages

DNA has been widely used as a structural material to construct supramolecular nanostructures. DNA origami approaches allow connecting DNA strands in predictable three-dimensional structures with stable inter- and intramolecular interactions. A functionalized tetrahedral DNA nanocage has been designed to serve as a stable three-dimensional scaffold for the coordination of electron transfer mediators, nanoparticles, and peptides. Design of the DNA nanocage provides a structural tool to spatially control and optimize position on the scaffold to facilitate effective electron transfer to electrodes. Each edge of the DNA tetrahedron contains 20 base pairs and is ∼6.8 nm long.

For microscopic visualization the DNA nanocages were self assembled with covalently attached Cy3 (green emission) or Cy 5 (red emission) fluorescent dyes. If the DNA tetrahedra were taken up by the nanoporous material then the bright background solution fluorescence under the confocal microscope should disappear and the nanoporous materias should show fluorescence from the dye. The critical experiments were designed to test a selective absorption of the DNA nanostructures with a hydrodynamic diameter of 9-10 nm into the metal oxide cavities.

Transparent ATO with controlled pore size

Don Seo and colleagues from Subtask 5 have a multistep plan for design of target nanoporous electrode materials. They have recently figured out that antimony-doped tin oxide (ATO) under certain conditions can be assembled with three-dimensionally interconnected pores within the metal oxide and highly tunable pore sizes on the nanoscale. The experimental procedure for preparation of the nanomaterial using sol gel method has been published recently (Volosin et al., 2011).

Tunability of the pore size in the nanostructured material is critical for a testing of selective entrapment of the DNA nanocages by the electrode material. Alex Volosin, a graduate student from the Seo lab has learned how to change the size of the nanopores. He has found that the average pore size can be controlled by varying the relative concentrations of starting precursor materials. Alex has prepared two types of materials, with narrow pores (7 nm) and broad pores (14 nm).

Fluorescence confocal microscopy images for the narrow porous ATO samples that were incubated with the Cy3-labeled nanocage indeed showed strong fluorescence background outside of the material with no observable uptake of the structure into the pores of the ATO. The ATO host matrix with an average pore size of 14 nm readily incorporates the DNA nanocage into pores throughout the material, with concurrent disappearance of the fluorescence in the solution and appearance in the nanocages.  The integrity of the entrapped nanocages was  verified using a Förster Resonance Energy Transfer (FRET) test. A self-assembled DNA tetrahedron was formed with covalently attached Cy3 and Cy5 dyes that demonstrate FRET in solution. Similar energy transfer efficiency from Cy3 to Cy5 in solution and within nanopores is evidence that the tetrahedra remain intact within the pores.

Achievement of a specific and stable entrapment of the DNA nanocages within the nanoporous ATO overcomes typical hurdles that are encountered when macromolecules are directly attached to electrodes including lack of solubility and denaturation. This now effectively lays the groundwork for potentially using the DNA scaffold systems for designing a bio-inspired solar fuel production cell via water splitting within the conductive and transparent ATO host matrix.

 

Source:

Simmons, C. R., Schmitt, D., Wei, X., Han, D., Volosin, A. M., Ladd, D. M., Seo, D.-K., Liu, Y., and Yan, H. (2011) Size-Selective Incorporation of DNA Nanocages into Nanoporous Antimony-Doped Tin Oxide Materials, ACS Nano, 5, 6060-6068 (Read online)

 

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