Single molecule atomic force microscopy studies of photosensitized singlet oxygen behavior on a DNA origami template.

DNA origami, the folding of a long single-stranded DNA sequence (scaffold strand) by hundreds of short synthetic oligonucleotides (staple strands) into parallel aligned helices, is a highly efficient method to form advanced self-assembled DNA-architectures. Since molecules and various materials can be conjugated to each of the short staple strands, the origami method offers a unique possibility of arranging molecules and materials in well-defined positions on a structured surface. Here we combine the action of light with AFM and DNA nanostructures to study the production of singlet oxygen from a single photosensitizer molecule conjugated to a selected DNA origami staple strand on an origami structure. We demonstrate a distance-dependent oxidation of organic moieties incorporated in specific positions on DNA origami by singlet oxygen produced from a single photosensitizer located at the center of each origami.

[1]  Hao Yan,et al.  Tiles for Label-Free RNA Hybridization Assays Self-Assembled Water-Soluble Nucleic Acid Probe , 2008 .

[2]  Yan Liu,et al.  DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires , 2003, Science.

[3]  J. Kjems,et al.  Self-assembly of a nanoscale DNA box with a controllable lid , 2009, Nature.

[4]  Reinhard Schmidt,et al.  Physical Mechanisms of Generation and Deactivation of Singlet Oxygen , 2003 .

[5]  T. Ohsaka,et al.  Use of Hydrodynamic Chronocoulometry for Simultaneous Determination of Diffusion Coefficients and Concentrations of Dioxygen in Various Media , 1994 .

[6]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[7]  Hao Yan,et al.  DNA-templated self-assembly of protein and nanoparticle linear arrays. , 2004, Journal of the American Chemical Society.

[8]  K. Gothelf,et al.  A nucleic acid dependent chemical photocatalysis in live human cells. , 2010, Chemistry.

[9]  Päivi Törmä,et al.  DNA origami as a nanoscale template for protein assembly , 2009, Nanotechnology.

[10]  P. Ogilby,et al.  Singlet Oxygen: There Is Indeed Something New under the Sun , 2010 .

[11]  P. Ogilby,et al.  Time‐resolved Singlet Oxygen Phosphorescence Measurements from Photosensitized Experiments in Single Cells: Effects of Oxygen Diffusion and Oxygen Concentration , 2008, Photochemistry and photobiology.

[12]  Shawn M. Douglas,et al.  Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.

[13]  Ralf Jungmann,et al.  DNA origami as a nanoscopic ruler for super-resolution microscopy. , 2009, Angewandte Chemie.

[14]  Hao Yan,et al.  Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. , 2008, Nature nanotechnology.

[15]  Masayuki Endo,et al.  Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. , 2010, Journal of the American Chemical Society.

[16]  H. Kautsky,et al.  Die Aufklärung der Photoluminescenztilgung fluorescierender Systeme durch Sauerstoff: Die Bildung aktiver, diffusionsfähiger Sauerstoffmoleküle durch Sensibilisierung , 1931, Naturwissenschaften.

[17]  Hao Yan,et al.  DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. , 2010, Angewandte Chemie.

[18]  Erik Winfree,et al.  Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. , 2010, Nature nanotechnology.

[19]  Hao Yan,et al.  Gold nanoparticle self-similar chain structure organized by DNA origami. , 2010, Journal of the American Chemical Society.

[20]  Akinori Kuzuya,et al.  Precisely Programmed and Robust 2D Streptavidin Nanoarrays by Using Periodical Nanometer‐Scale Wells Embedded in DNA Origami Assembly , 2009, Chembiochem : a European journal of chemical biology.

[21]  Mingdong Dong,et al.  DNA origami design of dolphin-shaped structures with flexible tails. , 2008, ACS nano.

[22]  Hao Yan,et al.  Scaffolded DNA origami of a DNA tetrahedron molecular container. , 2009, Nano letters.

[23]  Wael Mamdouh,et al.  Single-molecule chemical reactions on DNA origami. , 2010, Nature nanotechnology.

[24]  M. Davies.  Singlet oxygen-mediated damage to proteins and its consequences. , 2003, Biochemical and biophysical research communications.

[25]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[26]  T. Tachikawa,et al.  Real-Time Single-Molecule Imaging of the Spatial and Temporal Distribution of Reactive Oxygen Species with Fluorescent Probes: Applications to TiO2 Photocatalysts , 2008 .

[27]  J. Lambert,et al.  Lifetime and diffusion of singlet oxygen in a cell. , 2005, The journal of physical chemistry. B.

[28]  A. Rotaru,et al.  Nucleic acid binders activated by light of selectable wavelength. , 2007, Angewandte Chemie.