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ABSTRACT: Patterns of the protein streptavidin on DNA origami are printed onto a functionalized surface. The streptavidins are linked to DNA via a disulfide spacer and these conjugates self-organise into a predetermined pattern on DNA origami. The structure immobilises on a biotin-SAM-functionalized Au surface. By disulfide cleavage the origami is separated from the streptavidins, leaving the protein pattern at the surface.
Chemical Communications 01/2013; · 6.17 Impact Factor
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ABSTRACT: Low-energy electrons (LEEs) play an important role in nanolithography, atmospheric chemistry, and DNA radiation damage. Previously, the cleavage of specific chemical bonds triggered by LEEs has been demonstrated in a variety of small organic molecules such as halogenated benzenes and DNA nucleobases. Here we present a strategy that allows for the first time to visualize the electron-induced dissociation of single chemical bonds within complex, but well-defined self-assembled DNA nanostructures. We employ atomic force microscopy to image and quantify LEE-induced bond dissociations within specifically designed oligonucleotide targets that are attached to DNA origami templates. In this way, we use a highly selective approach to compare the efficiency of the electron-induced dissociation of a single disulfide bond with the more complex cleavage of the DNA backbone within a TT dinucleotide sequence. This novel technique enables the fast and parallel determination of DNA strand break yields with unprecedented control over the DNA's primary and secondary structure. Thus the detailed investigation of DNA radiation damage in its most natural environment, e.g., DNA nucleosomes constituting the chromatin, now becomes feasible.
ACS Nano 04/2012; 6(5):4392-9. · 10.77 Impact Factor
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ABSTRACT: 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.
ACS Nano 12/2010; 4(12):7475-80. · 10.77 Impact Factor
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ABSTRACT: The biologically and clinically important nuclear enzyme human topoisomerase I relaxes both positively and negatively supercoiled DNA and binds consequently DNA with supercoils of positive or negative sign with a strong preference over relaxed DNA. One scheme to explain this preference relies on the existence of a secondary DNA binding site in the enzyme facilitating binding to DNA nodes characteristic for plectonemic DNA. Here we demonstrate the ability of human topoisomerase I to induce formation of DNA synapses at protein containing nodes or filaments using atomic force microscopy imaging. By means of a two-dimensional (2D) DNA origami platform, we monitor the interactions between a single human topoisomerase I covalently bound to one DNA fragment and a second DNA fragment protruding from the DNA origami. This novel single molecule origami-based detection scheme provides direct evidence for the existence of a secondary DNA interaction site in human topoisomerase I and lends further credence to the theory of two distinct DNA interaction sites in human topoisomerase I, possibly facilitating binding to DNA nodes characteristic for plectonemic supercoils.
ACS Nano 10/2010; 4(10):5969-77. · 10.77 Impact Factor
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Nature Nanotechnology 10/2010; 5(11):760-1. · 27.27 Impact Factor
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Angewandte Chemie International Edition 08/2010; 49(33):5665-7. · 13.45 Impact Factor
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Niels V Voigt,
Thomas Tørring, Alexandru Rotaru,
Mikkel F Jacobsen,
Jens B Ravnsbaek,
Ramesh Subramani,
Wael Mamdouh,
Jørgen Kjems,
Andriy Mokhir,
Flemming Besenbacher,
Kurt Vesterager Gothelf
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ABSTRACT: DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally addressable solid supports.
Nature Nanotechnology 02/2010; 5(3):200-3. · 27.27 Impact Factor
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ABSTRACT: Hairpin-structured phosphorothioate oligodeoxyribonucleotides containing a singlet oxygen-sensitive linker in the loop were prepared. These compounds do not bind complementary nucleic acids in the dark. Upon irradiation with red light in the presence of chlorine e6 the linker within these compounds is cleaved and a single-stranded oligodeoxyribonucleotide is produced. The latter compound is an efficient binder of complementary nucleic acids. This is the first example of 'caged' phosphorothioate oligodeoxyribonucleotides, whose nucleic acid binding ability is triggered by red light.
Bioorganic & medicinal chemistry letters 07/2008; 18(15):4336-8. · 2.65 Impact Factor
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Angewandte Chemie International Edition 02/2007; 46(32):6180-3. · 13.45 Impact Factor
