Department of Food Processing Technology and Management

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Author: search.filters.author.Flemming, Besenbacher

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    TWO-DIMENSIONAL NETWORK STABILITY OF NUCLEOBASES AND AMINO ACIDS ON GRAPHITE UNDER AMBIENT CONDITIONS: ADENINE, L-SERINE AND L-TYROSINE
    (Royal Society of Chemistry, 2010-03-09) Ilko, Bald; Sigrid, Weigelt; Xiaojing, Ma; Pengyang, Xie; Ramesh, Subramani; Mingdong, Dong; Chen, Wang; Wael, Mamdouh; Jianguo, Wang; Flemming, Besenbacher
    We have investigated the stability of two-dimensional self-assembled molecular networks formed upon co-adsorption of the DNA base, adenine, with each of the amino acids, L-serine and L-tyrosine, on a highly oriented pyrolytic graphite (HOPG) surface by drop-casting from a water solution. L-serine and L-tyrosine were chosen as model systems due to their different interaction with the solvent molecules and the graphite substrate, which is reflected in a high and low solubility in water, respectively, compared with adenine. Combined scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations show that the self-assembly process is mainly driven by the formation of strong adenine–adenine hydrogen bonds. We find that pure adenine networks are energetically more stable than networks built up of either pure L-serine, pure L-tyrosine or combinations of adenine with L-serine or L-tyrosine, and that only pure adenine networks are stable enough to be observable by STM under ambient conditions.
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    BUILDING LAYER-BY-LAYER 3D SUPRAMOLECULAR NANOSTRUCTURES AT THE TEREPHTHALIC ACID/STEARIC ACID INTERFACE
    (Royal Society of Chemistry, 2011-07-14) Yinli, Li; Lei, Liu; Ramesh, Subramani; Yunxiang, Pan; Bo, Liu; Yanlian, Yang; Chen, Wang; Wael, Mamdouh; Flemming, Besenbacher; Mingdong, Dong
    By using the layer-by-layer deposition method, we build three dimensional (3D) supramolecular nanostructures by stacking small molecular species on top of the first buffer layer, which can be utilized to fabricate novel 3D supramolecular functional nanostructures.
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    A NOVEL SECONDARY DNA BINDING SITE IN HUMAN TOPOISOMERASE I UNRAVELLED BY USING A 2D DNA ORIGAMI PLATFORM
    (ACS Publications, 2010-09-09) Ramesh, Subramani; Sissel, Juul; Alexandru, Rotaru; Felicie F, Andersen; Kurt V., Gothelf; Wael, Mamdouh; Flemming, Besenbacher; Mingdong, Dong; Birgitta R, Knudsen
    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.
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    SINGLE-MOLECULE CHEMICAL REACTIONS ON DNA ORIGAMI
    (Nature Nanotechnology, 2010-02-28) Niels V, Voigt; Thomas, Tørring; Alexandru, Rotaru; Mikkel F, Jacobsen; Jens B, Ravnsbæk; Ramesh, Subramani; Wael, Mamdouh; Jørgen, Kjems; Andriy, Mokhir; Flemming, Besenbacher; Kurt, Vesterager Gothelf
    DNA nanotechnology1,2 and particularly DNA origami3, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures4,5,6,7,8,9,10. 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 imaged11,12,13. 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.
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    SELF-ASSEMBLY OF A NANOSCALE DNA BOX WITH A CONTROLLABLE LID
    (Nature Publishing Group UK, 2009-05-07) Ebbe S, Andersen; Mingdong, Dong; Morten M, Nielsen; Kasper, Jahn; Ramesh, Subramani; Wael, Mamdouh; Monika M, Golas; Bjoern, Sander; Holger, Stark; Cristiano L. P, Oliveira; Jan, Skov Pedersen; Victoria, Birkedal; Flemming, Besenbacher; Kurt V, Gothelf; Jørgen, Kjems
    The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a ‘bottom-up’ approach1. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures2,3,4,5,6,7,8. Recently, the DNA ‘origami’ method was used to build two-dimensional addressable DNA structures of arbitrary shape9 that can be used as platforms to arrange nanomaterials with high precision and specificity9,10,11,12,13. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures14,15. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 × 36 × 36 nm3 in size that can be opened in the presence of externally supplied DNA ‘keys’. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos