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- Banchelli, M., et al.
(author)
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Phospholipid membranes decorated by cholesterol-based oligonucleotides as soft hybrid nanostructures
- 2008
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:35, s. 10942-10952
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Journal article (peer-reviewed)abstract
- DNA monomers and oligomers are currently showing great promise as building blocks for supramolecular arrays that can self-assemble in a fashion preprogrammed by the base pairing code. The design and build-up of hybrid DNA/amphiphilic self-assemblies can expand the range of possible architectures and enhance the selectivity toward a well-specified geometry. We report on the self-assembly properties in aqueous solution of a cholesteryl-tetraethylenglycol single stranded 18-mer oligonucleotide (ON(1)TEG-Chol) and on its spontaneous insertion in fluid phospholipid membranes. Up to 500 units of these lipophilic ss-oligonucleotides can be incorporated in the outer leaflet of 350 A radius POPC vesicle. The insertion and hybridization with the complementary oligonucleotide are monitored through light scattering as an increase of hydrodynamic thickness, which is interpreted in terms of average distance between anchoring sites. The conformation of the ss-oligonucleotidic portion is strongly dependent on surface coverage, passing from a quasi-random coil to a more rigid configuration, as concentration increases. Interestingly, conformational details affect in a straightforward fashion the hybridization kinetics. Liposomes with single- and double-strand decorations remain stable within the experimental time window (about one week). The structure represents an example of successful and stable amphiphile/DNA supramolecular hybrid, where a DNA guest is held in a membrane by hydrophobic interactions. The lipophilic oligonucleotide under investigation is therefore a suitable building block that can effectively serve as a hydrophobic anchor in the fluid bilayer to assemble supramolecular constructs based on the DNA digital code.
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- Bombelli, F. B., et al.
(author)
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DNA Closed Nanostructures: A Structural and Monte Carlo Simulation Study
- 2008
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:48, s. 15283-15294
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Journal article (peer-reviewed)abstract
- DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution. © 2008 American Chemical Society.
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- Breimer, Michael, 1951, et al.
(author)
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Blood group A and B antigen expression in human kidneys correlated to A1/A2/B, Lewis, and secretor status.
- 2006
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In: Transplantation. - : Ovid Technologies (Wolters Kluwer Health). - 0041-1337. ; 82:4, s. 479-85
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Journal article (peer-reviewed)abstract
- BACKGROUND: In the revived interest in crossing ABO barriers in organ transplantation renal A/B antigen expression has been correlated with donor ABO, Lewis, and secretor subtype to predict antigen expression. METHODS: A/B antigen expression was explored by immunohistochemistry in LD renal biopsies. Donor A1/A2/B, Lewis, and secretor status were determined by serology and polymerase chain reaction. RESULTS: In the renal vascular bed, three distinct A antigen expression patterns with a major, minor, and minimal staining distribution, and intensity (designated as types 3+, 1+ and (+) respectively) were identified. Type 3+ had a strong A antigen expression in the endothelium of arteries, glomerular/peritubular capillaries and veins. The type 1+ showed an overall weaker antigen expression, whereas type (+) had faint staining of peritubular capillaries only. In all cases, distal tubular epithelium was focally stained, whereas proximal tubules were negative. Type 3+ were all from blood group A1 subtype individuals while A2 cases expressed either a 1+ or (+) pattern. The secretor gene did not appear to influence renal A antigen expression. All B kidneys examined showed a B antigen pattern slightly weaker but otherwise similar to A type 3+. CONCLUSION: Renal vascular A antigen expression correlates to donor A1/A2 subtypes, whereas B individuals show one singular antigen pattern. From antigen perspective, A1 and B donors are a "major" and A2 individuals a "minor" antigen challenge in ABO-incompatible renal transplantation.
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- Förster, A, et al.
(author)
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Baseline characterization of the CO2SINK geological storage site at Ketzin, Germany
- 2006
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In: Environmental Geosciences. - : American Association of Petroleum Geologists AAPG/Datapages. - 1075-9565 .- 1526-0984. ; 13:3, s. 145-161
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Journal article (peer-reviewed)abstract
- Since April 2004, preparatory work prior to CO2injection hasbeen conducted in the CO2SINK Project, the European Union’sfirst research and development activity on the in-situ testing ofgeological storage of CO2near the town of Ketzin, Germany.Carbon dioxide will be injected into a saline aquifer of the TriassicStuttgart Formation in an anticlinal structure of the northeastGerman Basin. The drilling of one injection and two observationwells will commence at the end of 2006. The predrilling phasefocuses on the baseline geological parameters of the anticline. TheStuttgart Formation is lithologically heterogeneous; it consists ofsandy channel-(string)-facies rocks, with good reservoir propertiesalternating with muddy flood-plain-facies rocks of poor reservoirquality. Playa-type rocks form the immediate cap rock above theCO2SINK reservoir. A geostatistical approach has been applied todescribe the reservoir architecture between and beyond well con-trol. This model forms the basis for the generation of reservoir-dynamic models of CO2injection that assist in the planning ofinjection operations and in the understanding of CO2plume evo-lution. A verification of the geometry of the reservoir and thestructural situation of its overburden is expected from a three-dimensional baseline seismic survey that was conducted in theautumn of 2005. Laboratory experiments under simulated in-situconditions were performed to evaluate the geophysical signatureof rocks saturated with CO2. The chemical composition of thegroundwater and the CO2flux in the soil were analyzed across theKetzin anticline, providing the baseline for a monitoring programduring and after injection of CO2, targeted at the detection ofpotential CO2leakage from the storage reservoir.
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- Starikov, Evgeni B., et al.
(author)
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Screw motion of DNA duplex during translocation through pore. I. Introduction of the coarse-grained model
- 2009
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In: Biophysical Reviews and Letters. - 1793-0480. ; 4:3, s. 209-230
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Journal article (peer-reviewed)abstract
- Based upon the structural properties of DNA duplexes and their counterion-water surrounding in solution, we have introduced here a screw model which may describe translocation of DNA duplexes through artificial nanopores of the proper diameter (where the DNA counterion-hydration shell can be intact) in a qualitatively correct way. This model represents DNA as a kind of "screw," whereas the counterion-hydration shell is a kind of "nut." Mathematical conditions for stable dynamics of the DNA screw model are investigated in detail. When an electrical potential is applied across an artificial membrane with a nanopore, the "screw" and "nut" begin to move with respect to each other, so that their mutual rotation is coupled with their mutual translation. As a result, there are peaks of electrical current connected with the mutual translocation of DNA and its counterion-hydration shell, if DNA is possessed of some non-regular base-pair sequence. The calculated peaks of current strongly resemble those observed in the pertinent experiments. An analogous model could in principle be applied to DNA translocation in natural DNA-protein complexes of biological interest, where the role of "nut" would be played by protein-tailored "channels." In such cases, the DNA screw model is capable of qualitatively explaining chemical-to-mechanical energy conversion in DNA-protein molecular machines via symmetry breaking in DNA-protein friction.
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