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11.
  • Ardhammar, Malin, 1970, et al. (författare)
  • In vitro membrane penetration of modified peptide nucleic acid (PNA)
  • 1999
  • Ingår i: Journal of Biomolecular Structure and Dynamics. - : Informa UK Limited. - 0739-1102 .- 1538-0254. ; 17:1, s. 33-40
  • Tidskriftsartikel (refereegranskat)abstract
    • Efficient cellular uptake is crucial for the success of any drug directed towards targets inside cells. Peptide nucleic acid (PNA), a DNA analog with a promising potential as a gene-directed drug, has been shown to display slow membrane penetration in cell cultures. We here used liposomes as an in vitro model of cell membranes to investigate the effect on penetration of a PNA molecule colvalently modified with a lipophilic group, an adamantyl moiety. The adamantyl attachment was found to increase the membrane-penetration rate of PNA three-fold, as compared to corresponding unmodified PNA. From the penetration behaviour of a number of small and large molecules we could conclude that passive diffusion is the mechanism for liposome-membrane passage. Flow linear dichroism (LD) of the modified PNA in presence of rod-shaped micelles, together with octanol-water distribution experiments. showed that the adamantyl-modified PNA is amphiphilic; the driving force behind the observed increased membrane-penetration rate appears to be an accumulation of the PNA in the lipid double layer.
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12.
  • Banchelli, M., et al. (författare)
  • Phospholipid membranes decorated by cholesterol-based oligonucleotides as soft hybrid nanostructures
  • 2008
  • Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:35, s. 10942-10952
  • Tidskriftsartikel (refereegranskat)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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13.
  • Becker, Hans-Christian, 1971, et al. (författare)
  • DNA Binding mode and sequence specificity of piperazinylcarbonyloxyethyl derivatives of anthracene and pyrene
  • 1999
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 121:51, s. 11947-11952
  • Tidskriftsartikel (refereegranskat)abstract
    • Four novel piperazinylcarbonyloxyethyl derivatives of anthracene and pyrene have been prepared and investigated with respect to sequence specificity and synergism between hydrophobic and electrostatic effects upon binding to DNA. Linear and circular dichroism spectroscopy was used to assess the orientation of the aromatic chromophores relative to the nucleobases. Anthracene and pyrene derivatives 2a and 3 are both concluded to bind to homo-polynucleotide poly(dA-dT)(2) by intercalation of their aromatic moieties between base pairs, with a binding constant K-AT of 4 x 10(5) M-1 and 2 x 10(6) M-1, respectively. Significantly reduced affinities (K-GC = 3 x 10(4) M-1 and 10(5) M-1, respectively) are observed with poly(dG-dC)(2), due to less favorable interactions of the piperazinium tail in the minor groove. Base pair specificity is reflected in the binding thermodynamics, with the binding to AT being more enthalpically driven than the binding to GC. Phenyl substitution at the quaternary piperazinium site of the anthracene derivative 2b, does not affect the ratio K-AT/K-GC, but reduces the affinity for both AT End GC slightly. Moreover, the phenyl group in the 10-position of 4 prevents intercalation, and apparently, this compound binds externally to both AT and GC duplex polynucleotides. The results are discussed in terms of general features of the interactions of the intercalating and minor-groove binding molecular moieties, and their interplay with each other, with potentials for tuning specificity.
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14.
  • Becker, Hans-Christian, 1971, et al. (författare)
  • DNA Binding Properties of 2,7-Diazapyrene and its N-methylated Cations Studied by Linear and Circular Dichroism Spectroscopy and Calorimetry
  • 1997
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 119:25, s. 5798-5803
  • Tidskriftsartikel (refereegranskat)abstract
    • The binding of 2,7-diazapyrene (DAP), N-methyl-2,7-diazapyrenium monocation (MDAP), and N,N'-dimethyl-2,7-diazapyrenium dication (DMDAP) to calf thymus DNA has been studied with respect to molecular geometry and thermodynamics. It is concluded from flow linear dichroism (LD) and induced circular dichroism (CD) spectra that the three diazapyrenes bind by intercalation to alternating AT as well as GC polynucleotide duplexes, as indicated by strong interactions with the transitions of the nucleobases in conjunction with approximately perpendicular orientations of the in-plane symmetry axes relative to the DNA helix axis. The reduced LD (LDt = LD/A(iso)) of the DNA complexes is characterized by marked fine structure, decreasing in the order DAP > MDAP > DMDAP. This finding is interpreted in terms of a microscopic heterogeneity associated with rotational mobility of the ligand in a tilted intercalation pocket, with the dication DMDAP having less rotational freedom than the neutral DAP has. Other distinct differences between the three diazapyrenes are revealed in their thermodynamic parameters of binding. DAP binds with a negative Delta H degrees (-9 kcal/mol) and a negative Delta S degrees (-7 cal/(mol K)), whereas the binding of the dication DMDAP is entropically driven (+43 cay(mol K)) but enthalpically disfavored (+5.2 kcal/mol), the monocation MDAP having an intermediate position (Delta H degrees = -3 kcal/mol, Delta S degrees = +12 cal/(mol K)).
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15.
  • Becker, Hans-Christian, 1971, et al. (författare)
  • DNA binding thermodynamics and sequence specificity of chiral piperazinecarbonyloxyalkyl derivatives of anthracene and pyrene
  • 2000
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 122:35, s. 8344-8349
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper we report the DNA binding proper ties of piperazinecarbonyloxy-2-propyl derivatives of anthracene (2), pyrene (3), and phenylanthracene (4). An intercalative binding mode is found for 2 and 3, while the phenyl group of 4 prevents intercalation and leads to external binding. Preferential binding of the (S)-enantiomers is found for both anthracene 2 and pyrene 3. However, the enantiomeric preference is small, with K-(R)/K-(S) being around 0.5 for both the anthracene and the pyrene compounds. This is interpreted in terms of orientation polarity in the binding, by which any intrinsic enantioselectivity is canceled by averaging of opposite binding orientations. The affinities for poly(dA-dT)(2) (AT) are 10(4) M-1 for anthracene derivative 2, and 5 x 10(5) M-1 for pyrene derivative 2. The affinities for poly(dG-dC)(2) (GC) are I order of magnitude lower than those for AT. This is explained by steric interference of the piperazinium tail with the exocyclic amino groups of guanine in the minor groove of GC, leading to a more shallow intercalation in GC than in AT, as also indicated by significantly less negative reduced linear dichroism of the intercalator absorption bands in the GC complexes. This behavior is consistent with that observed for the previously studied achiral analogues.(1) Binding thermodynamics support the difference in binding mode between AT and GC. The binding enthalpy of the AT complexes is significantly more negative than that of the corresponding GC complexes. This indicates a larger overlap of intercalating moiety and nucleobases in the AT complexes, consistent with the linear dichroism results.
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16.
  • Becker, Hans-Christian, 1971, et al. (författare)
  • Ground- and excited-state properties of molecular complexes between adenine and 2,7-diazapyrene and its N-methylated cations
  • 1997
  • Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 101:47, s. 8853-8860
  • Tidskriftsartikel (refereegranskat)abstract
    • It has recently been found that 2,7-diazapyrenes upon interaction with nucleic acids form stacked (''intercalation'') complexes, which for the methylated derivatives exhibit new absorption features assigned as charge-transfer (CT) transitions.' To better understand the basis of these interactions and associated optical properties, the geometries and electronic spectra of complexes of adenine (A) with 2,7-diazapyrene (DAP), N-methyl-2,7-diazapyrenium (MDAP(+)), and N,N-dimethyl-2,7-diazapyrenium (DMDAP(2+)) have been modeled using semiempirical AM1 and PM3 geometry optimizations, ab initio (vacuum and Onsager model) energy calculations, and ZINDO/S calculations. In addition, absorption spectra, fluorescence quenching, and H-1 NMR spectra for the complexes in aqueous solution have been measured. For the A-DAP complex, a coplanar, hydrogen-bonded complex is predicted by the calculations, while A-MDAP(+) and A-DMDAP(2+) complexes should have edge-to-face geometry. The association is predicted to be of electrostatic nature, mainly between the pyridinium nitrogen (MDAP(+), DMDAP(2+)) and N-1/NH2 of adenine. There seems to be a preference (6 kcal/mol) for the hydrogen-bonded A-DAP complex, and the energetic difference between face-to-face and edge-to-face A-MDAP(+) and A-DMDAP(2+) complexes is 3 and 8 kcal/mol, respectively (Onsager ab initio, epsilon = 79.5). By contrast, the H-1 NMR data and experimental absorption spectra in conjunction with calculated spectra instead indicate that all three adenine-diazapyrene complexes assume face-to-face arrangement in water because of hydrophobic effects. In agreement with the putative CT absorption of diazapyrenium-DNA complexes, absorption tails are also observed for A-DMDAP(2+) and A-MDAP(+), however not for the A-DAP complex. Most satisfactorily, charge-transfer transitions are predicted by the calculations to occur in the correct wavelength region for A-DMDAP(2+) (strongest) and A-MDAP(+), while A-DAP is predicted not to have any CT transitions. Correspondingly, the observation of quenching of fluorescence of MDAP(+) and DMDAP(2+) (but not DAP) by adenine can explained by charge transfer from adenine to the diazapyrenium.
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17.
  • Behravan, G., et al. (författare)
  • THE INTERACTION OF ELLIPTICINE DERIVATIVES WITH NUCLEIC-ACIDS STUDIED BY OPTICAL AND H-1-NMR SPECTROSCOPY - EFFECT OF SIZE OF THE HETEROCYCLIC RING
  • 1994
  • Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 34:5, s. 599-609
  • Tidskriftsartikel (refereegranskat)abstract
    • The DNA interaction of derivatives of ellipticine with heterocyclic ring systems with three, four, or five rings and a dimethylaminoethyl side chain was studied. Optical spectroscopy of drug complexes with calf thymus DNA, poly [(dA-dT).(dA-dT)], or poly [(dG-dC).(dG-dC)] showed a 10 nm bathochromic shift of the light absorption bands of the pentacyclic and tetracyclic compounds upon binding to the nucleic acids, which indicates binding by intercalation. For the tricyclic compound a smaller shift of 1-3 nm was observed upon binding to the nucleic acids. Flow linear dichroism studies show that the geometry of all complexes is consistent with intercalation of the ring system, except for the DNA and poly [(dG-dC).(dG-dC)] complexes of the tricyclic compound, where the average angle between the drug molecular plane and the DNA helix axis was found to be 65 degrees. One-dimensional H-1-nmr spectroscopy was used to study complexes between d(CGCGATCGCG)(2) and the tricyclic and pentacyclic compounds. The results on the pentacyclic compound show nonselective broadening due to intermediate chemical exchange of most oligonucleotide resonances upon drug binding. The imino proton resonances are in slow chemical exchange, and new resonances with upheld shifts approaching 1 ppm appear upon drug binding, which supports intercalative binding of the pentacyclic compound. The results on the tricyclic compound show more rapid binding kinetics and very selective broadening of resonances. The data suggest that the tricyclic compound is in an equilibrium between intercalation and minor groove binding, with a preference to bind close to the AT base pairs with the side chain residing in the minor groove. (C) 1994 John Wiley and Sons, Inc.
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18.
  • Beke-Somfai, Tamas, 1977, et al. (författare)
  • Double-lock ratchet mechanism revealing the role of alpha SER-344 in FoF1 ATP synthase
  • 2011
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:12, s. 4828-4833
  • Tidskriftsartikel (refereegranskat)abstract
    • In a majority of living organisms, FoF1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP + Pi. ATP + H2O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing to the complexity of this multisubunit enzyme. Based on quantum mechanical computations using recent high resolution X-ray structures, we propose that during ATP synthesis the enzyme first prepares the inorganic phosphate for the gamma P-O-ADP bond-forming step via a double-proton transfer. At this step, the highly conserved alpha S344 side chain plays a catalytic role. The reaction thereafter progresses through another transition state (TS) having a planar PO3- ion configuration to finally form ATP. These two TSs are concluded crucial for ATP synthesis. Using stepwise scans and several models of the nucleotide-bound active site, some of the most important conformational changes were traced toward direction of synthesis. Interestingly, as the active site geometry progresses toward the ATP-favoring tight binding site, at both of these TSs, a dramatic increase in barrier heights is observed for the reverse direction, i.e., hydrolysis of ATP. This change could indicate a "ratchet" mechanism for the enzyme to ensure efficacy of ATP synthesis by shifting residue conformation and thus locking access to the crucial TSs.
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19.
  • Beke-Somfai, Tamas, 1977, et al. (författare)
  • Energy phase shift as mechanism for catalysis
  • 2012
  • Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 535, s. 169-172
  • Tidskriftsartikel (refereegranskat)abstract
    • Catalysts are agents that by binding reactant molecules lower the energy barriers to chemical reaction. After reaction the catalyst is regenerated, its unbinding energy recruited from the environment, which is associated with an inevitable loss of energy. We show that combining several catalytic sites to become energetically and temporally phase-shifted relative to each other provides a possibility to sustain the overall reaction by internal 'energy recycling', bypassing the need for thermal activation, and in principle allowing the system to work adiabatically. Using an analytical model for superimposed, phase-shifted potentials of F-1-ATP synthase provides a description integrating main characteristics of this rotary enzyme complex.
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20.
  • Beke-Somfai, Tamas, 1977, et al. (författare)
  • Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites
  • 2010
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 49:3, s. 401-403
  • Tidskriftsartikel (refereegranskat)abstract
    • Despite exhaustive chemical and crystal structure studies, the mechanistic details of how F o F 1 -ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO 3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in β TP and, thus, promote ATP. © 2009 American Chemical Society.
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