| 1. |
- Höök, Fredrik, 1966, et al.
(författare)
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Characterization of PNA and DNA Immobilization and Subsequent Hybridization with DNA Using Acoustic-Shear-Wave Attenuation Measurements
- 2001
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 1520-5827 .- 0743-7463. ; 17:26, s. 8305-8312
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Tidskriftsartikel (refereegranskat)abstract
- We report here how the quartz crystal microbalance with dissipation monitoring (QCM-D) technique, simultaneously measuring changes in the induced energy dissipation, D (cf. viscoelastic properties), and the frequency, f (cf. coupled mass), can be used to characterize the bound state of single-stranded peptide nucleic acid (PNA) and deoxyribose nucleic acid (DNA) in relation to their ability to function as selective probe(s) for fully complementary and single-mismatch DNA. The possibility to use the QCM-D technique for detection of binding kinetics and structural differences in the formed duplexes is also presented. We found that thiol-PNA and thiol-DNA attached via a sulfur group directly on a bare-gold surface are less efficient as probes for DNA than are biotin-PNA and biotin-DNA, coupled on top of a two-dimensional (2-D) arrangement of streptavidin, formed on a biotinylated phospholipid bilayer on a SiO2 surface. The fully complementary and singly mismatched DNA oligomers hybridize with the immobilized PNA and DNA. A single mismatch is discriminated via a significant difference in the binding and dissociation kinetics, demonstrating a high selectivity and thus successful immobilization of functional single strands. The observed ratios between hybridization-induced energy dissipation (DeltaD) and the frequency shift (Deltaf) made it possible to discriminate thiol-PNA directly attached to a gold surface from biotin-PNA coupled to the streptavidin 2-D arrangement, where the former were shown to be inefficient for detecting subsequent hybridization. Structural differences of the immobilized layers composed of biotin-PNA-DNA and biotin-DNA-DNA were clearly reflected by the DeltaD and Deltaf response.
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| 2. |
- Wittung Stafshede, Pernilla, 1968, et al.
(författare)
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Detection of point mutations in DNA by PNA-based quartz-crystal biosensor
- 2000
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Ingår i: Colloids and Surfaces A: Physicochemical and Engineering Aspects. - 1873-4359 .- 0927-7757. ; 174:1-2, s. 269-273
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Tidskriftsartikel (refereegranskat)abstract
- Currently there is an extensive search for biosensors for detecting genetic defects by hybridisation to immobilised oligonucleotides. A concept able to detect a single mismatch in a 15mer single-strand target of the p53 tumor suppresser gene is presented (a mutation found in many types of cancer cells). In this method, the unique hybridisation properties of the DNA mimic peptide nucleic acid (PNA) are combined with electronically detected mass and shear dissipation at the surface of a quartz crystal. Cysteine-labeled PNA efficiently immobilises on crystal-gold surface at 20 degrees C. At 60 degrees C, addition of complementary DNA results in a signal response corresponding to hybridisation between DNA and the PNA-covered surface, whereas addition of DNA differing in only one of the 15 bases gives no response at all.
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| 3. |
- Ardhammar, Malin, 1970, et al.
(författare)
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Absolute configuration and electronic state properties of light-switch complex [Ru(phen)2dppz]2+ deduced from oriented circular dichroism in a lamellar liquid crystal host
- 2002
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Ingår i: Chemical Physics Letters. - 0009-2614. ; 354:1-2, s. 44-50
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Tidskriftsartikel (refereegranskat)abstract
- Circular dichroism (CD) of enantiomers of [Ru(phen)(2)dppz](2+) oriented in a octanoate-decanol-water lamellar liquid crystal has been measured parallel to the orientation axis. where the sample does not exhibit linear dichroism (LD). At an inclined incidence, the emerging LD shows that the chromophores have an along-chain orientation in the liquid crystal. The changes in the CD spectrum compared to an isotropic sample, in conjunction with CD calculations, allow us to assess the absolute configuration of the enantiomers and assign the CD bands to specific electronic transitions.
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| 4. |
- Ardhammar, Malin, 1970, et al.
(författare)
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DNA-Drug Interactions
- 2000
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Ingår i: Circular dichroism: principles and applications (Eds. Berova, N., Nakanishi, K. and Woody, R.W.). - 0471330035 ; , s. 741-768 (Chapter 26)
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Banchelli, M., et al.
(författare)
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Phospholipid membranes decorated by cholesterol-based oligonucleotides as soft hybrid nanostructures
- 2008
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:35, s. 10942-10952
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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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| 6. |
- Becker, Hans-Christian, 1971, et al.
(författare)
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DNA binding thermodynamics and sequence specificity of chiral piperazinecarbonyloxyalkyl derivatives of anthracene and pyrene
- 2000
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 122:35, s. 8344-8349
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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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| 7. |
- Bombelli, F. B., et al.
(författare)
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DNA Closed Nanostructures: A Structural and Monte Carlo Simulation Study
- 2008
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:48, s. 15283-15294
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Börjesson, Karl, 1982, et al.
(författare)
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A membrane anchored DNA-based energy/electron transfer assembly
- 2008
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Ingår i: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 691-691
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Tidskriftsartikel (refereegranskat)abstract
- In this work the trapping and conversion of visible light energy into chemical energy is examined using a supramolecular assembly. This consists of a light absorbing antenna and a porphyrin redox centre both covalently attached to a DNA strand, which in turn is bound to a lipid membrane. The excitation energy is finally trapped as a benzoquinone radical anion that could potentially be used in subsequent chemical reactions.
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| 9. |
- Börjesson, Karl, 1982, et al.
(författare)
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Membrane-Anchored DNA Assembly for Energy and Electron Transfer
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:8, s. 2831-2839
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Tidskriftsartikel (refereegranskat)abstract
- In this work we examine the trapping and conversion of visible light energy into chemical energy using a supramolecular assembly. The assembly consists of a light-absorbing antenna and a porphyrin redox center, which are covalently attached to two complementary 14-mer DNA strands, hybridized to form a double helix and anchored to a lipid membrane. The excitation energy Is finally trapped In the lipid phase of the membrane as a benzoquinone radical anion that could potentially be used In subsequent chemical reactions. In addition, In this model complex, the hydrophobic porphyrin moiety acts as an anchor into the liposome positioning the DNA construct on the lipid membrane surface. The results show the suitability of our system as a prototype for DNA-based light-harvesting devices, In which energy transfer from the aqueous phase to the interior of the lipid membrane Is followed by charge separation. © 2009 American Chemical Society.
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| 10. |
- Chiragwandi, Zackary, 1968, et al.
(författare)
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Properties of a bio-photovoltaic nano-device
- 2008
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 112:48, s. 18717-18721
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Tidskriftsartikel (refereegranskat)abstract
- Properties of an on-chip photovoltaic nanodevice are demonstrated. The dyes comprise green florescent proteins(GFP). Dependence of recently reported zero external potential bias (ZEPB) photocurrent (I) on temperature,power, and wavelength (λ) is shown. Correlation between UV-vis spectrum of the GFP and the ZEPB I(λ)of the device is reported. The temperature dependence suggests the ZEPB photocurrent to reflect a liquidcrystal type ordering where the current declines monotonically with increasing temperature. The influence ofan external bias on the photocurrent is demonstrated. The resulting light-induced current is analyzed in termsof resistive and quantum mechanical contributions.
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