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| 2. |
- 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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| 3. |
- 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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| 4. |
- Sandin, Peter, 1977, et al.
(författare)
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Highly efficient incorporation of the fluorescent nucleotide analogs tC and tC(O) by Klenow fragment
- 2009
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 37:12, s. 3924-3933
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Tidskriftsartikel (refereegranskat)abstract
- Studies of the mechanisms by which DNA polymerases select the correct nucleotide frequently employ fluorescently labeled DNA to monitor conformational rearrangements of the polymerase-DNA complex in response to incoming nucleotides. For this purpose, fluorescent base analogs play an increasingly important role because they interfere less with the DNA-protein interaction than do tethered fluorophores. Here we report the incorporation of the 5'-triphosphates of two exceptionally bright cytosine analogs, 1,3-diaza-2-oxo-phenothiazine (tC) and its oxo-homolog, 1,3-diaza-2-oxo-phenoxazine (tC(O)), into DNA by the Klenow fragment. Both nucleotide analogs are polymerized with slightly higher efficiency opposite guanine than cytosine triphosphate and are shown to bind with nanomolar affinity to the DNA polymerase active site, according to fluorescence anisotropy measurements. Using this method, we perform competitive binding experiments and show that they can be used to determine the dissociation constant of any given natural or unnatural nucleotide. The results demonstrate that the active site of the Klenow fragment is flexible enough to tolerate base pairs that are size-expanded in the major groove. In addition, the possibility to enzymatically polymerize a fluorescent nucleotide with high efficiency complements the tool box of biophysical probes available to study DNA replication.
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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. |
- Börjesson, Karl, 1982, et al.
(författare)
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Characterization and use of tricyclic fluorescent nucleic acid base analogues
- 2008
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Ingår i: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 3-4
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Tidskriftsartikel (refereegranskat)abstract
- The two recently developed nucleic acid probe molecules tC and tC(O) both have unique properties compared to other molecules in the family of fluorescent base analogues.(1-5) These tricyclic base analogues both form very stable base pairs with guanine and give minimal perturbations to the native structure of DNA.(2) We have found that tC(O) is the brightest fluorescent base analogue reported(4) and that tC also is very bright and has a fluorescence quantum yield that is virtually insensitive to its surrounding microenvironment within the nucleic acid(3). These base analogues have so far been used in FRET-studies of a DNA-polymerase system(6) and in initial anisotropy-studies of DNA-containing systems(4).
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| 7. |
- Börjesson, Karl, 1982, et al.
(författare)
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Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:12, s. 4288-4293
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Tidskriftsartikel (refereegranskat)abstract
- We present the first nucleobase analog fluorescence resonance energy transfer (FRET)-pair. The pair consists of tC O , 1,3-diaza-2- oxophenoxazine, as an energy donor and the newly developed tC nitro , 7-nitro-1,3-diaza-2-oxophenothiazine, as an energy acceptor. The FRET-pair successfully monitors distances covering up to more than one turn of the DNA duplex. Importantly, we show that the rigid stacking of the two base analogs, and consequently excellent control of their exact positions and orientations, results in a high control of the orientation factor and hence very distinct FRET changes as the number of bases separating tC O and tCnitro is varied. A set of DNA strands containing the FRET-pair at wisely chosen locations will, thus, make it possible to accurately distinguish distance- from orientation-changes using FRET. In combination with the good nucleobase analog properties, this points toward detailed studies of the inherent dynamics of nucleic acid structures. Moreover, the placement of FRET-pair chromophores inside the base stack will be a great advantage in studies where other (biomacro)molecules interact with the nucleic acid. Lastly, our study gives possibly the first truly solid experimental support to the dependence of energy transfer efficiency on orientation of involved transition dipoles as predicted by the Forster theory. © 2009 American Chemical Society.
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| 8. |
- Börjesson, Karl, 1982, et al.
(författare)
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Nucleic acid structure and sequence probing using fluorescent base analogue tCo
- 2009
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 1873-4200 .- 0301-4622. ; 139:1, s. 24-28
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Tidskriftsartikel (refereegranskat)abstract
- The fluorescent cytosine analog tC(o) is on average the brightest probe of its kind and, moreover, it introduces minimal perturbations to the normal secondary structure of DNA. Here several ways of how tC(o), with an advantage, can be used as a local fluorescent probe in nucleic acid systems are presented. Most importantly, we show that tCo is an excellent probe for the detection of individual melting processes of complex nucleic acid structures containing a large number of separate secondary structure motifs. Since conventional UV-melting investigations merely monitor the global melting process of the whole nucleic acid structure, e.g. multi-hairpin systems in RNA/DNA, and thus is incapable of estimating individual melting transitions of such systems, tC(o) represents a new method of characterization. Furthermore, we find that tCo may be used to detect bulges and loops in nucleic acids as well as to distinguish a matched base-pair from several of the mismatched.
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| 9. |
- Dyrager, Christine, 1975, et al.
(författare)
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2,6,8-Trisubstituted 3-hydroxychromone derivatives as fluorophores for live-cell imaging.
- 2009
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Ingår i: Chemistry (Weinheim an der Bergstrasse, Germany). - : Wiley. - 1521-3765 .- 0947-6539. ; 15:37, s. 9417-23
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Tidskriftsartikel (refereegranskat)abstract
- We present the synthesis and photophysical characterisation of a series of structurally diverse, fluorescent 2,6,8-trisubstituted 3-hydroxychromone derivatives with high fluorescence quantum yields and molar extinction coefficients. Two of these derivatives (9 and 10 a) have been studied as fluorophores for cellular imaging in HeLa cells and show excellent permeability and promising fluorescence properties in a cellular environment. In addition, we have demonstrated by photophysical characterisation of 3-isobutyroxychromone derivatives that esterification of the 3-hydroxyl group results in acceptable and useful fluorescence properties.
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| 10. |
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