1,721,177 research outputs found
Self-assembled DNA-based fluorescence waveguide with selectable output
No full textUsing the principle of self-assembly, a fluorescence-based photonic network is constructed with one input and two spatially and spectrally distinct outputs. A hexagonal DNA nanoassembly is used as a scaffold to host both the input and output dyes. The use of DNA to host functional groups enables spatial resolution on the level of single base pairs, well below the wavelength of light. Communication between the input and output dyes is achieved through excitation energy transfer. Output selection is achieved by the addition of a mediator dye intercalating between the DNA base pairs transferring the excitation energy from input to output through energy hopping. This creates a tool for selective excitation energy transfer on the nanometer scale with spectral and spatial control. The ability to direct excitation energy in a controlled way on the nanometer scale is important for the incorporation of photochemical processes in nanotechnology
Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue
No full textThis article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tCO, is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tCO is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm ({varepsilon} = 9000 M–1 cm–1) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tCO shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tCO, on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tCO a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET
Fluorescent properties of DNA base analogue tC upon incorporation into DNA - negligible influence of neighbouring bases on fluorescence quantum yield
No full textThe quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17-0.24 and 0.16-0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems
Membrane-Anchored DNA Assembly for Energy and Electron Transfer
No full textIn 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 separatio
Nucleic acid base analog fret-pair facilitating detailed structural measurements in nucleic acid containing systems
No full textWe present the first nucleobase analog fluorescence resonance energy transfer (FRET)-pair. The pair consists of tCO, 1,3-diaza-2-oxophenoxazine, as an energy donor and the newly developed tCnitro, 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 tCO 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 Frster theory
Platform for controlled supramolecular nanoassembly
No full textWe here present a two-dimensional (2D) micro/nano-fluidic technique where reactant-doped liquid?crystal films spread and mix on micro- and nanopatterned substrates. Surface-supported phospholipid monolayers are individually doped with complementary DNA molecules which hybridize when these lipid films mix. Using lipid films to convey reactants reduces the dimensionality of traditional 3D chemistry to 2D, and possibly to 1D by confining the lipid film to nanometer-sized lanes. The hybridization event was observed by FRET using single-molecule-sensitive confocal fluorescence detection. We could successfully detect hybridization in lipid streams on 250 nm wide lanes. Our results show that the number and density of reactants as well as sequence of reactant addition can be controlled within confined liquid crystal films, providing a platform for nanochemistry with potential for kinetic control
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Thermodynamic aspects of DNA nanoconstruct stability and design
No full textIn the present study, we use the fluorescent DNA base analog tC° to investigate the thermal stability of a small DNA hexagon and the thermodynamic factors that govern the formation of such a structure. The DNA molecule is becoming increasingly popular as a material for bottom-up construction of nanostructures; however, relatively little attention has been given to the thermodynamics of such biomacromolecule-based constructs. With the goal of increasing information density and structural complexity, the size of the nanoarchitectures decreases and, more importantly, the fine structure is becoming more detailed. In this process the thermal stability and formation of unwanted byproducts will become critical features to consider in the design and assembly of such structures. Using tC° as a fluorescent probe in fluorescence monitored DNA melting allows for individually observing the denaturing of each of the six 10-mer sides in the pseudohexagonal multicomponent system. Experimental results demonstrate that the ring-opening of the cyclized hexamer is virtually exclusive to one side and that the stability of this side is increased as a result of the cyclization. Moreover, a theoretical model describing the formation and melting of the nanostructure is presented. The results show that the cyclized structure is thermodynamically favored over linear polymeric structures under the conditions and concentrations used for the self-assembly
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