| 1. |
- Aissaoui, Nesrine, 1983, et al.
(author)
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FRET enhancement close to gold nanoparticles positioned in DNA origami constructs
- 2017
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In: Nanoscale. - Cambridge, United Kingdom : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 9:2, s. 673-683
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Journal article (peer-reviewed)abstract
- Here we investigate the energy transfer rates of a Förster resonance energy transfer (FRET) pair positioned in close proximity to a 5 nm gold nanoparticle (AuNP) on a DNA origami construct. We study the distance dependence of the FRET rate by varying the location of the donor molecule, D, relative to the AuNP while maintaining a fixed location of the acceptor molecule, A. The presence of the AuNP induces an alteration in the spontaneous emission of the donor (including radiative and non-radiative rates) which is strongly dependent on the distance between the donor and AuNP surface. Simultaneously, the energy transfer rates are enhanced at shorter D-A (and D-AuNP) distances. Overall, in addition to the direct influence of the acceptor and AuNP on the donor decay there is also a significant increase in decay rate not explained by the sum of the two interactions. This leads to enhanced energy transfer between donor and acceptor in the presence of a 5 nm AuNP. We also demonstrate that the transfer rate in the three "particle" geometry (D + A + AuNP) depends approximately linearly on the transfer rate in the donor-AuNP system, suggesting the possibility to control FRET process with electric field induced by 5 nm AuNPs close to the donor fluorophore. It is concluded that DNA origami is a very versatile platform for studying interactions between molecules and plasmonic nanoparticles in general and FRET enhancement in particular.
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| 2. |
- Björklund, Kicki, et al.
(author)
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An investigation of Property Price Studies
- 2002
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In: Real Estate Valuation Theory. - Boston, MA : Springer. ; , s. 63-93
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Book chapter (peer-reviewed)abstract
- Several delicate issues are connected to the question of how to compose scientific papers. A number of rules and guidelines apply — some interdisciplinary, others common for all sciences. The scientific policies of the academic journals, but also their space constraints, play an important role in forming the rules. Still, in several situations the question regarding what should be explained and interpreted explicitly and what may be left for the been discussed above, that can explain why it is reasonable not to find only “yes” answers to the questionnaire. In light of these objections, we find the overall result to be reasonably good. However, in two respects we found the results surprisingly poor, taking into account the emphasis that has been put on the topics in standard textbooks and earlier reviews.
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| 3. |
- Börjesson, Karl, 1982, et al.
(author)
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A membrane anchored DNA-based energy/electron transfer assembly
- 2008
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In: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 691-691
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Journal article (peer-reviewed)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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| 4. |
- Börjesson, Karl, 1982, et al.
(author)
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Characterization and use of tricyclic fluorescent nucleic acid base analogues
- 2008
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In: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 3-4
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Journal article (peer-reviewed)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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| 5. |
- Börjesson, Karl, 1982, et al.
(author)
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Membrane-Anchored DNA Assembly for Energy and Electron Transfer
- 2009
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:8, s. 2831-2839
-
Journal article (peer-reviewed)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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| 6. |
- Börjesson, Karl, 1982, et al.
(author)
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Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems
- 2009
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:12, s. 4288-4293
-
Journal article (peer-reviewed)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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| 7. |
- Celiker, Shemal, et al.
(author)
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A radiofrequency vs topical steroid treatment of chronic nasal obstruction : A prospective randomized study of 84 cases
- 2011
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In: Acta Oto-Laryngologica. - : Informa UK Limited. - 0001-6489 .- 1651-2251. ; 131:1, s. 79-83
-
Journal article (peer-reviewed)abstract
- Conclusions:Nasal congestion caused by mucosal swelling and conch hypertrophy impairs breathing and causes snoring and headaches. Treatment of conch hypertrophy with radiofrequency (RF) allows reduction of mucosal swelling, minimization of hyperplasia, and decreased mucus production. This treatment provides a clinically significant improvement in snoring, headaches, and mouth breathing.Objective:To compare the efficacy of RF surgery to nasal steroid; each method used separately and both in combination.Methods:This was a consecutive randomized study, which included 84 patients with 3 outpatient visits, where the first visit included a complete medical history, assessment of ENT status, and skin tests. Nasal flow measured with rhinomanometry was done at the first visit and then before and after each treatment. Patients were asked to respond to a questionnaire at the first visit and after each subsequent treatment. Thereafter the variables were analyzed with established statistical methods.Results:Measurement of variables and patient questionnaire responses showed a clear improvement in several symptoms, such as sneezing and headache, and a clinically significant improvement in nasal congestion and snoring.
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| 8. |
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| 9. |
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| 10. |
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| 11. |
- Engman, Cecilia, 1974, et al.
(author)
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DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization
- 2004
-
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 32:17, s. 5087-95
-
Journal article (peer-reviewed)abstract
- The influence of the highly fluorescent tricyclic cytosine base analogue (tC) on duplex DNA conformation is investigated. The duplex properties are characterized by absorbance and circular dichroism (CD) for all combinations of neighbouring bases to tC, and an NMR structure is determined for one tC-containing sequence. For the oligonucleotides with one tC incorporated instead of cytosine, the melting temperature is increased on average by 2.7 degrees C above that for the unmodified ones. CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. The root-mean-square distance for the nucleotides of the eight central base pairs between the 10 structures with lowest CYANA target functions and a mean structure is 0.45 +/- 0.17 A. The NMR data confirm correct base pairing for tC by the observation of both intrastrand and interstrand imino proton NOEs. Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems.
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| 12. |
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| 13. |
- Enström Öst, Cecilia, 1971-, et al.
(author)
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High house prices and homeownership rates
- 2013
-
Reports (other academic/artistic)abstract
- Earlier research have concluded that high house prices, relative to household income and wealth, and a tax on imputed rent are the most important causes of a countries low ownership rate. Given these findings, it is challenging to apply a similar analysis to a housing market characterized by comparatively high homeownership rates. One candidate for such a comparison is Sweden, where homeownership rates have exceeded 80% for at least the last two decades. From a particularly rich database covering all inhabitants of Sweden, we use observations of some 790,000 households (corresponding to some 2.9 million inhabitants) to analyze the Stockholm region housing market in 2008. The results suggest that high house prices relative to rents are unlikely to be the only key variable explaining the general ownership rate pattern in a housing market.
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| 14. |
- Enström Öst, Cecilia, et al.
(author)
-
Homeownership rates of finansially constrained households
- 2017
-
In: Journal of European Real Estate Research. - : Emerald Publishing. - 1753-9269 .- 1753-9277. ; 10:2
-
Journal article (peer-reviewed)abstract
- Purpose – This paper aims to examine tenure choice in the Swedish housing market with explicitconsideration of households’ credit constraints in combination with age and ethnic background.Design/methodology/approach – Observations of some 940,000 households were used to analyse theStockholm housing market in 2008, prior to the implementation of the mortgage cap. The tenure choicemodels were estimated using a two-stage instrument variable (IV) logit and probit model with ownership orrenting as outcome.Findings – The results suggest, as expected, that being financially restricted is negatively related toowning. In particular, financial restriction is more binding for young households and households with aforeign background than for other types of households. These two sub-groups are also known to havedifficulties establishing themselves in the rental housing market, and are therefore specifically vulnerable tofurther financial constraints such as borrowing restrictions or amortization requirements.Originality/value – The government in Sweden has become concerned with the rapid growth inhousehold indebtedness. As a response, a 0.85 loan-to-value ratio mortgage cap was introduced in 2010.However, critics are concerned with the effects this may have on the possibility for certain households topurchase a dwelling.
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| 15. |
- Enström Öst, Cecilia, et al.
(author)
-
Household allocation and spatial distribution in a market under ("soft") rent control
- 2014
-
In: Journal of Policy Modeling. - : Elsevier BV. - 0161-8938 .- 1873-8060. ; 36:2, s. 353-372
-
Journal article (peer-reviewed)abstract
- We analyse whether segregation exists in the rental housing market in Stockholm, Sweden, a market under persistent and all-embracing, yet "soft", rent control. We use segregation measures for the uncontrolled cooperative housing segment as benchmarks for analysing whether rent control counteracts segregation. We apply the analyses to a rich dataset encompassing some 400,000 households. We find that income segregation is significantly lower in the rent control segment than in the free market benchmark. However, when analysing segregation with respect to other segregation measures, the rental housing market is more segregated in these respects than in the non-regulated market for cooperatives. Rent control has arguably led to a comparatively flat rent gradient over the city and thus the comparatively low rents in the central, and most attractive, areas of the city provide a general subsidy to those who live in these areas. But according to our results this subsidy does not efficiently benefit households with low educated level, households with children, young households or households with a migrant background.
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| 16. |
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| 17. |
- Le, Hoang Ngoan, 1989, et al.
(author)
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Synthesis and photophysical characterization of a pH-sensitive quadracyclic uridine (qU) analogue
- 2024
-
In: Chemistry - A European Journal. - 1521-3765 .- 0947-6539. ; 30:18
-
Journal article (peer-reviewed)abstract
- Fluorescent base analogues (FBAs) have become useful tools for applications in biophysical chemistry, chemical biology, live-cell imaging, and RNA therapeutics. Herein, two synthetic routes towards a novel FBA of uracil named qU (quadracyclic uracil/uridine) are described. The qU nucleobase bears a tetracyclic fused ring system and is designed to allow for specific Watson-Crick base pairing with adenine. We find that qU absorbs light in the visible region of the spectrum and emits brightly with a quantum yield of 27 % and a dual-band character in a wide pH range. With evidence, among other things, from fluorescence lifetime measurements we suggest that this dual emission feature results from an excited-state proton transfer (ESPT) process. Furthermore, we find that both absorption and emission of qU are highly sensitive to pH. The high brightness in combination with excitation in the visible and pH responsiveness makes qU an interesting native-like nucleic acid label in spectroscopy and microscopy applications in, for example, the field of mRNA and antisense oligonucleotide (ASO) therapeutics.
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| 18. |
- Lundberg, Erik, 1981, et al.
(author)
-
Addressable molecular node assembly - high information density DNA nanostructures
- 2008
-
In: Nucleic acids symposium series (2004). - 1746-8272. ; :52, s. 683-684
-
Journal article (peer-reviewed)abstract
- The inherent self-assembly properties of DNA make it ideal in nanotechnology. We present a fully addressable DNA nanostructure with the smallest possible unit cell, a hexagon with a side-length of only 3.4 nm.(2,3) Using novel three-way oligonucleotides, where each side has a unique double-stranded DNA sequence that can be assigned a specific address, we will build a non-repetitive two-dimensional grid.
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| 19. |
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| 20. |
- Preus, S., et al.
(author)
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Characterization of Nucleobase Analogue FRET Acceptor tC(nitro)
- 2010
-
In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 114:2, s. 1050-1056
-
Journal article (peer-reviewed)abstract
- The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization Of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented similar to 27 degrees from the molecular long axis, This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum Of tC(nitro) is further characterized by density functional theory calculations.
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| 21. |
- Preus, S., et al.
(author)
-
FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids
- 2013
-
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 41:1, s. Article Number: e18-
-
Journal article (peer-reviewed)abstract
- Forster resonance energy transfer (FRET) is a technique commonly used to unravel the structure and conformational changes of biomolecules being vital for all living organisms. Typically, FRET is performed using dyes attached externally to nucleic acids through a linker that complicates quantitative interpretation of experiments because of dye diffusion and reorientation. Here, we report a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base-base FRET). These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.
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| 22. |
- Preus, S., et al.
(author)
-
Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family
- 2010
-
In: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 12:31, s. 8881-8892
-
Journal article (peer-reviewed)abstract
- Fundamental insight into the unique fluorescence and nucleobase-mimicking properties of the fluorescent nucleobase analogues of the tC family is not only vital in explaining the behaviour of these probes in nucleic acid environments, but will also be profitable in the development of new and improved fluorescent base analogues. Here, temperature-dependent fluorescence quantum yield measurements are used to successfully separate and quantify the temperature-dependent and temperature-independent non-radiative excited-state decay processes of the three nucleobase analogues tC, tC(O) and tC(nitro); all of which are derivatives of a phenothiazine or phenoxazine tricyclic framework. These results strongly suggest that the non-radiative decay process dominating the fast deactivation of tCnitro is an internal conversion of a different origin than the decay pathways of tC and tC(O). tCnitro is reported to be fluorescent only in less dipolar solvents at room temperature, which is explained by an increase in excited-state dipole moment along the main non-radiative decay pathway, a suggestion that applies in the photophysical discussion of large polycyclic nitroaromatics in general. New insight into the ground and excited-state potential energy surfaces of the isolated tC bases is obtained by means of high level DFT and TDDFT calculations. The S-0 potential energy surfaces of tC and tCnitro possess two global minima corresponding to geometries folded along the middle sulfur-nitrogen axis separated by an energy barrier of 0.05 eV as calculated at the B3LYP/6-311 + G(2d, p) level. The ground-state potential energy surface of tC(O) is also predicted to be shallow along the bending coordinate but with an equilibrium geometry corresponding to the planar conformation of the tricyclic framework, which may explain some of the dissimilar properties of tC and tC(O) in various confined (biological) environments. The S-1 equilibrium geometries of all three base analogues are predicted to be planar. These results are discussed in the context of the tC bases positioned in double-stranded DNA scenarios.
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| 23. |
- Preus, S., et al.
(author)
-
The photoinduced transformation of fluorescent DNA base analogue tC triggers DNA melting
- 2013
-
In: Photochemical and Photobiological Sciences. - : Springer Science and Business Media LLC. - 1474-9092 .- 1474-905X. ; 12:8, s. 1416-1422
-
Journal article (peer-reviewed)abstract
- While fluorescent analogues of the canonical nucleobases have proven to be highly valuable in a large number of applications, up until today, fluorescent DNA base analogues remain virtually inapplicable for single-molecule fluorescence experiments which require extremely bright and photostable dyes. Insight into the photodegradation processes of these fluorophores is thus a key step in the continuous development towards dyes with improved performances. Here, we show that the commercially available fluorescent nucleobase analogue tC under intense long-term illumination and in the presence of O-2 is degraded to form a single photoreaction product which we suggest to be the sulfoxide form of tC. The photoproduct is characterized by a blue-shifted absorption and a less intense fluorescence compared to that of tC. Interestingly, when tC is positioned inside double-stranded DNA this photodriven conversion of tC to its photoproduct greatly reduces the duplex stability of the overall double helix in which the probe is positioned. Since tC can be excited selectively at 400 nm, well outside the absorption band of the natural DNA bases, this observation points towards the application of tC as a general light-triggered switch of DNA duplex stability.
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| 24. |
- Sandin, Peter, 1977, et al.
(author)
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Characterization and Use of an Unprecedentedly Bright and Structurally Non-Perturbing Fluorescent DNA Base Analogue
- 2008
-
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 36:1, s. 157-167
-
Journal article (peer-reviewed)abstract
- This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tC(O), is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tC(O) 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 (epsilon = 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, tC(O) shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tC(O), 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 tC(O) 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).
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| 25. |
- Sandin, Peter, 1977, et al.
(author)
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Fluorescent Properties of DNA Base Analogue tC upon Incorporation into DNA - Negligible Influence of Neighboring Bases on Fluorescence Quantum Yield
- 2005
-
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 33:16, s. 5019-5025
-
Journal article (peer-reviewed)abstract
- The 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.
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| 26. |
- Sandin, Peter, 1977, et al.
(author)
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Thermodynamic Aspects of DNA Nanoconstruct Stability and Design
- 2009
-
In: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 113:15, s. 5941-5946
-
Journal article (peer-reviewed)abstract
- In the present study, we use the fluorescent DNA base analog tCå to investigate the thermal stability of a small DNA hexagon and the thermodynamie 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 tCå 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. © 2009 American Chemical Society.
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| 27. |
- Stengel, Gudrun, et al.
(author)
-
Conformational dynamics of DNA polymerase probed with a novel fluorescent DNA base analogue
- 2007
-
In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 46:43, s. 12289-12297
-
Journal article (peer-reviewed)abstract
- DNA polymerases discriminate between correct and incorrect nucleotide substrates during a "nonchemical" step that precedes phosphodiester bond formation in the enzymatic cycle of nucleotide incorporation. Despite the importance of this process in polymerase fidelity, the precise nature of the molecular events involved remains unknown. Here we report a fluorescence resonance energy transfer (FRET) system that monitors conformational changes of a polymerase-DNA complex during selection and binding of nucleotide substrates. This system utilizes the fluorescent base analogue 1,3-diaza-2oxophenothiazine (tC) as the FRET donor and Alexa-555 (A555) as the acceptor. The tC donor was incorporated within a model DNA primer/template in place of a normal base, adjacent to the primer 3' terminus, while the A555 acceptor was attached to an engineered cysteine residue (C751) located in the fingers subdomain of the Klenow fragment (KF) polymerase. The FRET efficiency increased significantly following binding of a correct nucleotide substrate to the KF-DNA complex, showing that the fingers had closed over the active site. Fluorescence anisotropy titrations utilizing tC as a reporter indicated that the DNA was more tightly bound by the polymerase under these conditions, consistent with the formation of a closed ternary complex. The rate of the nucleotide-induced conformational transition, measured in stopped-flow FRET experiments, closely matched the rate of correct nucleotide incorporation, measured in rapid quench-flow experiments, indicating that the conformational change was the rate-limiting step in the overall cycle of nucleotide incorporation for the labeled KF-DNA system. Taken together, these results indicate that the FRET system can be used to probe enzyme conformational changes that are linked to the biochemical function of DNA polymerase.
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| 28. |
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| 29. |
- Tumpane, John, 1983, et al.
(author)
-
Addressable high-information-density DNA nanostructures
- 2007
-
In: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 440:1-3, s. 125-129
-
Journal article (peer-reviewed)abstract
- We present a strategy for self-assembly of the smallest yet reported DNA nanostructures that are also addressable in terms of their DNA-base code. Using linear as well as novel branched three-way DNA., oligonucleotide building-blocks we demonstrate the formation of a nano-network's fundamental cell, a DNA pseudo-hexagon of side 4 nm. The network's inherent addressability will allow functionalization with sub-nanometer precision yielding unprecedented richness in information density, important in the context of Moore's Law and nano-chip technology. (c) 2007 Published by Elsevier B.V.
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| 30. |
- Tumpane, John, 1983, et al.
(author)
-
Triplex addressability as a basis for functional DNA nanostructures
- 2007
-
In: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 7:12, s. 3832-3839
-
Journal article (peer-reviewed)abstract
- Here, we present the formation of a fully addressable DNA nanostructure that shows the potential to be exploited as, for example, an information storage device based on pH-driven triplex strand formation or nanoscale circuits based on electron transfer, The nanostructure is composed of two adjacent hexagonal unit cells (analogous to naphthalene) in which each of the eleven edges has a unique double-stranded DNA sequence, constructed using novel three-way oligonucleotides. This allows each ten base-pair side, just 3.4 nm in length, to be assigned a specific address according to its sequence. Such constructs are therefore an ideal precursor to a nonrepetitive two-dimensional grid on which the "addresses" are located at a precise and known position. Triplex recognition of these addresses could function as a simple yet efficient means of information storage and retrieval. Future applications that may be envisaged include nanoscale circuits as well as subnanometer precision in nanoparticle templating. Characterization of these precursor nanostructures and their reversible targeting by triplex strand formation is shown here using gel electrophoresis, atomic force microscopy, and fluorescence resonance energy transfer (FRET) measurements. The durability of the system to repeated cycling of pH switching is also confirmed by the FRET studies.
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| 31. |
- Walker-Engström, Marie-Louise, et al.
(author)
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4-year follow-up of treatment with dental appliance or uvulopalatopharyngoplasty in patients with obstructive sleep apnea : A randomized study
- 2002
-
In: Chest. - : Elsevier BV. - 0012-3692 .- 1931-3543. ; 121:3, s. 739-746
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Journal article (peer-reviewed)abstract
- Study objectives: To evaluate the effects of treatment with a dental appliance or uvulopalato-pharyngoplasty, (UPPP) on somnographic variables in patients with mild-to-moderate obstructive sleep apnea (OSA) followed up for 4 years, and compliance,and complementary treatment.Design: Randomized study.Setting: Central Hospital, Västerås, Uppsala University, Sweden.Patients: Ninety-five male patients with confirmed mild-to-moderate OSA (apnea index (AI) > 5 and < 25) were randomized to treatment with a dental appliance or UPPP. Sleep studies were performed before and 1 year and 4 years after intervention. Thirty-two patients in the dental-appliance group and 40 patients in the UPPP group completed the 4-year follow-up.Results: The success rate (percentage of patients with at least 50% reduction in AI) in the dental-appliance group was 81%, which was significantly higher than in the UPPP group, 53% (p < 0.05). Normalization (AI < 5 or apnea/hypopnea index < 10) was observed in 63% of the dental-appliance group and 33% of the UPPP group after 4 years. The difference between the groups was significant (p < 0.05). The compliance to use of the dental appliance was 62% at the 4-year follow-up. Thirty patients (75%) in the UPPP group continued without complementary treatment. The dental appliances had few adverse effects on the stomatognathic system, and the number of adjustments and repairs of the appliances over time was moderate. Pronounced complaints of nasopharyngeal regurgitation of fluid and difficulty, with swallowing after UPPP were reported by 8% and 10%, respectively.Conclusions: The dental-appliance group showed significantly higher success and normalization rates regarding the somnographic variables compared to the UPPP group, but the effectiveness of the dental appliance was partly invalidated by the compliance of 62% at the 4-year follow-up. However, the appliances had few adverse effects on the stomatognathic system an required only moderate adjustments. Use of a dental appliance with regular follow-up can be recommended for long-term treatment of OSA.
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| 32. |
- Walker-Engström, Marie-Louise, et al.
(author)
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A prospective randomized study comparing two different degrees of mandibular advancement with a dental appliance in treatment of severe obstructive sleep apnea
- 2003
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In: Sleep and Breathing. - : Springer Science and Business Media LLC. - 1520-9512 .- 1522-1709. ; 7:3, s. 119-130
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Journal article (peer-reviewed)abstract
- The objective of this study was to compare the effect of two different degrees of mandibular advancement (MA), 75% versus 50%, on somnographic variables after 6 months of dental appliance treatment in patients with severe obstructive sleep apnea (OSA). A further purpose was to compare the number of adverse events on the stomatognathic system and the effects of dental appliance treatment on the presence of daytime sleepiness.Eighty-six males with severe OSA (apnea index ≥ 20) were randomly allocated to either 75% or 50% MA. Forty patients in the 75% MA group and 37 patients in the 50% MA group completed the 6-month follow-up.The effectiveness of treatment in terms of normalization (apnea index < 5 and apnea/hypopnea index < 10) with 75% MA was 52%, which was significantly higher (p = 0.04) than the 31% achieved with 50% MA. The dental appliance had few adverse events on the stomatognathic system regardless of group, and the number of adverse events did not differ between the two groups. Finally, the mean value of Epworth Sleepiness Scale scores decreased significantly from 11.6 at baseline to 8.0 at follow-up (p < 0.001). No significant difference was observed between the two groups. The results indicate that a dental appliance could be an alternative treatment for some patients with severe OSA.
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| 33. |
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| 34. |
- Wilhelmsson, Bo, et al.
(author)
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A Prospective Randomized Study of a Dental Appliance Compared with Uvulopalatopharyngoplasty in the Treatment of Obstructive Sleep Apnoea
- 1999
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In: Acta Oto-Laryngologica. - : Informa UK Limited. - 0001-6489 .- 1651-2251. ; 119:4, s. 503-509
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Journal article (peer-reviewed)abstract
- The enthusiasm for uvulopalatopharyngoplasty (UPPP) in the treatment of obstructive sleep apnoea (OSA) has declined in recent years, partly because of a lower success rate over time and partly because of adverse effects. Reports on the beneficial effects of dental appliances exist, but only one prospective randomized study has been published comparing dental appliances with nasal continuous positive airway pressure (CPAP) treatment. No study has been published comparing dental appliance treatment with UPPP. Ninety-five male patients with confirmed OSA, subjective daytime sleepiness and an apnoea index (AI) > 5 were randomized for subsequent treatment with either a dental appliance or UPPP. There were 49 patients in the dental appliance group and 46 in the UPPP group. Thirty-seven patients in the dental appliance group and 43 in the UPPP group completed the 12-month follow-up. The success rate (rate of patients with at least a 50% reduction in AI) for the dental appliance group was 95%, which was significantly higher (p < 0.01) than the 70% success rate for the UPPP group. According to the criteria for OSA (apnoea index > or = 5 or apnoea/hypopnoea index > or = 10), 78% of the dental appliance group and 51% of the UPPP group were normalized after 12 months. The difference between the groups was significant (p < 0.05). These findings suggest that the dental appliance technique is useful in the treatment of mild to moderate OSA.
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| 35. |
- Wilhelmsson, Marcus, 1974, et al.
(author)
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Photophysical Characterization of Fluorescent DNA Base Analogue, tC
- 2003
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 107:34, s. 9094-9101
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Journal article (peer-reviewed)abstract
- The novel fluorescent DNA cytosine base analogue 1,3-diaza-2-oxophenothiazine, tC, has previously been shown to have a remarkably preserved high quantum yield upon incorporation into a single strand of peptide nucleic acid, PNA, as well as when the latter is hybridized with a complementary DNA to form a PNA-DNA duplex. Here, we investigate fundamental photophysical properties of tC. Using fluorescence anisotropy, stretched film linear dichroism, and quantum chemical calculations, the transition moment polarizations of the lowest lying electronic states are determined. The neutral, base-pairing form of tC, having a fluorescence quantum yield of 0.2, is found to be the totally predominant species in a wide pH interval, 4-12. We show that the absorption band of tC at lowest energy, centered at 26 700 cm(-1) and well separated from the nucleobase absorption, is due to a single electronic transition polarized approximately at 35degrees from the long axis of the molecule. The 2-deoxyribonucleoside of 1,3-diaza-2-oxophenothiazine, synthesized for further incorporation into DNA, was found to display a fluorescence quantum yield nearly the same as in the form of tC that was incorporated into PNA, confirming the notion of the tC nucleoside being a probe with very promising fluorescence properties essentially invariant of environment, also upon incorporation into a DNA strand and upon hybridization.
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