Single-molecule fluorescence spectroscopy of TOTO on poly-AT and poly-GC DNA

Excited state lifetime and amplitude measurements were made on thiazole orange dimer (TOTO), a dimeric DNA-intercalating fluorophore, at single-molecule concentrations. As expected from previous study, the excited state lifetime of TOTO intercalated in DNA is dependent on the sequence of the double-stranded DNA, having values of 2.2 ns in poly-GC DNA and 1.8 ns in poly-AT DNA. The distribution of excited state lifetimes of single molecules of TOTO intercalated into oligonucleotides having varying proportions of poly-GC sequences relative to poly-AT sequences were analyzed as a function of the fraction of poly-GC. By using excited state lifetime distributions from the purely GC and purely AT oligonucleotides as a basis set, it was possible to estimate the GC content of oligonucleotides with intermediate GC composition to within a few percent error. This serves as a model for the analysis of equilibrium binding distributions in DNA using single-molecule methods.     

High-resolution detection of adulteration of maize oil using multi-component compound-specific delta13C values of major and minor components and discriminant analysis

Maize oil commands a premium price and is thus a target for adulteration with cheaper vegetable oils. Detection of this activity presents a particular challenge to the analyst because of the natural variability in the fatty acid composition of maize oils and because of their high sterol and tocopherol contents. This paper describes a method that allows detection of adulteration at concentrations of just 5% (m/m), based on the Mahalanobis distances of the principal component scores of the delta(13)C values of major and minor vegetable oil components. The method makes use of a database consisting of delta(13)C values and relative abundances of the major fatty acyl components of over 150 vegetable oils. The sterols and tocopherols of 16 maize oils and 6 potential adulterant oils were found to be depleted in (13)C by a constant amount relative to the bulk oil. Moreover, since maize oil contains particularly high levels of sterols and tocopherols, their delta(13)C values were not significantly altered when groundnut oil was added up to 20% (m/m) and it is possible to use the values for the minor components to predict the values that would be expected in a pure oil; therefore, comparison of the predicted values with those obtained experimentally allows adulteration to be detected. A refinement involved performing a discriminant analysis on the delta(13)C values of the bulk oil and the major fatty acids (16:0, 18:1 and 18:2) and using the Mahalanobis distances to determine the percentage of adulterant oil present. This approach may be refined further by including the delta(13)C values of the minor components in the discriminant analysis thereby increasing the sensitivity of the approach to concentrations at which adulteration would not be attractive economically.     

Rhetoric,Reality, and Possibilities: Interdisciplinary Teaching and Secondary Mathematics

The National Council of Teachers of Mathematics has proposed a broad core mathematics curriculum for all high school students. One emphasis in that core is on “mathematical connections” both among mathematical topics and between mathematics and other disciplines of study. It is suggested that mathematics should become a more integrated part of all students' high school education. In this article, working definitions for the terms curriculum, interdisciplinary, and integrated and a model of three categories of curriculum design based on the work of Harold Alberty are developed. This article then examines how a “connected” mathematics core curriculum might be situated within the different categories of curriculum organization. Examples from research on interdisciplinary education in high schools are presented. Issues arising from this study suggest the need for a greater emphasis on building and using models of curriculum integration both to frame and to give impetus to the work being done by teachers and administrators.     

Mechanism of carotenoid singlet excited state energy transfer in modified bacterial reaction centers

Ultrafast transient laser spectroscopy has been used to investigate carotenoid singlet excited state energy transfer in various Rhodobacter (Rb.) sphaeroides reaction centers (RCs) modified either genetically or chemically. The pathway and efficiency of energy transfer were examined as a function of the structures and energies of the donor and acceptor molecules. On the donor side, carotenoids with various extents of pi-electron conjugation were examined. RCs studied include those from the anaerobically grown wild-type strain containing the carotenoid spheroidene, which has 10 conjugated carbon-carbon double bonds; the GA strain containing neurosporene, which has nine conjugated double bonds; and aerobically grown wild-type cells, as well as aerobically grown H(M182)L mutant, both containing the carbonyl-containing carotenoid spheroidenone, which has 11 conjugated double bonds. By varying the structure of the carotenoid, we observed the effect of altering the energies of the carotenoid excited states on the rate of energy transfer. Both S(1)- and S(2)-mediated carotenoid-to-bacteriochlorophyll energy transfer processes were observed. The highest transfer efficiency, from both the S(1) and S(2) states, was observed using the carotenoid with the shortest chain. The S(1)-mediated carotenoid-to- bacteriochlorophyll energy transfer efficiencies were determined to be 96%, 84%, and 73% for neurosporene, spheroidene, and spheroidenone, respectively. The S(2)-mediated energy transfer efficiencies follow the same trend but could not be determined quantitatively because of limitations in the time resolution of the instrumentation. The dependence of the energy transfer rate on the energetics of the energy transfer acceptor was verified by performing measurements with RCs from the H(M182)L mutant. In this mutant, the bacteriochlorophyll (denoted B(B)) located between the carotenoid and the RC special pair (P) is replaced by a bacteriopheophytin (denoted phi(B)), where the Q(X) and Q(Y) bands of phi(B) are 1830 and 1290 cm(-1), respectively, higher in energy than those of B(B). These band shifts associated with phi(B) in the H(M182)L mutant significantly alter the spectral overlap between the carotenoid and phi(B), resulting in a significant decrease of the transfer efficiency from the carotenoid S(1) state to phi(B). This leaves energy transfer from the carotenoid S(2) state to phi(B) as the dominant channel. Largely because of this change in mechanism, the overall efficiency of energy transfer from the carotenoid to P decreases to less than 50% in this mutant. Because the spectral signature of phi(B) is different from that of B(A) in this mutant, we were able to demonstrate clearly that the carotenoid-to-P energy transfer is via phi(B). This finding supports the concept that, in wild-type RCs, the carotenoid-to-P energy transfer occurs through the cofactor located at the B(B) position.     

Electronic transitions of the Soret band of reaction centers from Rhodobacter sphaeroides studied by femtosecond transient absorbance spectroscopy

The Soret band of reaction centers from Rhodobacter sphaeroides has been systematically studied using femtosecond transient absorption spectroscopy. When the excitation wavelength was scanned over the entire Soret band, the approximate absorption spectra of the bacteriochlorophyll dimer, the monomer bacteriochlorophylls, and the bacteriopheophytins within the Soret band were determined by analyzing the ground state bleaching with about 100 fs resolution. The main contribution of H is on the blue end of the spectrum, peaking near 350 nm, P absorbs mostly on the red side of the spectrum, but probably has multiple bands, and the main absorbance of B likely lies between H and P, overlapping with P on the red side (particularly near 390 nm). The energy transfer from B to P in the QY band takes about 300 fs when Soret-band excitation is used and the time constant of overall energy transfer from H to B to P in the QY band when H is specifically excited near 350 nm is about 500 fs. Internal conversion after Soret-band excitation is the rate-limiting step for the energy-transfer process. The time constant of internal conversion for B and P is less than 300 fs, and for H it is about 500 fs.     

TOTO binding affinity analysis using single-molecule fluorescence spectroscopy

The sequence dependence of the double-stranded DNA (dsDNA)-binding affinity of TOTO, a thiazole orange dimer that functions as a DNA-intercalating fluorophore, was measured using single-molecule methods. An analysis was performed of the distribution of excited-state lifetimes of single molecules of TOTO intercalated into dsDNA fragments containing four-base pair sequences shown previously to have high affinity for TOTO under conditions used in nuclear magnetic resonance (NMR) spectroscopy. For the current studies, the putative binding sites were located centrally in 30-base pair-long dsDNA fragments in which the remaining sequence was either all poly-AT or poly-GC. The lifetime of TOTO fluorescence when bound to these fragments was entirely determined by the background sequence, i.e. DNA fragments with a poly-AT background predominantly gave a fluorescence lifetime of 1.7 ns, whereas DNA fragments with a poly-GC background gave a lifetime of 2.0 ns, independent of the presence or absence of the putative binding sequence. By performing competitive binding experiments in which these DNA fragments competed for TOTO binding with pure poly-AT fragments and using single-molecule fluorescence methods to determine the number of each type of DNA fragment having a TOTO bound in an equilibrium mixture, the relative binding affinity of each putative binding site was determined. The results of these experiments showed clearly that TOTO has no preference for binding to the putative binding sites over binding poly-AT or poly-GC under the conditions of these measurements. This suggests that there is very little sequence dependence of TOTO binding under conditions that would likely predominate in most biological applications of this intercalating dye.     

Excitation wavelength dependence of primary charge separation in reaction centers from Rhodobacter sphaeroides

The excitation wavelength dependence of the initial electron transfer rate in both wild type and mutant reaction centers from Rhodobacter sphaeroides has been studied between 840 and 920 nm as a function of temperature (10-295 K). The dynamics of primary charge separation show no resolvable excitation wavelength dependence at room temperature over this spectral range. A small variation in rate with excitation wavelength is observed at cryogenic temperatures. The low temperature results cannot be explained in terms either of a nonequilibrium model that assumes that the primary charge separation starts from a vibrationally hot state or a model that assumes a static inhomogeneous distribution of electron transfer driving forces. Instead these results are consistent with the concept that primary charge separation kinetics are controlled by the dynamics of protein conformational diffusion.     

Light-directed movement of polymer microstructures

Light has been used to induce photochemical changes in the surface chemistry of porous polymer microstructures giving rise to a substantial change in volume. When illumination is asymmetric, this results in light-directed motion of the structure. Swellable trimethylolpropane trimethacrylate cross-linked poly(2-hydroxylethyl methacrylate) microstructures were constructed by azo-bis-isobutyronitrile photopolymerization using a 20 x 0.5 NA microscope objective and 365 nm laser excitation. Structures were aminiated with glycine and protected with the photolabile group 4-nitroveratryloxycarbanyl (NVOC). Addition of NVOC resulted in a volume increase >10% when performed in the solvent N,N'-dimethylformamide. Photochemical cleavage of NVOC using asymmetric illumination of a cone-shaped microstructure with a 365 nm laser induced polymer shrinkage in excess of 4% at the base of the cone and resulted in a maximum velocity of 1 mm/s at the tip of the cone. Symmetric illumination gave rise to displacement of solvent from the microstructure due to shrinkage with a velocity in excess of 0.01 mm/s. This system could in principle be used for light-directed movement of micromechanical systems, optical control of microfluidics, or light activated chemical delivery.     

Photoactuation from a carbon nanotube-nafion bilayer composite

A bilayer composite of single walled carbon nanotubes (SWNTs) deposited onto Nafion exhibits substantial mechanical motion upon exposure to visible or near-infrared light. The magnitude of the actuation parallels the absorption spectrum of the SWNTs in the near-infrared, but the actuation diminishes in the visible and disappears in the UV portions of the spectrum. In the near-infrared region, the photoactuation is linear with respect to the light intensity. The photoactuation also appears to be associated with a photocurrent across the nanotube/Nafion interface. The proposed mechanism for the actuation is that band bending of the semiconducting SWNTs induces polarization of mobile hydrogen ions at the Nafion interface, which then causes swelling of the polymer.