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Displacement of the loosely encapsulated fluorescent indicator coumarine 343 (F) from a dicopper(II) cryptate enables the selective fluorimetric detection of the HCO3 (-) ion (A) in water (see scheme, •○=Cu(2+) ). The fluorophore is quenched when encapsulated, but displays its full emission when released to the solution.
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Well-defined supramolecular assemblies of Zn and free-base porphyrins are constructed through the formation of amidinium-carboxylate salt bridges. A one-to-one donor-acceptor pair and a four-to-one antenna-type assembly are investigated. The steady-state and time-resolved fluorescence measurements unequivocally showed that efficient singlet-singlet excited energy transfer from the Zn-porphyrin complex to the free-base porphyrin takes place in these assemblies. Indeed, the observed energy-transfer rates in both types of assemblies are much faster than those the Förster mechanism would suggest, implying the involvement of an intermolecular through-bond mechanism.
Novel photo- and electroactive triads, in which pi-conjugated p-phenylenevinylene oligomers (oPPVs) of different length are connected to a photoexcited-state electron donor (i.e., zinc tetraphenylporphyrin) and an electron acceptor (i.e., C(60)), were designed, synthesized, and tested as electron-transfer model systems. A detailed physicochemical investigation, concentrating mainly on long-range charge separation and charge recombination and kinetics, revealed small attenuation factors beta of 0.03+/-0.005 A(-1). Energy matching between the HOMO levels of C(60) and oPPVs emerged as a key parameter for supporting molecular-wire-like behavior: It favors rapid and efficient electron or hole injection into the oPPV wires. Large electronic coupling values were determined as a result of paraconjugation in the oPPV moieties.
Two triads (donor-spacer-acceptor), exTTF-BN-C60 (6) and ZnP-BN-C60 (7), in which electron donors (i.e., exTTF or ZnP) are covalently linked to C60 through a chiral binaphthyl bridge (BN), have been prepared in a multistep synthetic procedure starting from a highly soluble enantiomerically pure binaphthyl building block (1). Unlike other oligomeric bridges, with binaphthyl bridges, the conjugation between the donor and the acceptor units is broken and geometric conformational changes are facilitated. Consequently, distances and electronic interactions between the donor and C60 are drastically changed. Both donor-spacer-acceptor (D-s-A) systems (i.e., 6 and 7) exhibit redox processes that correspond to all three constituent electroactive units, namely, donor, BN, and C60. Appreciable differences were, however, observed when comparing triad 6, in which no significant exTTF-C60 interactions were noted, with D-s-A 7, whose geometry favors donor-acceptor and pi-pi interactions that result in ZnP-C60 electronic communication. This through-space interaction is, for example, reflected in the redox potentials. Excited-state studies, carried out by fluorescence and transient absorption spectroscopy, also support through-space rather than through-bond interactions. Although both triads form the corresponding radical-ion pair, that is, exTTF*+-BN-C60*- and ZnP*+-BN-C60*-, dramatic differences were found in their lifetimes: 165 micros and 730 ns, respectively.
BACKGROUND: Fluorescence Correlation Spectroscopy is a powerful method to analyze densities and diffusive behavior of molecules in membranes, but effects of photodegradation can easily be overlooked. METHOD: Based on experimental photophysical parameters, calculations were performed to analyze the consequences of photobleaching in fluorescence correlation spectroscopy (FCS) cell surface experiments, covering a range of standard measurement conditions. RESULTS: Cumulative effects of photobleaching can be prominent, although an absolute majority of the fluorescent molecules would pass the laser excitation beam without being photo-bleached. Given a distribution of molecules on a cell surface with different diffusive properties, the fraction of molecules that is actually analyzed depends strongly on the excitation intensities and measurement times, as well as on the size of the reservoir of freely diffusing molecules. Both the slower and the faster diffusing molecules can be disfavored. CONCLUSIONS: Apart from quantifying photobleaching effects, the calculations suggest that the effects can be used to extract additional information, for instance about the size of the reservoirs of free diffusion. By certain choices of measurement conditions, it may be possible to more specifically analyze certain species within a population, based on their different diffusive properties, different areas of free diffusion, or different kinetics of possible transient binding.
The cis-syn cyclobutane pyrimidine dimer (CPD) is the major photoproduct induced in DNA by low wavelength ultraviolet radiation. An improved method was developed to detect CPD formation and removal in genomic DNA that avoids the problems encountered with the standard method of endonuclease detection of these photoproducts. Since CPD-specific endonucleases make single-strand cuts at CPD sites, quantification of the frequency of CPDs in DNA is usually done by denaturing gel electrophoresis. The standard method of ethidium bromide staining and gel photography requires more than 10 microg of DNA per gel lane, and correction of the photographic signal for the nonlinear film response. To simplify this procedure, a standard Southern blot protocol, coupled with phosphorimage analysis, was developed. This method uses random hybridization probes to detect genomic sequences with minimal sequence bias. Because of the vast linearity range of phosphorimage detection, scans of the signal profiles for the heterogeneous population of DNA fragments can be integrated directly to determine the number-average size of the population.
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Thermodynamic integration is a widely used method to calculate and analyze the effect of a chemical modification on the free energy of a chemical or biochemical process, for example, the impact of an amino acid substitution on protein association. Numerical fluctuations can introduce large uncertainties, limiting the domain of application of the method. The parametric energy function describing the chemical modification in the thermodynamic integration, the "Alchemical path," determines the amplitudes of the fluctuations. In the present work, I propose a measure of the fluctuations in the thermodynamic integration and an approach to search for a parametric energy path minimizing that measure. The optimal path derived with this approach is very close to the theoretical minimum of the measure, but produces nonergodic sampling. Nevertheless, this path is used to guide the design of a practical and efficient path producing correct sampling. The convergence with this practical path is evaluated on test cases, and compares favorably with that of other methods such as power or polynomial path, soft-core van der Waals, and some other approaches presented in the literature.
When retrieving information from memory, a number of contextual cues may interact to determine which ideas will be easily accessible. Even the simplest case in which joint cue action obtains (two cues) is very revealing of the principles of memory access and representation of compounds. Mechanisms by which dual cues interact to constrain retrieval from episodic memory are considered. A holistic mechanism of cue integration is contrasted with two nonholistic mechanisms: a multiplicative or intersection mechanism and an independent-contributions mechanism. Holistic- and intersection-cuing mechanisms are consistent with different variants of compound cue models of priming. The independent cuing mechanism is consistent with spreading activation models of priming. Data from four experiments which examined dual-cued recognition of items from (newly learned) triples demonstrated strongly configural, holistic, action of dual cues. The two cues and test item must form an encoded compound to yield cuing advantages. Two independent cues to the test item are ineffective if the two cues and test were not learned together as a triple; one valid and one invalid cue are also ineffective. This is so despite the availability of pairwise information for each cue-test relation, and despite the fact that these cues are effective when operating alone. A compound cue model which predicts precisely this surprising pattern of priming is developed. The compound cue model also predicts previously obtained configural priming of associative judgments, as well as the bias priming generally observed in item recognition and similar paradigms.
Using a density functional method we study how the correlations between particles adsorbed in neighboring pores, forming a network of slit-like pores, influence the capillary condensation and the structure of adsorbed Lennard-Jones fluid. The calculations indicate that if the distance between two pores is small enough, these correlations lead to pronounced changes in the density profiles, to an increase of the critical temperature, and to the modifications in the coexistence envelope. Copyright 2000 Academic Press.
We discuss the formulation of free energy functionals that describe the formation of structure in partially folded proteins. These free energy functionals take into account the inhomogeneous nature of contact energies, chain entropy and cooperative contributions reflecting the many body character of some folding forces like hydrophobicity, but do not directly account for non-native contacts because they assume the validity of the minimal frustration principle. We show how the free energy functionals can be used to interpret experiments on partially folded proteins that probe the fractional occupancy of specific local structures. In particular, we study the hydrogen protection factors in lysozyme studied in transient experiments by Gladwin and Evans and by Nash and Jonas using equilibrium pressure denaturation and the NMR order parameters measured by Dobson and Kim for the homologous protein alpha-lactalbumin.
Novel heterodimeric coiled-coil pairs were selected simultaneously from two DNA libraries using an in vivo protein-fragment complementation assay with dihydrofolate reductase, and the best pair was biophysically characterized. We randomized the interface-flanking e and g positions to Gln, Glu, Arg or Lys, and the core a position to Asn or Val in both helices simultaneously, using trinucleotide codons in DNA synthesis. Selection cycles with three different stringencies yielded sets of coiled-coil pairs, of which 80 clones were statistically analyzed. Thereby, properties most crucial for successful heterodimerization could be distinguished from those mediating more subtle optimization. A strong bias towards an Asn pair in the core a position indicated selection for structural uniqueness, and a reduction of charge repulsions at the e/g positions indicated selection for stability. Increased stringency led to additional selection for heterospecificity by destabilizing the respective homodimers. Interestingly, the best heterodimers did not contain exclusively complementary charges. The dominant pair, WinZip-A1B1, proved to be at least as stable in vitro as naturally occurring coiled coils, and was shown to be dimeric and highly heterospecific with a K(D) of approximately 24 nM. As a result of having been selected in vivo it possesses all characteristics required for a general in vivo heterodimerization module. The combination of rational library design and in vivo selection presented here is a very powerful strategy for protein design, and it can reveal new structural relationships.