Spectroscopic and photophysical properties of dUTP and internally DNA bound fluorophores for optimized signal detection in biological formats

Efficient signal generation in DNA-based assays requires understanding of the influence of fluorophore's interactions on the spectroscopic properties. The resulting changes in fluorescence intensity, quantum yield, emission anisotropy, and fluorescence lifetime provide straightforward tools for the study of molecular dynamics and interaction between labels and nucleic acids. Searching for bright fluorescent reporters for rolling circle amplification (RCA) as efficient signal enhancement strategy for biological formats, we investigated the spectroscopic properties of seven dyes: cyanines, rhodamines, and BODIPYs. They spectrally resemble Cy3, the most frequently used fluorophore in biodetection formats, and are measured in six samples (free dye, dye-dUTP, internally labeled ssDNA and dsDNA-single- and triple-labeled) using steady-state and time-resolved fluorometry. Special emphasis was dedicated to characterizing the nature of the interaction of these fluorophores differing in dye class, charge, and rigidity. Our results suggest dye charge and structure as main factors governing the dye's interactions, with DY-555 and Cy3B presenting the best candidates for our envisaged signal amplification strategy. This label comparison underlines the importance of a proper understanding of structure-property relations and dye-biomolecule interactions for reporter choice and presents a road map towards the design and interpretation of experiments using these labels on DNA of known sequence.     

Determination of gadolinium-based MRI contrast agents in biological and environmental samples: A review

The development of analytical methods and strategies to determine gadolinium and its complexes in biological and environmental matrices is evaluated in this review.     

Ordinary Papers

This paper deals with the systems of algebraic equations arising in the application of implicit Runge-Kutta methods.Equivalent conditions under which three wide classes of differential equations have unique solutions are presented. In addition, sufficient conditions for their existence are given.     

Continuous production of butanol with immobilized cells ofClostridium acetobutylicum

Spores ofClostridium acetobutylicum were immobilized in calcium alginate. An active gel preparation was obtained after outgrowth of the spores to vegetative cells within the gel matrix. A 100 mL column containing the immobilized cells was used for continuous production. At steady-state conditions the productivity of butanol was 67 g/L reactor volume/day.     

The recognition of nucleotides with model beta-hairpin receptors: investigation of critical contacts and nucleotide selectivity

[reaction: see text] We have investigated the factors that contribute to binding of ATP by a designed 12-residue beta-hairpin peptide, WKWK, and have determined its selectivity for binding to the naturally occurring nucleotide triphosphates. We have previously shown that WKWK creates an ATP binding pocket on one face of the beta-hairpin consisting of two Trp and two Lys residues. Mutation of the two Lys residues on the binding face of the beta-hairpin resulted in a lower affinity, indicating that each is involved in ATP binding and that each residue contributes approximately -1.5 kcal/mol to the energy of complexation. Replacement of either Trp residue of the ATP binding pocket with Phe or Leu destabilizes the complex formed with ATP by approximately 1 kcal/mol, indicating that both Trp residues participate in interactions with ATP. For binding to the nucleotide triphosphates, the order of binding affinity was shown to follow dTTP > GTP > ATP > CTP, with differences in binding energies spanning as much as 1.6 kcal/mol. NMR analysis demonstrates that both aromatic interactions with the Trp side chains and CH-pi interactions between the ribose protons and the Trp residues may contribute significantly to binding. The results from our model system provide useful thermodynamic information regarding protein-nucleic acid interactions that occur at the surface of a beta-sheet.     

A study of the stereochemistry of 2-aryl-4,5-dimethyl-1,3-dioxolanes by cholesteric induction in nematic phases and circular dichroism spectroscopy

[Chemical reaction: See text] The circular dichroism spectra and the twisting ability of a series of 2-aryl-4,5-dimethyl-1,3-dioxolanes used as dopants in nematic solvents have been related to their absolute configuration. Whereas the circular dichroism (CD) spectra are deeply affected by the substituents present in the aromatic ring, which in several cases cause sign inversion, the helical twisting power beta is only marginally influenced. The values of beta also seem not very sensitive to the rotamer population around the aromatic ring; this indicates the predominant importance of the chiral dioxolane ring in determining the cholesteric induction. These facts can be explained by the different nature of the two observables: in CD, the chirality is read by the absorbing chromophore and is deeply influenced even by small changes of this group. In cholesteric induction we are dealing instead with chiral solute-solvent interactions that determine a twist in the solvent. In light of the present and previous results, this process seems predominantly determined by short-range interactions, which are modulated by the molecular shape. From a practical point of view, a configurational correlation using CD for the present series of compounds seems problematic, while the values of beta are nicely correlated to the absolute configurations. Calculations with the surface chirality method predict well the sign and order of magnitude of beta and their limited sensitivity to the phenyl substituents and rotamer population.     

An acid-catalyzed Michael-aldol reaction

A tricyclic ketone is formed from cyclohexanone and cyclohexenone in strong acid solutions. The structure is confirmed by X-ray crystallography.