Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

We report the design, synthesis, and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy, and fluorescence depolarization measurements. The three-dye binary probe (BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system (BP-2d) was constructed with Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively slow FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.     

Reversible microwave-assisted cycloaddition of aziridines to carbon nanotubes

We report a new approach that uses microwaves to rapidly functionalize carbon nanotubes by using 1,3-dipolar cycloaddition of aziridines, well-known precursors to azomethine ylides, in solvent-free conditions. The efficiency of our microwave-mediated protocol is confirmed by comparison to a similar protocol in classical conditions for the azomethine ylides in DMF. Under these latter conditions, the reaction proceeds in 5 days (against 1 h under microwave irradiation), and the functionalization degree is much lower, as confirmed by thermogravimetric analysis and Raman spectroscopy. With our procedure, we easily scale-up the reaction up to 250 mg of functionalized MWNT in 1 h. We also provide an indirect proof of the covalent sidewall functionalization of the tubes.     

Quantitative carbamylation as a stable isotopic labeling method for comparative proteomics

A method was developed that uses urea to both solublize and isotopically label biological samples for comparative proteomics. This approach uses either light or heavy urea ((12)CH(4)(14)N(2)O or (13)CH(4)(15)N(2)O, respectively) at a concentration of 8 M and a pH of 7 to dissolve the samples prior to digestion. After the sample is digested using standard proteomic protocols and dried, isotopic labeling is completed by resuspending the sample in a solution of 8 M urea at a pH of 8.5, using the same isotopic species of urea as used for digestion and incubating for 4 h at 80 degrees C. Under these conditions, carbamylation occurs only on the primary amines of the peptides. The effects of complete carbamylation on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS) (collision-induced dissociation (CID)) were examined. Peptides that had a C-terminal carbamylated lysine residue were found to have a reduced intensity when viewed by MALDI-TOFMS. CID of a tryptic peptide that was carbamylated on both the N-terminus and the C-terminus was found to have a more uniform distribution of b- and y-ions, as well as prominent ions from loss of water. Reversed-phase chromatography coupled to ESI-MS/MS was used to identify and quantify the isotopically labeled standard proteins, bovine serum albumin (BSA), bovine transferrin, and bovine alpha-casein. Quantitative error between theoretical and observed data ranged from 1.7-10.0%. Relative standard deviations for protein quantitation ranged from 5.2-27.8% over a dynamic range from 0.1-10 (L/H). The development of a method utilizing urea-assisted carbamylation of lysines and N-termini to globally labeled samples for comparative proteomics may prove useful for samples that require a strong chaotrope prior to proteolysis.     

Structures of the high-temperature solid phases of the odd-numbered fatty acids from tridecanoic acid to tricosanoic acid

Crystal structures of the high-temperature phases of odd-numbered fatty acids (C(n)H(2n-1)OOH) from tridecanoic acid (C(13)H(25)OOH) to tricosanoic acid (C(23)H(45)OOH) are presented in this article. They have been determined from high-quality X-ray powder-diffraction patterns. Two types of high-temperature phases are adopted: one monoclinic A2/a with Z=8 for the fatty acids with n=13 and n=15, denoted as C', and one monoclinic P2(1)/a with Z=4 for the longer-chain fatty acids, denoted as C'. It appears that the packing arrangement of the alkyl chains and of the carboxyl groups is similar in all of the structures. However, the arrangement at the methyl-group interface differs between the C' and C' forms. A survey of the intermolecular interactions involved in these polymorphs coupled with a study of the effects of temperature on the structures have led us to a better understanding of the arrangement of the molecules within the high-temperature solid phases of odd-numbered fatty acids.     

Analysis of mitochondrial DNA for authentication of meats from chamois (Rupicapra rupicapra), pyrenean ibex (Capra pyrenaica), and mouflon (Ovis ammon) by polymerase chain reaction-restriction fragment length polymorphism

The prevention of fraudulent labeling of game meat constitutes an important part of food regulatory control and quality assurance systems. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis based on mitochondrial deoxyribonucleic acid (DNA) was developed for authentication of meats from chamois (Rupicapra rupicapra), pyrenean ibex (Capra pyrenaica), and mouflon (Ovis ammon). Amplification and restriction site analysis of a DNA fragment about 720 base pairs (bp) from the mitochondrial 12S rRNA gene of all analyzed species permitted the selection of Msel and Apol endonucleases for meat speciation. The 12S rRNA restriction profiles obtained allowed the unequivocal identification of chamois, pyrenean ibex, and mouflon/sheep and their differentiation from meats of domestic species such as cattle, goat, and swine. The highly variable mitochondrial D-loop gene was also targeted to attempt discrimination between mouflon and sheep meats. A D-loop region (700-1000 bp) was amplified and sequenced in all game and domestic species analyzed, and a primer set was designed for the selective amplification of a 370 bp DNA fragment from mouflon and sheep. PCR-RFLP analysis with the selected Maell enzyme generated a single electrophoretic profile characteristic for sheep, whereas 3 different fragment patterns were obtained for mouflon meats. Consequently, the PCR-RFLP technique developed can be routinely applied in inspection programs in order to verify the correct labeling of game species.     

Temperature and pH-Sensitive Polymers with Hydrophobic Spacers for the Controlled Delivery of Drugs

Summary: Acid methacrylates containing hydrophobic aliphatic and aromatic spacers were used to prepare pH-sensitive ampholytic hydrogels and bidimensional temperature- (T) and pH-sensitive hydrogels. Their swelling behaviour was studied by changing the pH and temperature of buffer solutions. Salicylamide, salicylic acid and green fluorescent protein (GFP) as model drugs were loaded into the gels and their release kinetics studied under simulated gastric and intestinal conditions. T- and pH-sensitive hydrogels containing aliphatic spacers show sustained release of analgesics depending on pH (e.g. 7.4); while longer aliphatic spacers resulted in drug release depending on pH and temperature (T < transition T). GFP was released from temperature- and pH-sensitive ampholytic hydrogels after different lag times depending on hydrogel composition.     

Quantum semiempirical studies on the formation of aromatic polyamides, 1. Effect of structural parameters of diamines on the polyamidation reaction

A semiempirical quantum-mechanical study of structural and electronic parameters of aromatic diamines was performed using the method AM1. The diamines have been considered as condensation monomers, and the reactivities of both amino groups against acyl chlorides have been computed. The study shows that the amidation reaction is controlled mainly by the global charge on the amino group and, in a much smaller extent, by the frontier orbitals. This behaviour is consistent with the large energy gap between the HOMO 1

1 HOMO: highest occupied molecular orbital.

of the diamine and the LUMO 2

2 LUMO: lowest unoccupied molecular orbital.

of the acyl chloride. It has been found also that the electronic nature of the substituents, affecting the charge of the amino groups, greatly affects the carbons directly joined to these groups. This permits to correlate the reactivities with the calculated charges on these carbons:     

Energetic Cost of Statistical Order-Degree Change in a Fermions’ Set

We discuss novel many-fermions thermodynamics’ features. They refer to the energy cost associated to order-disorder changes. Our thermal quantum statistical scenario is controlled by suitable fermion-fermion interactions. We deal with two well-known quantum interactions that operate within an exactly solvable model. This model is able to adequately describe some aspects of fermion-dynamics, particularly level-crossings. We describe things via employment of Gibbs’ canonical ensemble strictures. We show that judicious manipulation of the energy cost associated to statistical order (disorder) variations generates useful information-quantifiers. The underlying idea is that changes in the degree of order are intimately linked to level-crossings energetic costs.