General and facile purification of dye-labeled oligonucleotides by pH-controlled extraction.

Previously, we reported a method for facile purification of oligonucleotides labeled with hydrophobic dyes, based on the solubility difference between the hydrophilic DNA and unreacted dye. Here, we present a new purification method applicable to any dye regardless of its hydrophobicity. We exploited the population shift of a fluorescent dye in a low-pH aqueous solution from its anionic form toward its neutral form. When the pH of an aqueous solution containing dye-labeled DNA and unreacted free dye is lowered, and the solution is mixed with a hydrophobic organic solvent (butanol), the neutral free dye is preferentially dissolved in the organic phase, leaving behind the hydrophilic dye-labeled DNA in the aqueous phase. We experimentally verified that our new method results in high yields of dye-labeled oligonucleotides and the efficient removal of free dye.

Characterizing changes in snow crab (Chionoecetes opilio) cryptocyanin protein during molting using matrix-assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry.

RATIONALE: We report the matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) characterization of the cryptocyanin proteins of the juvenile Chionoecetes opilio crabs during their molting and non-molting phases. In order to assess the structural cryptocyanin protein differences between the molting and non-molting phases, the obtained peptides were sequenced by MALDI low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS). METHODS: The cryptocyanin protein was isolated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed by MALDI-TOF/TOF-MS. The purified cryptocyanin protein was sequenced, using the 'bottom-up' approach. After tryptic digestion, the peptide mixture was analyzed by MALDI-QqTOF-MS/MS and the data obtained were used for the peptide mass fingerprinting (PMF) identification by means of the Mascot database. RESULTS: It was demonstrated using MALDI-TOF/TOF-MS that the actual molecular weights of the non-molting and molting cryptocyanin proteins were different; these were, respectively, 67.6 kDa and 68.1 kDa. Using low-energy CID-MS/MS we have sequenced the trytic peptides to monitor the differences and similarities between the cryptocyanin molecular structures during the molting and non-molting stages. CONCLUSIONS: We have demonstrated for the first time that the actual molecular masses of the cryptocyanin protein during the molting and non-molting phases were different. The MALDI-CID-MS/MS analyses allowed the sequencing of the cryptocyanins after tryptic digestion, during the molting and non-molting stages, and showed some similarities and staggering differences between the identified cryptocyanin peptides.

Fluorescence characteristics of isolated dye molecules within silicalite-1 channels.

Fluorescence characteristics of hemicyanine dye molecules isolated from neighboring molecules and strongly restricted inside nanosized pores of zeolite (silicalite-1) crystal were investigated. For samples in which the molecules were sufficiently far away from the others, the fluorescence decay lifetime of the molecules was about 2.2 ns. As the intermolecular distance was reduced, the steady-state fluorescence peak shifted toward the longer wavelength and the fluorescence efficiency decreased markedly. The fluorescence decay lifetime also decreased to 0.8 ns for a sample with the smallest intermolecular distance of 2.1 nm. These results were explained in terms of a dipole-dipole interaction between pairs of dye molecules. From the relation between the intermolecular distances and the fluorescence decay lifetimes of the molecules, the radius of energy transfer of hemicyanine donor-acceptor pair in zeolite matrix was determined to be 2.2 nm, in fair agreement with the calculated Förster radius between dye molecules of the same species.

Utility of array CGH in molecular diagnosis of mitochondrial disorders.

Array comparative genomic hybridization (aCGH) is a powerful clinical diagnostic tool that can be used to evaluate copy number changes in the genome. Targeted aCGH provides a much higher resolution in targeted gene regions to detect copy number changes within single gene or single exon. A custom-designed oligonucleotide aCGH platform (MitoMet(®)) has been developed to provide tiled coverage of the entire 16.6-kb mitochondrial genome and high-density coverage of a set of nuclear genes associated with metabolic and mitochondrial related disorders, for quick evaluation of copy number changes in both genomes (1). The high-density probes in mitochondrial genome on the MitoMet(®) array allow estimation of mtDNA deletion breakpoints and deletion heteroplasmy (2). This technology is particularly useful as a complementary diagnostic test to detect large deletions in genes related to mitochondrial disorders.

Protein-protein interactions: an application of Tus-Ter mediated protein microarray system.

In this chapter, we present a novel, cost-effective microarray strategy that utilizes expression-ready plasmid DNAs to generate protein arrays on-demand and its use to validate protein-protein interactions. These expression plasmids were constructed in such a way so as to serve a dual purpose of synthesizing the protein of interest as well as capturing the synthesized protein. The microarray system is based on the high affinity binding of Escherichia coli "Tus" protein to "Ter," a 20 bp DNA sequence involved in the regulation of DNA replication. The protein expression is carried out in a cell-free protein synthesis system, with rabbit reticulocyte lysates, and the target proteins are detected either by labeled incorporated tag specific or by gene-specific antibodies. This microarray system has been successfully used for the detection of protein-protein interaction because both the target protein and the query protein can be transcribed and translated simultaneously in the microarray slides. The utility of this system for detecting protein-protein interaction is demonstrated by a few well-known examples: Jun/Fos, FRB/FKBP12, p53/MDM2, and CDK4/p16. In all these cases, the presence of protein complexes resulted in the localization of fluorophores at the specific sites of the immobilized target plasmids. Interestingly, during our interactions studies we also detected a previously unknown interaction between CDK2 and p16. Thus, this Tus-Ter based system of protein microarray can be used for the validation of known protein interactions as well as for identifying new protein-protein interactions. In addition, it can be used to examine and identify targets of nucleic acid-protein, ligand-receptor, enzyme-substrate, and drug-protein interactions.

Study of optimal temperature, pH and stability of dragon fruit (Hylocereus polyrhizus) peel for use as potential natural colorant.

The peel of Hylocereus polyrhizus is often regarded as a waste hence this study was aimed at exploring the feasibility of using the peel as a natural colorant using simple water extraction method. Samples were subjected to a series of temperatures: Room temperature (RT), 50, 80 and 100 degrees C; varied length of heating time from 1, 2, 3, 4, 5 and 10 min and a varied range of pH using 1 M of citric acid solution. The best condition to obtain highest betacyanin content was heating samples at 100 degrees C for 5 min in a pH 5 citric acid solution. The next part of this study involved the stability test of the pigments obtained through the best method determined earlier. The pigments were dried and resuspended in distilled water. The samples were then exposed to light to monitor pigment changes. Initial resuspension of the dried pigments yielded a comparable high content of betacyanins to its juice counterpart. The results showed that resuspended pigments had high pigment retention and were stable up to 7 days. These initial findings must be further studied in more controlled conditions to understand the stability of betacyanin. Nevertheless, the results show that betacyanin obtained from the peel of dragon fruit has a high potential to be used as a natural dye.

Application of microfluidic chip with integrated optics for electrophoretic separations of proteins.

This paper describes the fabrication, the characterization and the applications of a capillary electrophoresis microchip. This hybrid device (glass/PDMS) features channels and optical waveguides integrated in one common substrate. It can be used for electrophoretic separation and fluorimetric detection of molecules. The microfluidic performance of the device is demonstrated by capillary zone and gel electrophoresis of proteins.

Betacyanins and phenolic compounds from Amaranthus spinosus L. and Boerhavia erecta L.

Stem bark extracts of Boerhavia erecta L. (erect spiderling) and Amaranthus spinosus L. (spiny amaranth), two wild growing weed plants used in traditional African medicine, were characterized with respect to their phenolic profile including the betalains. While the main betalains in A. spinosus were identified as amaranthine and isoamaranthine, the major betacyanins in B. erecta were betanin, isobetanin together with neobetanin. The latter showed higher betalain concentrations amounting to 186 mg/100 g, while the former contained 24 mg betacyanins in 100 g of the ground plant material. Extracts of A. spinosus were found to contain hydroxycinnamates, quercetin and kaempferol glycosides, whereas catechins, procyanidins and quercetin, kaempferol and isorhamnetin glycosides were detected in B. erecta. The amounts of these compounds ranged from 305 mg/100 g for A. spinosus to 329 mg/100 g for B. erecta.

Cyanine-labeling reagents: sulfobenzindocyanine succinimidyl esters.

A synthetic method for shifting the absorption and emission wavelengths of cyanine dye labels by 15-30 nm to the red has been developed. This step significantly increases the potential for preparing fluorescent probes for multiparameter analysis in cytometry and diagnostics. The new sulfobenzindocyanine dyes contain succinimidyl esters as reactive groups and can be readily conjugated to antibodies, avidin, modified DNA, and other amino group-containing materials. The labeling reagents are water soluble, and their fluorescence is not sensitive to pH. One of the reagents, Cy3.205, can be optimally excited with the 568 nm Kr laser line and is useful for confocal microscopy and flow cytometry. Another dye, Cy5.205, can be excited with the 633 He-Ne or 647 nm Kr laser lines available with many flow cytometers and laser-scanning microscopes. New laser diodes emitting near 660-690 nm should also be excellent excitation sources for Cy5.205.