We have developed a microfabricated analytical device on a glass chip that performs a protein sizing assay, by integrating the required separation, staining, virtual destaining, and detection steps. To obtain a universal noncovalent fluorescent labeling method, we have combined on-chip dye staining with a novel electrophoretic dilution step. Denatured protein-sodium dodecyl sulfate (SDS) complexes are loaded on a chip and bind a fluorescent dye as the separation begins. At the end of the separation channel, an intersection is used to dilute the SDS below its critical micelle concentration before the detection point. This strongly reduces the background due to dye molecules bound to SDS micelles and also increases the peak amplitude by 1 order of magnitude. Both the on-chip staining and SDS dilution steps occur in the 100-ms time scale and are approximately 10(4) times faster than their conventional counterparts in SDS-PAGE. This represents a much greater speed increase due to microfabrication than has been obtained in other assay steps such as electrophoretic separations. We have designed and tested a microchip capable of sequentially analyzing 11 different samples, with sizing accuracy better than 5% and high sensitivity (30 nM for carbonic anhydrase).

A scanning mobility particle sizer (SMPS) allows size separation of gas phase particles according to their electrophoretic mobilities. The addition of an electrospray source (ES) recently allowed extension of SMPS analysis to the macromolecular range. We demonstrate here the application of ES-SMPS to nucleic acids analysis. Single- and double-stranded DNA molecules ranging from 6.1 kDa (single-stranded DNA 20 nucleotides in length) to 300 kDa (500 base-pair double-stranded DNA) were separated and detected by ES-SMPS at the picomole to femtomole levels. The measured electrophoretic mobility diameters were found to correlate with the analytes' molecular weights, while the peak areas could yield quantitative information. No fragmentation of DNA was observed under the conditions employed. Different apparent densities were observed for single-stranded and double-stranded DNAs, showing a different behavior for each type of biomolecule. The total analysis time was about 3 min/spectrum. Further optimization of ES-SMPS is expected to make it a fast and sensitive technique for biopolymer characterization.

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Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has in recent years significantly advanced the field of polymer analysis. However, the mechanisms of the desorption and ionization processes, and in particular the critical role played by the matrix, remain unclear. In the present work, the usual matrix is replaced with a self-assembled monolayer consisting of a UV absorbing matrix-like compound covalently linked to a gold surface. Analytes such as proteins or oligonucleotides are directly deposited on the covalently modified probe tips and mass analyzed by laser desorption time of flight (TOF) mass spectrometry. Several types of monolayers were investigated and tested for their ability to produce positive and negative analyte ions. Molecular ion signals were obtained for dT10 oligonucleotides and proteins as large as cytochrome C on monolayers of methyl N-(4-mercaptophenyl)carbamate (MMPC). The amenability of this model system to characterization with established physical and chemical methods should help investigate the processes involved in MALDI.