Poor detection limits and strong salt effects are two of the main problems encountered in the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric analysis of DNA. This work demonstrates that a probe tip with a paraffin wax film (Parafilm) surface improves the MALDI performance in DNA analysis compared to the commonly used metal surface. First, the use of Parafilm increases the detection sensitivity. It was found that the detection limit achieved with Parafilm was 5 times better than that obtained using stainless steel for a 85mer. More importantly, the Parafilm method could improve detection of larger DNA components in the presence of a large excess of a smaller DNA component or in a DNA mixture. This feature is important to analyses of PCR and sequencing products. Second, we found that the use of Parafilm increased the salt tolerance limits for the 17-, 41-, and 85mers studied in this work and that the salt effect was less sensitive to the DNA size. Third, this method offers other analytical benefits, including producing a more homogeneous coverage of matrix/DNA, adding no extra cost and time to sample preparation, and eliminating the commonly required step for cleaning the probe after analysis. In this paper, we will also present our perspectives on why the use of Parafilm can improve the MALDI-TOF performance in DNA analysis.

Although atomic-resolution crystal structures of the conserved C-terminal domain of several species of TBP and their complexes with DNA have been determined, little information is available concerning the structure in solution of full-length TBP containing both the conserved C-terminal and nonconserved N-terminal domains. Quantitation of the amino acid side chain oxidation products generated by synchrotron X-ray radiolysis by mass spectrometry has been used to determine the solvent accessibility of individual residues in monomeric Saccharomyces cerevisiae TATA binding protein (TBP) free in solution and in the TBP-DNA complex. Amino acid side chains within the C-terminal domain of unliganded full-length TBP that are predicted to be accessible from crystal structures of the isolated domain are protected from oxidation. Residues within the N-terminal domain are also protected from oxidation in both the absence and presence of DNA. Some residues within the DNA-binding "saddle" of the C-terminal domain are protected upon formation of a TBP-DNA complex as expected, while others are protected in both the absence and presence of bound DNA. In addition, residues on the upper side of the beta-sheets undergo reactivity changes as a function of DNA binding. These data suggest that the DNA-binding saddle of monomeric unliganded yeast TBP is only partially accessible to solvent, the N-terminal domain is partially structured, and the N- and C-terminal domains form a different set of contacts in the free and DNA-bound protein. The functional implications of these results are discussed.

The main problem encountered in the MALDI-TOF analysis of polydisperse polymers is mass discrimination against high-mass oligomers. This work investigated some of the causes of this problem by using PMMAs as the polymer analytes. It was found that both instrumental and matrix factors could lead to this problem. Among the instrumental factors, detector saturation resulting from strong signals of matrix-related and low-mass oligomer ions can be a potential major cause of this problem. Since most of the ion detectors do not have an adequate dynamic range to avoid saturation, detection saturation could be a fundamental limitation, especially when the molar ratio of high- to low-mass oligomers is small. A quantitative analysis was also performed to examine the matrix effect. IAA and HABA were selected for this study. It was found that mass discrimination occurred in both cases, but the use of HABA led to more profound mass discrimination. This shows that the use of improper matrixes could be another source causing mass discrimination. Hence, unless new approaches are developed, one must be cautious in using MALDI-TOF for directly measuring MWDs of polydisperse polymers, especially those highly polydisperse polymers.

The effect of the matrix on poly(ethylene glycol) (PEG) cationization was investigated using an equimolar mixture of CsCl and LiCl as cationizing agents. It was observed that for both carboxylic acid and non-carboxylic acid matrices used, PEG cationization by a given alkali metal ion depends on the matrix used. For example, cesiated PEG ion intensities were much stronger than those of the corresponding lithiated PEG ions when equimolar concentrations of Cs(+) and Li(+) were present and IAA (indolacrylic acid) was the matrix. However, an opposite result was obtained when the same experimental conditions were utilized, but with HABA (2-(4-hydroxyphenylazo)benzoic acid) in place of IAA as the matrix.

Structural effects on polyether cationization in matrix-assisted laser desorption/ionization (MALDI) are investigated using three different polyethers: PEG (polyethylene glycol), PPG (polypropylene glycol), and PTHF (polytetrahydrofuran). This study was performed using equimolar cesium and lithium chlorides as the cationizing agent. It was observed that the polyether structure variation led to a substantial change in polyether selectivity for alkali metal ion complexation. Moreover, it was found that like PEG, PPG displays a different selectivity for Cs+ and Li+ with different matrices. Discussion of these results and their implication in MALDI are given.