No abstract

Peptide nucleic acids (PNAs) are a new class of DNA mimics in which the regular nucleobases of adenine, thymine, cytosine, and guanine are connected via a peptide-like backbone. PNA molecules retain the same Watson-Crick base pairing as regular oligonucleotides, with the added benefits of greater specificity and resistance to enzymatic digestion. While the use of PNAs has grown rapidly because of their potential applications in biotechnology, little work has been done on developing analytical procedures for characterizing them. We have found matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to be an effective tool for PNA analysis. PNA molecules survive the MALDI process intact and are easily ionized with almost no multiply-charged species. These features allow mixtures to be easily characterized. Traditional protein matrices (e.g., sinapinic acid,2,5-dihydroxybenzoic acid, alpha-cyano-4-hydroxycinnamic acid) were found to be superior to DNA matrices (e.g., trihydroxy-acetophenone, 3-hydroxypicolinic acid, picolinic acid). In addition, the new DNA matrix 6-aza-2-thiothymine worked well. The ability of MALDI-TOF-MS to ascertain PNA purity and sequence information at low picomole levels will be important as greater quality control of PNA synthesis is needed (e.g., when PNAs are used as antisense or antigene drugs).

The method of preparation and methods of analysis of a narrow distribution polystyrene of ∼7 ku used in an interlaboratory comparison of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) of synthetic polymers is described. Size exclusion chromatography was used to measure the polystyrene sample variability. Fourier transform infrared spectroscopy and MALDI-TOF-MS were used to analyze end groups on the polymer. The polystyrene was analyzed by MALDI-TOF-MS and classical methods of polymer characterization. The number (M n) and mass (M w) average of the molecular mass distribution (MMD) determined by the classical methods (light scattering and NMR) were compared with those obtained by MALDI-TOF-MS. Agreement between classical methods to obtain the moments of the MMD and the MALDI is found to be good overall. However, all the experimental values obtained by MALDI fell below the classical values. A discussion of why these values are lower is included. We discuss the statistical analysis of the data from the interlaboratory comparison conducted by NIST, which includes data from 23 different laboratories. Analysis of variance is used to examine the influences of the independent parameters (laboratory, matrix, instrument manufacturer, instrument mode) on the data. The parameters, laboratory and instrument manufacturer, were determined to have an influence on the MMD, where matrix and instrument mode were found not to have a significant influence.

A novel analytical method using PNA probes detected by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) was applied to type sequence polymorphisms within the human leukocyte antigen (HLA), DQA locus. Streptavidin-coated magnetic beads were used to immobilize biotinylated DNA. PNA probes representing possible alleles were then prepared for the immobilized DNA hybridization. The nonspecific PNA probes were removed with stringent washes. The PNA/DNA/beads conjugate was analyzed by MALDI-TOFMS. The genotype of the DNA was determined by the detected molecular masses of the released PNA probes. Reproducible and accurate genotyping was achieved by this analytical method.