PEPTIDE NUCLEIC-ACID CHARACTERIZATION BY MALDI-TOF MASS-SPECTROMETRY

Peptide nucleic acids (PNAs) are a new class of DNA mimics in which th e regular nucleobases of adenine, thymine, cytosine, and guanine are c onnected via a peptide-like backbone, PNA molecules retain the same Wa tson-Crick base pairing as regular oligonucleotides, with the added be nefits of greater specificity and resistance to enzymatic digestion, W hile the use of PNAs has grown rapidly because of their potential appl ications in biotechnology, little work has been done on developing ana lytical procedures for characterizing them, We have found matrix-assis ted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectr ometry to be an effective tool for PNA analysis. PNA molecules survive the MALDI process intact and are easily ionized with almost no multip ly-charged species. These features allow mixtures to be easily charact erized. Traditional protein matrices (e.g., sinapinic acid, 2,5-dihydr oxybenzoic acid, alpha-cyano-4-hydroxycinnamic acid) were found to be superior to DNA matrices (e.g., trihydroxy-acetophenone, 3-hydroxypico linic acid, picolinic acid). In addition, the new DNA matrix 6-aza-2-t hiothymine worked well. The ability of MALDI-TOF-MS to ascertain PNA p urity and sequence information at low picomole levels will be importan t as greater quality control of PNA synthesis is needed (e.g., when PN As are used as antisense or antigene drugs).