Qualitative and quantitative DNA and RNA analysis by matrix-assisted laser desorption/ionization time-of-flight mass...

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) gives extremely precise reading of mass-to-charge ratios (two analytes differ by 1 Da can be distinguished) and provides high sensitivity (less than 1 fmole of a DNA oligonucleotide can be detected), allowing DNA quantifications with single base specificity and single DNA molecule sensitivity (coupled with polymerase chain reaction [PCR]). To quantify a DNA sequence of interest, a competitive synthetic (60-80 bases) oligonucleotide standard with an artificial single base mutation in the middle is introduced, and these two virtually identical sequences are co-amplified by PCR. A third primer (extension primer) is designed to anneal to the region immediately upstream of the mutation site. Depending on the specific mutation introduced and the ddNTP/dNTP mixtures used, either one or two bases are added to the extension primer to produce two extension products from the two templates. Last, the two extension products are detected and quantified by high-throughput MALDI-TOF MS. In addition, with an improved primer extension method called single allele base extension reaction (SABER), rare mutant DNA can be robustly detected even when normal DNA is present at 50-fold or more than the DNA mutants.