Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the analysis of RNase H cleavage products

RNase H is an endonuclease which cleaves RNA at points of hybridization wit h DNA. However, certain ambiguities exist in terms of its specificity and l ocation of cleavage along the RNA strand. The analysis of RNase H reaction products of an oligoribonucleotide hairpin by matrix-assisted laser desorpt ion/ionization time-of-flight mass spectrometry (MALDI/TOF-MS) is demonstra ted. The oligoribonucleotide studied has a highly stable secondary structur e which reduces the efficiency of hybridization with the chimeric oligonucl eotide used to direct RNase H cleavage. By monitoring the reaction products under different conditions using MALDI/TOF-MS, the optimum variables for c leavage of this highly stable hairpin structure can be determined. (C) 1998 John Whey & Sons, Ltd.