title: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the analysis of RNase H cleavage products.
abstract: RNase H is an endonuclease which cleaves RNA at points of hybridization with DNA. However, certain ambiguities exist in terms of its specificity and location of cleavage along the RNA strand. The analysis of RNase H reaction products of an oligoribonucleotide hairpin by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF-MS) is demonstrated. The oligoribonucleotide studied has a highly stable secondary structure which reduces the efficiency of hybridization with the chimeric oligonucleotide used to direct RNase H cleavage. By monitoring the reaction products under different conditions using MALDI/TOF-MS, the optimum variables for cleavage of this highly stable hairpin structure can be determined.
authors.affiliation: Department of Chemistry, Louisiana State University, Baton Rouge 70803, USA.
authors.forename: L M
authors.initials: LM
authors.lastname: Polo
authors.forename: P A
authors.initials: PA
authors.lastname: Limbach
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002851:Chromatography, High Pressure Liquid; D066298:In Vitro Techniques; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D016914:Ribonuclease H / Q000378:metabolism*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D013379:Substrate Specificity
chemical_list: D009843:Oligoribonucleotides; D016914:Ribonuclease H