Comparison of direct infusion and on-line liquid chromatography/electrospray ionization mass spectrometry for the analysis of nucleic acids.
The applicability of ion-pair reversed-phase high-performance liquid chromatography/electrospray ionization mass spectrometry (IP-RP-HPLC/ESI-MS) and direct infusion/ESI-MS to the characterization of nucleic acid mixtures was evaluated by the analysis of the reaction products obtained from solid-phase synthesis of a 39-mer oligonucleotide. IP-RP-HPLC/ESI-MS was performed using 200 microm i.d. capillary columns packed with octadecylated, micropellicular poly(styrene-divinylbenzene) particles and applying gradients of acetonitrile in 50 mM triethylammonium bicarbonate (TEAB). Three different solvent systems were utilized for direct infusion/ESI-MS with removal of metal cations by on-line cation exchange: (1) 10 mM triethylamine (TEA) in 50% aqueous acetonitrile, (2) 2.2 mM TEA, 400 mM hexafluoro-2-propanol (HFIP) in 20% aqueous methanol and (3) 50 mM TEAB in 10% aqueous acetonitrile. Owing to its separation capability, the highest selectivity and specificity were achieved with IP-RP-HPLC/ESI-MS, which, apart form the 39-mer target sequence, allowed the identification of two isobutyryl-protected target sequences and a 10-mer and 20-mer failure sequence. Direct infusion/ESI-MS with TEA-acetonitrile or TEA-HFIP-methanol as solvent revealed signals for the 39-mer in the m/z range 700-1600. The presence of derivatives containing one, two, three and four isobutyryl groups indicated that the hydrolysis of the protecting groups after solid-phase synthesis was not complete. Failure sequences could not be identified by direct infusion/ESI-MS under conditions favoring multiple charging of the analytes owing to the high chemical background and coincidental overlapping of m/z signals. However, efficient charge state reduction upon addition of carbonic acid to the electrosprayed solvent shifted the signals of the 39-mer and derivatives to m/z values >2400 and allowed the detection of seven different failure sequences, ranging from the 8-mer to the 23-mer, in the mixture.
Institute of Analytical Chemistry and Radiochemistry, Leopold Franzens University, Innsbruck, Austria. Christian.Huber@uibk.ac.at
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Krajete
D001483:Base Sequence; D001639:Bicarbonates; D002197:Capillary Action; D002852:Chromatography, Ion Exchange / Q000379:methods; D002853:Chromatography, Liquid / Q000379:methods; D007202:Indicators and Reagents; D013058:Mass Spectrometry / Q000379:methods; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011137:Polystyrenes; D012997:Solvents
D001639:Bicarbonates; D007202:Indicators and Reagents; D009838:Oligodeoxyribonucleotides; D011137:Polystyrenes; D012997:Solvents; C041737:triethylammonium bicarbonate; C003771:Amberlite XAD-2 resin