Negative ionization micro electrospray mass spectrometry of oligonucleotides and their complexes

The utility of negative ionization micro electrospray (microspray) mass spectrometry is demonstrated for detection of oligonucleotides and their non-covalent complexes. A simple microspray ionization source is fabricated from an outer stainless-steel needle and an inner fused-silica capillary. Under these conditions, the liquid flow rate can be reduced 15-fold from 7.5 microL/min to 0.5 microL/min. Studies of a 14-mer DNA oligonucleotide show no change in the charge-state distribution and quantity of adducted salt ions during the microspray process compared to pneumatically assisted electrospray mass spectrometry. The microspray ion source is less sensitive to the presence of solution buffers, and an 11-fold increase in integrated ion abundance from oligonucleotide analyte is observed with a 10 mM concentration of ammonium acetate, compared to pneumatically assisted nebulization (PAN). A > 100-fold increase in the duplex:single strand ratio for a 14-mer oligodeoxynucleotide and its complementary strand is observed using the microspray ion source relative to experiments performed with PAN. Studies of duplexes between DNA and a peptide nucleic acid suggest that this effect may be related to the degree of adduction of counterions to the DNA during ionization.