NONCOVALENT PROTEIN-OLIGONUCLEOTIDE INTERACTIONS MONITORED BY MATRIX-ASSISTED LASER DESORPTION IONIZATION MASS-SPECTROMETRY/

Positive ion mode matrix-assisted laser desorption/ionization mass spe ctrometry (MALDI-MS) was used to explore nonspecific interactions betw een proteins and oligonucleotides. The formation of noncovalent comple xes showed correlation with the type of oligonucleotide bases and with the amino acid composition of the proteins, Among the four DNA homool igomers, abundant protein-nucleic acid complexes were detected for pd( T)(n), whereas negligible attachment was evident for pd(A)(n), pd(C)(n ), and pd(G)(n). Mixed base sequence nucleic acids (pd(AGCTCAGCTT) and d(TTAGCAGCTT)) also showed affinity to Arg-Lys, The protein affinity of pd(T)(n) turned out to be nonspecific and produced a larger variety of complexes when the number of basic residues in the protein was inc reased. Complexation of pd(T)(n) with small basic dipeptides (Arg-Lys or His-His) led to significant improvement in the mass resolution for positive ions. For example, the mass resolution of the pd(T)(20)/Arg-L ys complex exhibited about 4 times improvement over pd(T)(20) alone. T he protein-oligonucleotide interactions were also pH and matrix depend ent. Lowering the pH from its original value (pH = 1.7) led to diminis hing complex related signal, whereas increasing the pH resulted in the appearance of a larger variety of complexes. 2,5-Dihydroxybenzoic aci d matrix demonstrated much greater tendency to produce complex ions th an did the three other matrix materials we tested. A possible explanat ion of the observed phenomena was based on pH-controlled ion pair form ation between oligonucleotides and proteins.