Structural characterization of oligonucleotide strands using electrospray ionization mass spectrometry

The structural diversity of deoxyribonucleie acid (DNA) plays a critical role in gene expression. Although a number of biophysical techniques have been used for the analysis of DNA structures and related binding, Electrospray Ionization Mass Spectrometry (ESI-MS) has demonstrated several unique advantages. The intrinsic features of the ESI MS for detection of the accurate molecular mass allow for the unambiguous identification of various complexes and binding stoichiometries. Fragmentation produced under collisional activation provides further information for investigating the binding sites and structural features. In addition, ESI MS produces multiple charged ions for a macromolecule and the charge state distributions of these macromolecules in the gas phase reflect their conformation in solution to a certain extent.;Secondly we found optimal conditions and detected the DNA duplexes, triplexes, and G-quadruplex. It was observed that the formation of the multi-stranded complexes depended on the concentration of ammonium acetate in solution. The formation of the triplex also depended on the pH. The strands produced intense peaks of complex ion in the gas phase also have a higher melting temperature in solution.;Finally, we studied the structure of an argininamide (Arm) binding DNA and its binding properties with Arm. The higher charge state distributions of the selected DNA aptamer suggested that the interactions of residues in the loop region. The intense peaks produced by DNA aptamer-Arm complex ion confirmed the specific binding. We also observed that the aptamer and its derivatives non-specifically bind with several Arms by electrostatic interactions. The ESI-MS spectra provided new insight into the interactions between DNA and Arms.;In this work, firstly we developed an ESI MS method to measure the charge state distributions of negative oligonucleotide ions with hairpin and linear structures. The results showed that the hairpin DNA demonstrated more intense peaks with higher charge state values than the linear strands. Furthermore it was observed that strands demonstrated higher charge state distributions in the gas phase also have a higher melting temperature in solution. The charge state distributions of the negative oligonucleotide ions in the gas phase reflected their conformation and stabilization in solution.