Hairpin vs. Linear Conformation of DNA Strands Studied by Electrospray Ionization Mass Spectrometry

Development of electrospray ionization mass spectrometry (ESIMS) has demonstrated a wide range of applications in analysis of nucleic acid, which include precise determination of molecular mass of various DNA strands and detection of noncovalent DNA complexes. An intrinsic property of ESI-MS is that generates multiply charged ions for macromolecules. This has been applied for structural conformational determination of proteins. However, little work addressed using ESI-MS how to determine DNA association in a single stranded chain. In this work we designed three sets of DNA strands, each set of DNA strands have same base composition but different sequences, therefore, some of strands can fold into hairpin conformation and some absent of complementary base pairing and keep linear conformation. Results demonstrated folded hairpin strands intend to generate higher negative charged ions in the gas phase in contrast to linear strands. And results obtained by ESI-MS demonstrate well consistence with the results performed by UV-spectroscopy.