Determination of noncovalent interactions of PNA/DNA by electrospray mass spectrometry

Abstract

The structure of peptide nucleic acid is similar to DNA, whereas it differs in phosphate and sugar groups, which improves the hybridization property. The stabilities of the PNA-DNA complexes were previously found to be more stable than the complexes of PNA-DNA or PNA-DNA because the charge repulsion between PNA-DNA complexes did not appear. In this research, the relationships between the stability of 6 species of acpcPNA were investigated. The groups of PNA were divided into 2 sets. The firs set consisted of 4 bases (T, A, C, G) which differed on positions 4 and 7 on the strand of the acpcPNA. For the second set, two PNAs in this set conclude more than 70% of G and C base. The stability of PNA-DNA complexes in the gas phase can be measured by centre-of-mass collision energy (ECM) using electrospray mass spectrometry (ESI-MS). The obtained ECM values go in the same direction as the melting temperature (Tm) measured by UV-vis spectroscopy (UV-vis), indicating that the stability of PNA-DNA complexes in the gas phase correlates well with that in the solution phase. On the contrary, the obtained ECM values of the first set of acpcPNA-DNA complexes (G or C base on positions 4 and 7) go in the inverse direction as they are influenced by base stacking and hydrogen bonding. The experiment confirms that the stability of PNA-DNA complexes can be explained by the inner energy of the complexes. The most striking aspect of our data is the disparity between the solution phase and gas phase stabilities. We hope that this data information will be used for further study and applied for in vitro use such as PCR primers and hybridization probes.