Metastable fragmentation of a thymidine-nucleotide and its components

Abstract

In aqueous biological environment DNA is typically deprotonated. The metastable deprotonated DNA nucleobases are important reaction intermediates in low-energy electron induced damage to DNA. By comparing the metastable decay of small deprotonated DNA building blocks (thymine, thymidine, d-ribose, d-ribose 5-monophosphate) with the metastable decay of thymidine 5′-monophosphate and the hexameric oligonucleotide dT6 we show that the most intense fragmentation pathways of the individual components are inherited to their next larger compositions of one step further in complexity, i.e., from thymine and ribose to thymidine, from thymidine and 2-deoxyribose 5-monophosphate to thymidine 5′-monophosphate, and from thymidine 5′-monophosphate to thymine oligonucleotides. However, fragmentation channels that are dominant in the smaller, principle building blocks such as d-ribose and thymidine do not necessarily prevail beyond their composition, i.e., in thymidine 5′-monophosphate and thymine oligonucleotides. The comparison of the metastable decay mass spectra of molecules of increasing complexity reveals detailed fragmentation mechanisms and shows that the individual fragmentation pathways are determined by the initial deprotonation sites.