title: Fragmentation mechanisms of oligodeoxynucleotides: effects of replacing phosphates with methylphosphonates and thymines with other bases in T-rich sequences.
abstract: This article reports another step in an ongoing effort to understand the fragmentation of T-rich oligodeoxynucleotides. We extended an earlier investigation of T-rich 4-mers to T-rich 6-mers, 8-mers and 10-mers by using four different tandem mass spectrometric methods. The methods include low-energy collisionally activated decomposition (CAD) of electrospray ionization (ESI)-produced ions, source-CAD of ESI-produced ions, post-source decay (PSD), and CAD of matrix assisted laser desorption ionization (MALDI)-generated ions. The most abundant fragment ions produced from [M - 2H]2- precursors upon low-energy CAD in an ion trap are the [a - B]- and their complementary w ions. The predominant cleavage sites for T-rich oligodeoxynucleotides are always the 3' C-O bonds adjoining a non-T nucleobase (i.e., a base with a higher proton affinity (PA) than that of T). The relative abundance of [a - B]- correlates with the PAs of the nucleobases, underscoring the importance of proton transfer to the base. The propensity to form [a - B]- ions falls in the order of G > C approximately A >> T. Structural isomers up to 10-mers can be readily sequenced and distinguished with each of the four tandem mass spectrometric methods applied. The fragmentation of oligodeoxynucleotides in which various phosphates were replaced with methylphosphonate is a measure of the participation of the phosphate proton in the formation of [a - B] ions. For 4 and 5-mers, transfer of an acidic proton from the 5'-phosphate to the departing base is the initiating step in the formation of [a - B]- ions.
authors.affiliation: Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA.
authors.forename: K X
authors.initials: KX
authors.lastname: Wan
authors.forename: M L
authors.initials: ML
authors.lastname: Gross
mesh_terms: D007536:Isomerism; D008958:Models, Molecular; D015394:Molecular Structure; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D063065:Organophosphonates / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013329:Structure-Activity Relationship; D013941:Thymine / Q000737:chemistry*
chemical_list: D009838:Oligodeoxyribonucleotides; D063065:Organophosphonates; D010710:Phosphates; D013941:Thymine