Structures and Activation Energies for Glycosidic Bond Cleavage of Protonated Nucleosides: A Synergy of Theory and Threshold Collision-Induced Dissociation Experiments

摘要

Nature makes use of deprotonation, protonation and noncovalent interactions to alter the structures and reactivities of molecules to facilitate various biological functions and chemical transformations. For example, protonation of a nucleic acid can occur along the phosphate backbone, or to the nucleobases and sugar moieties. Intramolecular hydrogen bonding interactions between the nucleobase, phosphate, and sugar moieties stabilize the excess proton and result in changes in the conformation of the phosphate backbone, orientations of the nucleobases, and puckering of the sugars. As the basic building blocks of nucleic acids, the DNA and RNA nucleosides are excellent model systems for elucidating the role that protonation plays in facilitating changes in structure and reactivity associated with the biological processes in which nucleic acids participate. In particular, the effects of protonation on the structures and stabilities of the N-glycosidic bond of the common 2'-deoxyribonucleosides and ribonucleosides are of great interest as these molecules are ubiquitious in nature. A variety of minor or modified nucleosides are also found in nature and/or have been synthesized for pharmaceutical applications. Studies of the effects of various modifications on the stability of the N-glycosidic bond are also important as such knowledge would provide an understanding of the biological reasons for these modifications. In this study, the collision-induced dissociation (CID) behavior of protonated DNA and RNA nucleosides with Xe was studied as a function of kinetic energy using guided ion beam tandem mass spectrometry techniques. Theoretical electronic structure calculations were also performed to support and enhance the experimental studies. The four common DNA nucelosides (2′-deoxyadenosine (dAdo), 2′-deoxycytidine (dCyd), 2′-deoxyguanosine (dGuo), thymidine (thd) and 2′-deoxyuridine) and the four common RNA nucleosides (adenosine (Ado), cytidine (Cyd), guanosine (Guo), and uridine (Urd)) are included in this work to investigate the influence of the nucleobase identity on the structure and stability of their protonated forms. In addition, we also include two minor nucleosides, 2′-deoxyuridine and 5-methyluridine, to determine the effects of 5-methylation on the stability of the uridine/thymidine nucleosides in an effort to understand why nature uses a different form of this nucleobase for the DNA and RNA nucleic acids.