Hydrogen/Deuterium Exchange of Nucleotides in the Gas Phase

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Abstract
Gas-phase hydrogen/deuterium exchange reactions have been performed on the 5‘- and 3‘-nucleotide monophosphates and on the 3‘,5‘-cyclic nucleotides. Following negative mode electrospray ionization and transport to a Fourier transform ion cyclotron resonance cell, each nucleotide was reacted with gaseous D2O for up to 600 s. Extensive deuterium exchange was observed for the 3‘- and 5‘-nucleotides in negative ion mass spectra with relative rates of exchange following the trend 5‘-dCMP > 5‘-dAMP > 5‘-dTMP ≫ 5‘-dGMP and 3‘-dGMP >3‘-dAMP ≈ 3‘-dCMP ≈ 3‘-dTMP. At least two classes of exchanging protons are observed. The more facile class is assigned to the amino protons of the bases, with a slower class attributed to the phosphate and/or hydroxyl proton. Overall, the 3‘-nucleotides exchange more quickly than the 5‘-oligonucleotides. The cyclic nucleotides did not undergo deuterium exchange, suggesting that a charged phosphate group proximate to the base is required to catalyze the exchange reaction. Exchange through tautomerization of the bases is not observed, although molecular modeling suggests an energy barrier of <30 kcal.

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