Strong Hydration and Salt Association Complicate Nucleotide Oligomer Analysis by Mass Spectrometry

Abstract The abiotic synthesis of nucleotide oligomers via wet–dry cycling may have provided a source of nucleic acids necessary for the origin of primitive forms of life. Mass spectrometry (MS) is an important analytical tool used to investigate such oligomers, but the products are surprisingly complex because of water molecules and salt ions adsorbed to ionic and polar groups on the molecules. There are also aggregates of monomers stabilized by noncovalent forces, and differentiating between covalent polymers and noncovalent aggregates remains a subject of technical debate. This study addresses methods for identifying peaks in mass spectra by investigating the adsorption of water and sodium during the ionization of uridine monophosphate and 3′,5′-cyclic guanosine monophosphate (UMP and cGMP). Using 18O-labeled water and increasing the temperature of the heated capillary inlet, we demonstrated that hydrogen-bonded water molecules persist even under high temperatures up to 450 °C. Furthermore, we identified the salt enrichment effect, where increasing chain length leads to a binomial accumulation of sodium ions even in an acidic (pH 2.5) environment. By employing field-asymmetric ion mobility MS, we successfully deconvoluted isobaric ions, distinguishing between massive noncovalent UMP 35-mer aggregates and true covalent 36-mer UMP polymers. These results confirm that water and salt involvement are intrinsic to the MS signature of nucleotide monomers and oligomers. Our findings provide a rigorous analytical framework for validating prebiotic polymerization and highlight the necessity of advanced separation techniques in the characterization of nucleic acid polymers synthesized nonenzymatically on the prebiotic Earth.