Fingerprints of Both Watson–Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H⁺ Pair

Abstract

Gas phase protonated guanine-cytosine (CGH) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base pairs.

Theoretical Comparison of the Stabilities of Hoogsteen and Watson–Crick Conformations for Proton‐bound Base‐pairing of Nucleic Acid Bases and Nucleosides in the Gas Phase

“…However, recent NMR studies have observed transient sequence-specific base-pairing other than the WC type, which occurred inside canonical DNA double helixes. 10,11,18 In an extensive exploration of the conformations of [C:G:H] + complexes, proton-bound Hoogsteen conformations were predicted to be the most stable, and they were far more stable than protonated WC base pairs. In particular, base-pairing in proton-bound Hoogsteen base pairs of C and G, [C:G:H] + , involves two hydrogen bonds of which one is ionic.…”

“…In particular, base-pairing in proton-bound Hoogsteen base pairs of C and G, [C:G:H] + , involves two hydrogen bonds of which one is ionic. 10,11,18 In an extensive exploration of the conformations of [C:G:H] + complexes, proton-bound Hoogsteen conformations were predicted to be the most stable, and they were far more stable than protonated WC base pairs. Due to the electrostatic interaction, the ionic hydrogen bonding offers a stronger interaction than neutral hydrogen bonding.…”

“…5 The ionic hydrogen bond, which is formed by the extra proton obtained by protonation that bridges between the basic sites of two nucleic acid bases, possesses quite a different property from that of neutral hydrogen bonds. [9][10][11] On the other hand, the attachment of a proton to WC base pairs is also known to significantly strengthen neutral hydrogen bonds participating in WC basepairing. 6 In addition, unlike neutral hydrogen bonding, it possesses a very low energy barrier for proton transfer along the ionic hydrogen bond.…”

“…6 In addition, unlike neutral hydrogen bonding, it possesses a very low energy barrier for proton transfer along the ionic hydrogen bond. For experimental approaches, (IRMPD) spectroscopy 11,14,15 and energyresolved collision-induced dissociation (ER-CID) experiments 10,16,17 in combination with quantum chemical calculations have yielded accurate elucidation of the structures and base-pairing energies of proton-bound dimers of nucleic acid bases. [9][10][11] On the other hand, the attachment of a proton to WC base pairs is also known to significantly strengthen neutral hydrogen bonds participating in WC basepairing.…”

“…5,7,8 The mobile nature of the attached proton also causes intriguing anomalous behaviors in the dissociation of proton-bound base pairs by altering dissociation pathways, leading to the generation of isomeric fragments of proton-transferred products. 10,11,18 In an extensive exploration of the conformations of [C:G:H] + complexes, proton-bound Hoogsteen conformations were predicted to be the most stable, and they were far more stable than protonated WC base pairs. 12,13 The investigation of proton-bound base pairs in the gas phase offers a model system to deepen our understanding of base-pairing interactions at the molecular level, in which protonation is deeply involved.…”