Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study

Abstract

Protonated nucleobases have significant roles in facilitating catalytic functions of RNA, and in stabilizing different structural motifs. Reported pKa values of nucleobase protonation suggest that the population of neutral nucleobases is 10(3)-10(4) times higher than that of protonated nucleobases under physiological conditions (pH ∼ 7.4). Therefore, a molecular level understanding of various putative roles of protonated nucleobases cannot be achieved without addressing the question of how their occurrence propensities and stabilities are related to the free energy costs associated with the process of protonation under physiological conditions. With water as the proton donor, we use advanced QM methods to evaluate the site specific protonation propensities of nucleobases in terms of their associated free energy changes (ΔGprot). Quantitative follow up on the energetics of base pair formation and database search for evaluating their occurrence frequencies, reveal a lack of correlation between base pair stability and occurrence propensities on the one hand, and ease of protonation on the other. For example, although N7 protonated adenine (ΔGprot = 40.0 kcal mol(-1)) is found to participate in stable base pairing, base pairs involving N7 protonated guanine (ΔGprot = 36.8 kcal mol(-1)), on geometry optimization, converge to a minima where guanine transfers its extra proton to its partner base. Such observations, along with examples of weak base pairs involving N3 protonation of cytosine (ΔGprot = 37.0 kcal mol(-1)) are rationalized by analysing the protonation induced charge redistributions which are found to significantly influence, both positively and negatively, the hydrogen bonding potentials of different functional sites of individual nucleobases. Protonation induced charge redistribution is also found to strongly influence (i) the aromatic character of the rings of the participating bases and (ii) hydrogen bonding potential of the free edges of the protonated base pair. Comprehensive analysis of a non-redundant RNA crystal structure dataset further reveals that, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities.

Single‐stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation

“…In negative mode, several phosphates are protonated by interactions with ammonium ions, leaving the rest deprotonated . The better‐defined IMS bands observed in positive mode suggest that nucleobase protonation restricts the number of potential conformers via stabilization of non‐canonical base‐pairing, in good agreement with previous theoretical studies . This is in contrast to certain broader bands in positive mode (i.e.…”

“…52 The better-defined IMS bands observed in positive mode suggest that nucleobase protonation restricts the number of potential conformers via stabilization of non-canonical base-pairing, in good agreement with previous theoretical studies. 53,54 This is in contrast to certain broader bands in positive mode (i.e. bands D and L) which are indicative of less tightly folded conformers, similar to those previously observed in nESI-TIMS experiments on DNA structures.…”

Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

“…We have considered both the possibilities and have observed that (Figure 6 C, D, Table 2) , N3 protonated cytosine results in a nonplanar triple with lower interaction energy (-32.1 kcal/mol) whereas, the triple with adenine N7 protonation (-49.3 kcal/mol) is more stable. This is due to the fact that, although cytosine N3 is easier to protonate than adenine N7 protonation in solution, 68 protonation induced charge redistribution in cytosine disfavors hydrogen bonding interactions via O2 of cytosine. On the other hand, protonation at N7 of adenine favors the hydrogen bonding interactions via N6 of adenine 68 .…”

“…This is due to the fact that, although cytosine N3 is easier to protonate than adenine N7 protonation in solution, 68 protonation induced charge redistribution in cytosine disfavors hydrogen bonding interactions via O2 of cytosine. On the other hand, protonation at N7 of adenine favors the hydrogen bonding interactions via N6 of adenine 68 . Higher charge dipole interaction between neutral cytosine and protonated adenine, compared .…”

The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study

“…Halder et al have benchmarked the conventional formalisms for modeling the process of protonation and concluded that considering water as a proton donor might provide a physicochemically relevant picture of the relative order of protonation propensity of different sites of the nucleobases. Also, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities (Halder et al, 2014). Specifically, the protonation of adenine, adenosine, and adenine-containing nucleotides have been studied extensively in both gas and condensed phases by theoretical and experimental means (Russo et al, 1998;van Zundert et al, 2011).…”