Formic acid catalyzed isomerization of protonated cytosine: a lower barrier reaction for tautomer production of potential biological importance

Abstract

Tautomerism in nucleotide bases is one of the possible mechanisms of DNA mutation. In spite of numerous studies on the structure and energy of protonated cytosine tautomers, little information is available on the process of their intra- and intermolecular tautomerizations. The catalytic ability of HO, HCOOH, and the HCOOHHO group to facilitate the tautomerism of the Cyt2t to CytN3 isomer has been studied. It is shown that the activation free energies of tautomerism in the gas phase are 161.17, 58.96, 26.06, and 15.69 kJ mol, respectively, when the reaction is carried out in the absence and presence of HO, HCOOH, or the HCOOHHO group. The formation of a doubly hydrogen bonded transition state is central to lowering the activation free energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of intramolecular tautomerization, the isomerization of the Cyt2t to CytN3 isomer remains unfavorable, and the HCOOH and HCOOHHO group mediated mechanisms are still more favorable. Meanwhile, conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the product complex (CytN3HCOOH) is in the rapid tautomeric equilibrium with the reaction complex (Cyt2tHCOOH) (τ = 3.84 × 10 s), which is implemented by the mechanism of the concerted synchronous double proton transfer. Its lifetime of the formed CytN3HCOOH complex (τ = 8.33 × 10 s) is almost one order of magnitude larger than the time required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication (several ns), which is further dissociated into the CytN3 and HCOOH monomers. The results of the present study demonstrate the feasibility of acid catalysis for DNA base isomerization reactions that would otherwise be forbidden.

The isomerization of cytosine: Intramolecular hydrogen atom transfer mediated through formic acid

“…Based on the previous work, the activation free energy of direct hydrogen transfer is obviously reduced by the contribution of a single water molecule. Then, the H 2 O‐mediated mechanism has been investigated.…”

“…The recent theoretical researches and our previous work indicate that the activation energy is likely to be further lowered in the presence of formic acid (HCOOH). Then, the ∆ G ≠ of direct tautomerization of KA to KIt isomer may be further affected by the contribution of the formic acid molecule.…”

“…The previously theoretical works have also demonstrated that the presence of the protic molecule significantly contributes to facilitating the intramolecular hydrogen atom transfer of the direct isomerization of KA to KIt isomer. Our recently theoretical work has also suggested that the formation of a doubly hydrogen‐bonded transition state is central to lowering the activation free energy of the isomerization for Cyt under acid condition when the reaction is performed in the absence and presence of formic acid (HCOOH). Even though formic acid is not present in biological environment, it also presents a donor/acceptor profile.…”

The C5‐substituent effects on the formic acid‐assisted tautomerization of protonated cytosine: A lower isomerization barrier and potential biological importance

“…As outlined in a previous work, [ 22–25 ] HCOOH acted as both donor and acceptor groups to imitate the interacting group of amino acid residues is of considerable interest in the intermolecular proton transfer from the hydroxo‐amino tautomer into the oxo‐amino one. Brovarets′ et al [ 26 ] have imitated the acetic acid involved in diproton transfer between canonical and mutagenic tautomers of DNA bases by the theoretical study.…”

“…The formic acid has recently been demonstrated that it could reduce the barriers for unimolecular isomerization involving hydrogen atom transfer in modeling biological molecules. [ 22–25 ] Taken HCOOH as a typical catalyst, the isomerization of other protonated isomers for new DNA bases into another canonical one is one of the great concerns.…”