Mispair formation in DNA can involve rare tautomeric forms in the template

Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets

The functionality of a semisynthetic DNA in the biological environment will depend on the base pair nature of its complementary base pairs. To understand this, base pair interactions between complementary bases of recently proposed eight second-generation artificial nucleobases are studied herein by considering their rare tautomeric conformations and a dispersion-corrected density functional theoretic method. It is found that the binding energies of two hydrogen-bonded complementary base pairs are more negative than those of the three hydrogen-bonded base pairs. However, as the former base pairs are endothermic, the semisynthetic duplex DNA would involve the latter base pairs.

Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases

Single-subunit RNA polymerases (RNAPs) are present in phage T7 and in mitochondria of all eukaryotes. This RNAP class plays important roles in biotechnology and cellular energy production, but we know little about its fidelity and error rates. Herein, we report the error rates of three single-subunit RNAPs measured from the catalytic efficiencies of correct and all possible incorrect nucleotides. The average error rates of T7 RNAP (2 × 10^-6), yeast mitochondrial Rpo41 (6 × 10^-6), and human mitochondrial POLRMT (RNA polymerase mitochondrial) (2 × 10^-5) indicate high accuracy/fidelity of RNA synthesis resembling those of replicative DNA polymerases. All three RNAPs exhibit a distinctly high propensity for GTP misincorporation opposite dT, predicting frequent A→G errors in RNA with rates of ∼10^-4 The A→C, G→A, A→U, C→U, G→U, U→C, and U→G errors mostly due to pyrimidine-purine mismatches were relatively frequent (10^-5-10^-6), whereas C→G, U→A, G→C, and C→A errors from purine-purine and pyrimidine-pyrimidine mismatches were rare (10^-7-10^-10). POLRMT also shows a high C→A error rate on 8-oxo-dG templates (∼10^-4). Strikingly, POLRMT shows a high mutagenic bypass rate, which is exacerbated by TEFM (transcription elongation factor mitochondrial). The lifetime of POLRMT on terminally mismatched elongation substrate is increased in the presence of TEFM, which allows POLRMT to efficiently bypass the error and continue with transcription. This investigation of nucleotide selectivity on normal and oxidatively damaged DNA by three single-subunit RNAPs provides the basic information to understand the error rates in mitochondria and, in the case of T7 RNAP, to assess the quality of in vitro transcribed RNAs.

Assessment of the tautomeric population of benzimidazole derivatives in solution: a simple and versatile theoretical-experimental approach

Herein, we present a simple and versatile theoretical-experimental approach to assess the tautomeric distribution on 5(6)-aminobenzimidazole (5(6)-ABZ) derivatives in solution via one-photon absorption. The method is based on the optimized weighted sum of the theoretical spectra of the corresponding tautomers. In this article we show how the choice of exchange-correlation functional (XCF) employed in the calculations becomes crucial for the success of the approach. After the systematic analysis of XCFs with different amounts of exact-exchange we found a better performance for B3LYP and PBE0. The direct test of the proposed method on omeprazole, a well-known 5(6)-benzimidazole based pharmacotherapeutic, demonstrate its broader applicability. The proposed approach is expected to find direct applications on the tautomeric analysis of other molecular systems exhibiting similar tautomeric equilibria.

Mechanism of Escherichia coli resistance to Pyrrhocoricin

Due to their lack of toxicity to mammalian cells and good serum stability, proline-rich antimicrobial peptides (PR-AMPs) have been proposed as promising candidates for the treatment of infections caused by antimicrobial-resistant bacterial pathogens. It has been hypothesized that these peptides act on multiple targets within bacterial cells, and therefore the likelihood of the emergence of resistance was considered to be low. Here, we show that spontaneous Escherichia coli mutants resistant to pyrrhocoricin arise at a frequency of approximately 6 × 10(-7). Multiple independently derived mutants all contained a deletion in a nonessential gene that encodes the putative peptide uptake permease SbmA. Sensitivity could be restored to the mutants by complementation with an intact copy of the sbmA gene. These findings question the viability of the development of insect PR-AMPs as antimicrobials.

Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch

Structural diversification of canonical nucleic acid bases and nucleotide analogues by tautomerism has been proposed to be a powerful on/off switching mechanism allowing regulation of many biological processes mediated by RNA enzymes and aptamers. Despite the suspected biological importance of tautomerism, attempts to observe minor tautomeric forms in nucleic acid or hybrid nucleic acid-ligand complexes have met with challenges due to the lack of sensitive methods. Here, a combination of spectroscopic, biochemical, and computational tools probed tautomerism in the context of an RNA aptamer-ligand complex; studies involved a model ligand, oxythiamine pyrophosphate (OxyTPP), bound to the thiamine pyrophosphate (TPP) riboswitch (an RNA aptamer) as well as its unbound nonphosphorylated form, oxythiamine (OxyT). OxyTPP, similarly to canonical heteroaromatic nucleic acid bases, has a pyrimidine ring that forms hydrogen bonding interactions with the riboswitch. Tautomerism was established using two-dimensional infrared (2D IR) spectroscopy, variable temperature FTIR and NMR spectroscopies, binding isotope effects (BIEs), and computational methods. All three possible tautomers of OxyT, including the minor enol tautomer, were directly identified, and their distributions were quantitated. In the bound form, BIE data suggested that OxyTPP existed as a 4'-keto tautomer that was likely protonated at the N1'-position. These results also provide a mechanistic framework for understanding the activation of riboswitch in response to deamination of the active form of vitamin B1 (or TPP). The combination of methods reported here revealing the fine details of tautomerism can be applied to other systems where the importance of tautomerism is suspected.

Observation of two N2-isobutyrylguanine tautomers by NMR spectroscopy

N(2)-isobutyrylguanine was prepared by treatment of guanine with isobutyryl chloride. Two tautomers, 1,7-dihydro-2-(isobutyroyl)amino-6H-purin-6-one and 1,9-dihydro-2-(isobutyroyl)amino-6H-purin-6-one, were identified in almost 1:1 ratio in dichloromethane-dimethyl sulfoxide (1:1 v/v) by NMR spectroscopy. By using the selective-inversion experiments, enthalpy, entropy, and free energy for activation were determined. This work represents the first report of guanine tautomers observed directly by NMR spectroscopy.

Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+

The tautomeric equilibrium and hydrogen bonding in nucleotide 2'-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O.Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ and B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. The Mg2+ ion forms two inner-shell contacts with the nucleotide, similar to small phosphorylated molecules under physiological conditions. The presence of the phosphate group and the hydrated magnesium cation leads to a change in guanine tautomeric equilibrium of 4H2O.Mg[dGMP] in comparison to free guanine. The influence of the phosphate group and the magnesium cation on tautomeric equilibrium is larger in the anti conformation where the P=O-->Mg and Mg<--N7 coordinate bonds are formed. The canonical oxo form of guanine is more stable (by 6-8 kcal/mol) than the O6-hydroxo form in anti conformation. Thus, the interaction with Mg2+ ion is capable of further suppressing the likelihood of a spontaneous transient formation of the rare tautomer. In the syn conformation of 4H2O.Mg[dGMP], the interaction of the guanine nucleobase with the phosphate group and the magnesium cation is not as strong as in the anti conformation, and the relative stability of guanine tautomers is close to those in free guanine.

Tautomerism in computer-aided drug design

Tautomers are often disregarded in computer-aided molecular modeling applications. Little is known about the different tautomeric states of a molecule and they are rarely registered in chemical databases. Tautomeric forms of a molecule differ in shape, functional groups, surface, and hydrogen-bonding pattern. Calculation of physical-chemical properties and molecular descriptors differ from one tautomeric state to the other as it is demonstrated with an example of the log P calculation, similarity index, and the complementarity pattern to the targeted protein. Considering tautomery in ligand-protein interactions therefore has a significant impact on the prediction of the ligand binding using various docking techniques. This article points on hitherto unaddressed issue of tautomerism in computer-aided drug design.

The biological equilibrium of base pairs

An inherent feature of double-stranded DNA is the possible replacement of any base pair by another one upon replication. A replication-dependent substitution mutation of a matched base pair requires the temporary formation of a mismatched base pair (mispair). A functionally complementary pair of mispairs is ascribed to each of the four types of substitution mutations. Provided that all types of mispairs can be formed, a dynamic biological equilibrium between the four matched base pairs must exist in all DNA, which is directly related to the formation and stability of the corresponding eight mispairs in vivo. Each nucleotide position in a genome can therefore be described as a system of six dynamic equilibria between the four matched base pairs. After a sufficient number of replications, these equilibrium states will express an overall mutation-selection balance for each individual base pair. In a thermodynamic context, the mispairs represent intermediate states on the transformation pathways between the matched base pairs. Catalysts change the stability and probability of formation of intermediate states. Mutagenic proteins are proposed as hypothetical substitution mutation catalysts in vivo. Functionally, they would be capable of recognizing a particular DNA sequence, tautomerizing a nucleotide base thereof, and hence efficiently inducing a specific misincorporation. Phenomenologically such catalysts would accelerate the rates of substitution mutations and provide pathways for directional mutation pressure.