Tautomeric forms, nucleobases

Abstract IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computatitMial techniques. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen-bonding patterns. 

The Mg+ complexes of cytosine, thymine and uracil are the most complex system studied via photodissociation spectroscopy to date . A complication for these systems is that these nucleobases can exist in various tautomeric forms and that complexation of a metal can change the stability order of the tautomers. DFT calculations located four tautomeric Mg(cytosine)+ complexes, and three of these (29, 30, and 31) were suggested to be responsible for the four reactive photofragment ions 32-35 observed at a wavelength of 360 nm (Scheme 4) . Related photofragmentation reactions were observed for the Mg(thymine)+" and Mg(uracil)+" complexes . ... 

Mass fragmentation of modified nucleobases of 6-methyl tetrazolo[l,5-c]pyrimidin-5(6fl)-one and its 7 and 8-methyl derivatives suggested the occurrence of both azide and tetrazole tautomeric forms of M (661 and 662). For the 8-halo derivatives, only the of the tetrazole form was proposed (930MS643) (Scheme 135). 

Figure 1. (Top) Lewis formulas of nucleobases A, G, C, U (T) in different protonation states. Only single mesomeric and preferred tautomeric forms are given. Additionally, protonated forms of A, G, U (T) and twofold deprotonated form of G are not shown. (Bottom) Distribution of protonation states of nucleobases with pH. The pA a values of A -nucIcotides are used as boundaries for the neutral form.

Among the species produced upon radiolysis of water, hydroxyl radical ( OH) is the most reactive. Indeed, its reaction rate with the four bases and related nucleosides is diffusion-controlled. The main reactive sites of hydroxyl radicals on nucleobases are the double-bonds of the heterocycles. Accordingly, addition of OH at the C8 position of adenine and guanine yields the corresponding reducing 8-hydroxy-7,8-dihydropurin-7-yl radical (Fig. 2). Oxidation of this intermediate leads to the formation of related 8-hydroxypurines that are in dynamic equilibrium with their more stable 8-oxo-7,8-dihydropurine tautomeric form. Competitive reduction of the latter purine radical gives rise to imidazole ring opened compounds the... 

A further option is given by application of bases with inexact base-pairing properties. Due to tautomeric structures, nucleobase P forms hydrogen bridges with adenine and guanine, and nucleobase K with cytidine and thymine (Fig. 34). Thus, a mixture of phosphorami-dites P and K may be used at positions of unknown bases instead of the mixture of the phor-phoramidites dA, dG, dT, dC. 

In Fourier transform microwave spectroscopy, isomeric analysis is derived from rotational spectra see [16]. Alonso and coworkers have combined this approach with laser desorption jet cooling for the study of tautomeric forms of nucleobases. 

The nucleobase monomers can adopt a variety of tautomeric forms and IR spectroscopy in the near IR is diagnostic for this property, especially with the NH and OH stretch frequencies as fingerprints of keto, imino, or enol forms. 

A major use of IR data is structure determination, which for nucleobases includes tautomeric forms and cluster structures to model base pair interactions and microhydration. This capability also makes it possible to follow other properties as a function of structure. For the nucleobases, it turns out that self-protection against UV photodamage by internal conversion depends dramatically on molecular structure. Comparison with solution experiments probably further elucidates these findings and stimulates further research. 

To verify the feasible stabilization of noncanonical forms of the protonated adenine nucleobase, we extended our B3LYP/6-31G(d) calculations to the study of the tautomeric forms of isolated cations on a water-simulated dielectric medium and including different metal-oxalato surroundings simulating those experimentally found in the eompoimds. 

Table 4 presents the proton affinities PA and deprotonation enthalpies DPE of thiouracils calculated at the B3LYP/6-31+G(d,p) computational level. Inspecting this Table, we find that first, the thio substitution of uracil systematically increases its PAs by 3-6 kcal/mol and second, it decreases the DPEs of uracil by 6-13 kcal/mol. As far as the base pair A thioU is considered, it particularly implies a lowering, on the one hand, of the potential well at the Sio atom of thiouracil corresponding to the proton transfer from the N8 atom of adenine to the Sio of thiouracil and, on the other one, a raising of the potential well at the N3 atom of thiouracil involved in the proton transfer from the N3-H bond to the Ni atom of adenine. Therefore, summarizing, the thio substitution of uracil is in a favor to the double proton transfer mechanism of the occurrence of the spontaneous point mutations proposed by Lowdin [19]. Table 4 also includes the PAs of the T2 tautomer of uracil and thiouracils. A comparison with the corresponding PAs of the parental normal nucleobases shows that their tautomerization to the T2 form is accompanied by an increase of the proton affinity by 20-23 kcal/mol. 

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