Excited-State Proton Transfer and Phototautomerism in Nucleobase and Nucleoside Analogs: A Mini-Review

Abstract

Intermolecular excited-state proton transfer (ESPT) has been observed in several fluorescent nucleobase and/or nucleoside analogs. In the present work, some new examples of ESPT in this class of compounds are presented together with a brief recapitulation of the previously published data. The nucleobases, nucleosides, and their analogs contain many basic and acidic centers and therefore their ESPT behavior may be complex. To interpret the complex data, it is usually necessary to determine the microscopic pK* values for each (or most) of the possible ESPT centers. Typical approach to solve this problem is by analysis of the alkyl derivatives, in which the possibility of the ESPT is reduced. Of particular interest are examples of "phototautomerization via the cation," observed in several systems, which in the neutral media do not undergo ESPT. Protonation of the molecule in the ground state facilitates the two-step phototautomerism in several systems, including formycin A and 2-amino-8-azadenine. Fluorescence of the nucleobase and nucleoside analogs undergoing ESPT is usually solvent-, isotope-, and buffer-ion sensitive, and in some systems the ESPT can be promoted by environmental factors, e.g., the presence of buffer ions. This sensitivity to the microenvironment parameters makes the ESPT systems potentially useful for biological applications.

Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution

“…The photophysics of several azabase derivatives in aqueous solution and at different pHs have been studied to some extent [218][219][220][221][222][223] and reviewed recently [224]. The interpretation of the photophysical results is complicated by the fact that aza-substitution lowers the pK a of the bases significantly, thus resulting in a mixture of tautomers in the ground state and at different pHs (Table 18) [224].…”

“…The interpretation of the photophysical results is complicated by the fact that aza-substitution lowers the pK a of the bases significantly, thus resulting in a mixture of tautomers in the ground state and at different pHs (Table 18) [224]. The nitrogen atom in place of the methine group at position 6 (C6H) of the uracil or thymine ring of the nucleosides lowers the pK a of the N3 hydrogen considerably relative to its pK a in uridine and thymidine [225][226][227][228][229][230].…”

“…Hence, unlike the uracil and thymine nucleosides that are found as neutral species at pH 7, 6-azauridine and 6-azathymidine are significantly deprotonated at neutral pH. Evidence for excited-state proton transfer and phototautomerism has been presented [224], but further experimental (particularly time-resolved) and computational work are needed to understand fully their photochemistry in aqueous solution. On the other hand, the photophysics of the azabase derivatives can be significantly simplified by using acetonitrile as the solvent.…”

Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes

“…2AP and PyC exhibit substantial and moderate quenching, respectively, of the fluorescence upon incorporation into oligonucleotides, and further quenching of fluorescence is also observed upon duplex formation. 5a,6,18 This results in decreased R 0 values for the two FRET pairs inside oligonucleotide systems (see Table 2). Our R 0 estimation shows that 5 and 8 are good FRET pair candidates with either 2AP or PyC also following incorporation into oligonucleotides.…”

“…3,4 However appealing, efforts to develop fluorescent nucleoside probes are often hampered by synthetic challenges and the unpredictability of their spectroscopic properties, particularly features pertinent to their excited-state dynamics. 5 Furthermore, the fluorescence of emissive nucleosides is frequently substantially quenched upon incorporation into oligonucleotides and even further upon duplex formation, 1a,5a,6 rendering this development and use a tedious and empirical process.…”