Change in Electronic Structure upon Optical Excitation of 8-Vinyladenosine: An Experimental and Theoretical Study

Abstract

8-Vinyladenosine (8VA) is an adenosine analog, like 2-aminopurine (2AP), that has a red-shifted absorption and high fluorescence quantum yield. When introduced into double-stranded DNA (dsDNA), its base-pairing and base-stacking properties are similar to those of adenine. Of particular interest, the fluorescence quantum yield of 8VA is sensitive to base stacking, making it a very useful real-time probe of DNA structure. The fundamental photophysics underlying this fluorescence quenching by base stacking is not well understood, and thus exploring the excited state electronic structure of the analog is warranted. In this study, we report on changes in the electronic structure of 8VA upon optical excitation. Stark spectroscopy was performed on 8VA monomer in frozen ethanol glass at 77 K to obtain the direction and degree of charge redistribution in the form of the difference dipole moment, Deltamu(01) = 4.7 +/- 0.3 D, and difference static polarizability, tr(Delta(alpha)01) = 21 +/- 11 A(3), for the S(0)-->S(1) transition. In addition, solvatochromism experiments were performed on 8VA in various solvents and analyzed using Bakhshiev's model. High level ab initio methods were employed to calculate transition energies, oscillator strengths, and dipole moments of the ground and excited states of 8VA. The direction of Deltamu(01) was assigned in the molecular frame for the lowest optically accessible state. Our study shows that the angle between ground and excited state dipole moment plays a critical role in understanding the change in electronic structure upon optical excitation. Compared to 2AP, 8VA has a larger difference dipole moment which, with twice the extinction coefficient, suggests that 8VA is superior as a two-photon probe for microscopy studies. To this end, we have measured the ratio of the two-photon fluorescence yields of the two analogs by excitation at the respective monomer absorption maxima. We show that 8VA is indeed a significantly brighter two-photon fluorophore, based on our experimental and computational results.

Comparing ultrafast excited state quenching of flavin 1,N6-ethenoadenine dinucleotide and flavin adenine dinucleotide by optical spectroscopy and DFT calculations

“…The ground-state geometries and molecular orbital energies of 9-CH 3 -εAde and 9-CH 3 -Ade radicals were optimized as before [44,45] using the Density Functional Theory (DFT) package in Gaussian 16 [46], with UB3LYP/6-311 + G(d,p) functional and basis set respectively, as well as lumiflavin anionic semiquinone as a control. B3YLP/6-311 + G(d,p) calculations for neutral lumiflavin, 9-CH 3 -ε-Ade, and 9-CH 3 -Ade were performed as additional checks on the radical calculations.…”

8-(p-CF3-cinnamyl)-modified purine nucleosides as promising fluorescent probes

“…1) results in a longer emission wavelength and higher quantum yield as compared to adenosine (l em 388 nm; f 0.66 vs. l em 319 nm; f 0.00026). [16][17][18] The purine p-system was also extended upon conjugation with aromatic moieties. Specifically, 8-(p-hydroxy-phenyl) nucleosides, 2-4 emit at ~390 nm with high quantum yields ranging from 0.25 to 0.56 in aqueous solution (pH 7).…”

Measuring electronic structure properties of flavins and flavoproteins by electronic Stark spectroscopy

“…For flavins though, higher levels of theory are sometimes useful. These approaches and results have been described in detail in previous papers (Kodali, Kistler, Matsika, & Stanley, 2008;Kodali, Kistler, Narayanan, Matsika, & Stanley, 2010;Kodali, Narayanan, & Stanley, 2012;Kodali et al, 2009; Pauszek III, Kodali, & Stanley, 2014;Pauszek, Kodali, Caldwell, et al, 2013;Pauszek et al, 2016;Rohwer et al, 2018). We believe that we are on the threshold of elucidating how the unique electrostatic cavity fields in proteins affect flavin energetics and catalysis.…”