Density Functional Theoretical Study on the Acid Dissociation Constant of an Emissive Analogue of Guanine

Lee, Yong-Jae; Jang, Yun Hee; Kim, Yong-Seong; Hwang, Sungu

doi:10.5012/bkcs.2012.33.12.4255

Cited by 12 publications

(4 citation statements)

References 12 publications

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“…The keto‐amino th G–H1 tautomer (Figure a) appears largely dominant over the other tautomers (Figures b–e), with the exception of water where it is only 0.11 eV more stable than th G–H3, when including only bulk solvent effects. Therefore, the two th G keto‐amino tautomers, analogous to the most stable tautomer of guanine in solution, are likely populated in water.…”

Section: Figuresupporting

confidence: 84%

Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels

et al. 2016

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Thienoguanosine ( th G) is an isomorphic nucleoside analogue acting as a faithful fluorescent substitute of G, with respectable quantum yield in oligonucleotides. Photophysical analysis of th G reveals the existence of two ground-state tautomers with significantly shifted absorption and emission wavelengths, and high quantum yield in buffer. Using (TD)-DFT calculations, the tautomers were identified as the H1 and H3 keto-amino tautomers. When incorporated into the loop of (−)PBS, the (−)DNA copy of the HIV-1 primer binding site, both tautomers are observed and show differential sensitivity to protein binding. The red-shifted H1 tautomer is strongly favored in matched (−)/(+)PBS duplexes, while the relative emission of the H3 tautomer can be used to detect single nucleotide polymorphisms. These tautomers and their distinct environmental sensitivity provide unprecedented information channels for analyzing G residues in oligonucleotides and their complexes. Keywordsab initio calculations; fluorescence; molecular modeling; nucleic acids; tautomerismThe structure, acid-base features, and tautomeric equilibria of the canonical and noncanonical nucleobases found in nucleic acids have been the subject of intense investigation for decades. [1] While the role of minor tautomers in mutagenesis has been one of the primary foci, [2] recent observations suggest that such isomeric nucleobases also play key roles in regular nucleic acid structure and function. [3] As the population of distinct tautomeric forms is impacted by their micro-environment, this added level of complexity also provides opportunities to further advance our understanding of nucleic acid structure and dynamics.In this context, emissive nucleoside analogues, which have become powerful biophysical tools, [4] provide unique prospects. A tautomerizable nucleoside analogue, where the tautomers would have distinct absorption and emission spectra, could be instrumental for [5] and identify two environmentally sensitive ground-state tautomeric forms ( Figure 1) which display distinct absorption and emission spectra. The equilibrium between the two tautomers is mainly governed by the hydrogen-bond donor properties of the solvent. Their observed sensitivity to the microenvironment was rationalized by ab initio calculations. By exploring single-and double-stranded th Gcontaining oligonucleotides, as well as DNA-protein complexes, we illustrate that this probe provides compelling biophysical information and greater insight compared to monochromatic or ratiometric fluorescent nucleosides.The emission spectra of either th G or d th G in water and methanol are surprisingly complex. [5a,b] Excitation at both λ=360 and 380 nm gives a similar emission spectrum (Figure 2a, orange) centered at λ=468 nm. When the excitation energy is progressively increased, a blue-shifted emission with a maximum at λ=400 nm appears and becomes dominant for excitation below λ=300 nm ( Figure 2a, magenta and blue). The simplest interpretation is that th G exhibits two ground-state ...

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Section: Figuresupporting

confidence: 84%

Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels

et al. 2016

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“…In fact, since we started this work, a number of theoretical studies of the 1P photophysics of fluorescent nucleobases have appeared, including some of the molecules described herein. [9] New probe designs that incorporate structure–photophysics property relationships, and developments in optical instrumentation, such as the use of new ultrafast lasers for multiphoton excitation, [10] could facilitate the realization of fluorescent nucleobase labels that can probe the structure and dynamics of nucleic acids at the single-molecule level.…”

Section: Resultsmentioning

confidence: 99%

Two‐Photon‐Induced Fluorescence of Isomorphic Nucleobase Analogs

et al. 2014

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Five isomorphic fluorescent uridine mimics have been subjected to two-photon (2P) excitation analysis to investigate their potential applicability as non-perturbing probes for the single-molecule detection of nucleic acids. We find that small structural differences can cause major changes in the two-photon excitation probability, with the 2P cross sections varying by over one order of magnitude. Two of the probes, both furan-modified uridine analogs, have the highest 2P cross sections (3.8 GM and 7.6 GM) reported for nucleobase analogs, using a conventional Ti:sapphire laser for excitation at 690 nm; they also have the lowest emission quantum yields. In contrast, the analogs with the highest reported quantum yields have the lowest 2P cross sections. The structure-photophysical property relationship presented here is a first step towards the rational design of emissive nucleobase analogs with controlled 2P characteristics. The results demonstrate the potential for major improvements through judicious structural modifications.

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“…A number of theoretical studies of the 1P and 2P photophysics of fluorescent nucleobases have appeared recently. 22,[45][46][47][48] However, the influence of the local electric field on the 2P cross section in DNA has not been addressed. We hope that the results of the present work will stimulate theoretical studies of this effect.…”

Section: Discussionmentioning

confidence: 99%

Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity

Fisher

Nobis

Füchtbauer

et al. 2018

Phys. Chem. Chem. Phys.

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Density Functional Theoretical Study on the Acid Dissociation Constant of an Emissive Analogue of Guanine

Cited by 12 publications

References 12 publications

Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels

Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels

Two‐Photon‐Induced Fluorescence of Isomorphic Nucleobase Analogs

Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity

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