Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions

Dziuba, Dmytro; Pospíšil, Petr; Matyašovský, Ján; Brynda, J.; Nachtigallová, Dana; Rulı́s̆ek, Lubomı́r; Pohl, Radek; Hof, Martin; Hocek, Michal

doi:10.1039/c6sc02548j

Cited by 60 publications

(42 citation statements)

References 115 publications

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“…1–16 Recent highlights include Tor’s isomorphic RNA alphabet, 17,18 Wilhelmsson’s internucleobase FRET pair, 12,19 Sasaki’s fluorescent sensors for nucleobase damage, 20 and a number of examples of nucleobase surrogates that can report on events in the major groove, such as protein binding. 21,22 Still, significant unmet needs persist. For example, most fluorescent nucleobase analogues are quenched when base stacked, emit only at wavelengths <525 nm, and many perturb duplex structure.…”

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confidence: 99%

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

et al. 2017

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Most fluorescent nucleoside analogues are quenched when base stacked and some maintain their brightness, but there has been little progress toward developing nucleoside analogues that markedly increase their fluorescence upon duplex formation. Here, we report on the design and synthesis of a new tricyclic cytidine analogue, 8-diethylamino-tC (8-DEA-tC), that responds to DNA duplex formation with up to a 20-fold increase in fluorescent quantum yield as compared with the free nucleoside, depending on neighboring bases. This turn-on response to duplex formation is the greatest of any reported nucleoside analogue that can participate in Watson–Crick base pairing. Measurements of the quantum yield of 8-DEA-tC mispaired with adenosine and, separately, opposite an abasic site show that there is almost no fluorescence increase without the formation of correct Watson–Crick hydrogen bonds. Kinetic isotope effects from the use of deuterated buffer show that the duplex protects 8-DEA-tC against quenching by excited state proton transfer. These results, supported by DFT calculations, suggest a rationale for the observed photophysical properties that is dependent on duplex integrity and the electronic structure of the analogue.

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confidence: 99%

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

et al. 2017

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“…Thus, they can be used to detect polarity changes upon duplex formation and to detect microenvironmental changes in major and minor grooves . Emissions from ethynylfluorene‐containing U FL become more red‐shifted with increasing solvent polarity 10b . Therefore, we first measured U FT UV absorption and fluorescence in various solvents (Figure ).…”

Section: Resultsmentioning

confidence: 97%

“…Fluorescent nucleosides and the corresponding ODNs are sensitive to solvent properties such as polarity and viscosity. Thus, they can be used to detect polarity changes upon duplex formation and to detect microenvironmental changes in major and minor grooves . Emissions from ethynylfluorene‐containing U FL become more red‐shifted with increasing solvent polarity 10b .…”

Section: Resultsmentioning

confidence: 99%

“…On the other hand, U FT exhibited different emission intensities and emission maxima in different solvents, indicating that this nucleoside is environmentally sensitive. The emission maxima and Stokes shifts ( ν abs – ν em ) observed for U FL in different solvents, against Dimroth's E T (30) as a parameter of solvent polarity, exhibited a linear correlation 10b . Thus, these parameters were plotted against E T (30) (Table S1 and Figure S1).…”

Section: Resultsmentioning

confidence: 99%

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Photophysical Study of 2‐Fluorenyl‐1,2,3‐Triazole‐labeled 2′‐Deoxyuridine and Its Oligonucleotide

Hong

Hwang

2017

Bulletin Korean Chem Soc

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In this study, we prepared 2‐fluorenyl‐1,2,3‐triazol‐4‐yl‐2′‐deoxyuridine (U FT) and inserted it at the central position of an oligodeoxynucleotide (ODN) to investigate whether the triazole group is an efficient linker between fluorene and uracil. U FT displays different fluorescence intensities and emission maxima in different solvents, indicating its potential for application as an environmentally sensitive probe. Moreover, excimer emission from U FT was observed in water. However, U FT containing ODN did not exhibit selective thermal stability and fluorescence changes upon duplex formation with matched and single‐base mismatched targets. This highlighted the importance of selecting the appropriate linker to connect the fluorophore to the nucleobase when developing such DNA probes.

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“…[20][21][22] Ongoing efforts by an umber of groups are focused on developing nucleoside analogues with useful fluorescence changes in response to base stacking, base pairing, changes in nucleic acid secondary and tertiary structure, as well as environmental changes associatedw ith protein binding or changes in nucleic acids olvation. [1,5,[23][24][25][26][27][28][29][30][31] But probablyt he greatesti mpediment to the development of new generationso ff luorescent nucleoside analogues with radically improved properties is that robust methods for predictingp hotophysics based on structure are largely unavailable, especially when one is targeting the complex, anisotropic environment of the base stack. [3] An umber of research groups have studied the relationships between structure andf luorescenceo fn ucleoside analogues, using ac ombination of empirical observations and computation.…”

Section: Introductionmentioning

confidence: 99%

Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing

Teppang

Lee

Burns

et al. 2018

Chemistry A European J

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The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of ag eneral method to predict their photophysics, ap roblem that is especially acute when base pairing and stacking changef luorescence. To better understand these effects, as eries of tricyclic cytidine (tC and tC O )a nalogues ranging from electron-rich to electron-deficient was designed and synthesized.T hey were then incorporated into oligonucleotides,a nd photophysical responses to base pairing and stackingw ere studied.W hen insertedi nto double-stranded DNA oligonucleotides, electron-rich analogues exhibit af luorescencet urn-on effect, in contrast with the electron-deficient compounds, whichs how diminished fluorescence. The magnitude of these fluores-cence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover,m atched base pairing enhances fluorescenceturn-on for the electron-rich compounds, and it causesaf luorescence decrease for the electron-deficientc ompounds. For the tC O compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering ap otentialn ew tool for studying nucleic acid structurea nd dynamics. These results, supported by DFT calculations,h elp to rationalize fluorescencec hangesi n the base stacka nd will be useful for selectingt he best fluorescent nucleoside analogues for ad esired application.

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Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions

Abstract: Color-changing fluorescent nucleotide and oligonucleotide probes for studying interactions with other biomolecules were designed and prepared, and perform better than currently known environment-sensitive fluorophores.

Cited by 60 publications

References 115 publications

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

Photophysical Study of 2‐Fluorenyl‐1,2,3‐Triazole‐labeled 2′‐Deoxyuridine and Its Oligonucleotide

Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing

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