7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein

Tokugawa, Munefumi; Yoshio, Masaki; Canggadibrata, Jan Christian; Kaneko, Kazuhei; Shiozawa, Takashi; Kanamori, Takashi; Grøtli, Morten; Wilhelmsson, L. Marcus; Sekine, Mitsuo; Seio, Kohji

doi:10.1039/c5cc09700b

Cited by 33 publications

(16 citation statements)

References 43 publications

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“…In fact, it has to be considered that in solution already two atropisomeric molecules are present. This is not only valid for compound 1, but is a general phenomenon occurring in related purine and pyrimidine nucleosides with unsymmetric heterocycles as side chains, as reported by Tor (Greco & Tor, 2007) and others (Tokugawa et al, 2016).…”

Section: Hirshfeld Surface Analysis Of Fur Imidc (1)supporting

confidence: 69%

8-Furylimidazolo-2′-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence

Budow-Busse¹,

Jana²,

Kondhare³

et al. 2022

Acta Crystallogr C

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8-Furylimidazolo-2′-deoxycytidine (furImidC), C14H14N4O5, is a fluorescent analogue of 2′-deoxycytidine, also displaying the same recognition face. As a constituent of DNA, furImidC forms extraordinarily strong silver-mediated self-pairs. Crystal structure determination revealed that furImidC adopts two types of disordered residues: the sugar unit and the furyl moiety. The disorder of the sugar residue amounts to an 87:13 split. The disorder of the furyl ring results from axial chirality at the C8—C2′′ bond connecting the nucleobase to the heterocycle. The two atropisomers are present in unequal proportions [occupancies of 0.69 (2) and 0.31 (2)], and the nucleobase and the furyl moiety are coplanar. Considering the atomic sites with predominant occupancy, an anti conformation with χ = − 147.2 (7)° was found at the glycosylic bond and the 2′-deoxyribosyl moiety shows a C2′-endo (S, 2 T 1) conformation, with P = 160.0°. A 1H NMR-based conformational analysis of the furanose puckering revealed that the S conformation predominates also in solution. In the solid state, two neighbouring furImidC molecules are arranged in a head-to-tail fashion, but with a notable tilt of the molecules with respect to each other. Consequently, one N—H...N hydrogen bond is found for neighbouring molecules within one layer, while a second N—H...N hydrogen bond is formed to a molecule of an adjacent layer. In addition, hydrogen bonding is observed between the nucleobase and the sugar residue. A Hirshfeld surface analysis was performed to visualize the intermolecular interactions observed in the X-ray study. In addition, the fluorescence spectra of furImidC were measured in solvents of different polarity and viscosity. furImidC responds to microenvironmental changes (polarity and viscosity), which is explained by a hindered rotation of the furyl residue in solvents of high viscosity.

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Section: Hirshfeld Surface Analysis Of Fur Imidc (1)supporting

confidence: 69%

8-Furylimidazolo-2′-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence

Budow-Busse¹,

Jana²,

Kondhare³

et al. 2022

Acta Crystallogr C

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“…Environment‐sensitive fluorophores [2] can sense changes in the microenvironment, secondary structures or intramolecular interactions and respond by changing the emission wavelength (solvatochromism) or intensity (light‐up probes) and/or the lifetime. Diverse viscosity‐sensitive fluorophores, mostly based on molecular rotors, were used to detect hybridisation or mismatches, [3] secondary structure changes, [4] or protein‐DNA interactions [5–7] . Nucleotides bearing solvatochromic labels can sense changes in polarity of the microenvironment by changing the colour of emission [8,9] .…”

Section: Methodsmentioning

confidence: 99%

“…Diverse viscositysensitive fluorophores, mostly based on molecular rotors, were used to detect hybridisation or mismatches, [3] secondary structure changes, [4] or protein-DNA interactions. [5][6][7] Nucleotides bearing solvatochromic labels can sense changes in polarity of the microenvironment by changing the colour of emission. [8,9] Previously, we reported push-pull fluorene-linked nucleotide which changed the colour in a less polar environment of a protein.…”

mentioning

confidence: 99%

Acetophenyl‐thienyl‐aniline‐Linked Nucleotide for Construction of Solvatochromic Fluorescence Light‐Up DNA Probes Sensing Protein‐DNA Interactions

Güixens-Gallardo

Hocek

2021

Chemistry A European J

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The synthesis of 2'-deoxycytidine and its 5'-Otriphosphate bearing solvatochromic acetophenyl-thienylaniline fluorophore was developed using the Sonogashira cross-coupling reaction as the key step. The triphosphate was used for polymerase synthesis of labelled DNA. The labelled nucleotide or DNA exerted weak red fluorescence when excited at 405 nm, but a significant colour change (to yellow or green) and light-up (up to 20 times) was observed when the DNA probes interacted with proteins or lipids.

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“…2 for chemical structures) include C8 to S8 thio-RNA analogue th A [ 23 ], the C8-naphtalene substituted adenines cn A and dn A [ 24 ], as well as our own quadracyclic qAN1 [ 25 ]. A handful of fluorescent guanine analogues has been synthesized and characterized and includes the recent turn-on probe BFdG, 3-MI, 2PyG, as well as the emissive RNA analogue th G [ 23 , 26 – 28 ]. Some notable pyrimidine analogues include our tricyclic analogues tC and tC O [ 29 – 31 ], pyrrolo-dC [ 32 ] and its derivatives [ 33 ] as well as th U, th C [ 23 ] and DMA C [ 34 ].…”

Section: Reviewmentioning

confidence: 99%

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

Bood¹,

Sarangamath²,

Wranne³

et al. 2018

Beilstein J. Org. Chem.

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Förster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base–base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been complemented with among others the adenine analogue FRET pair, qAN1–qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ 2, have a different distance window of opportunity than external fluorophores, and, thus, have the potential to facilitate better structure resolution. Netropsin DNA binding and the B-to-Z-DNA transition are examples of structure investigations that recently have been performed using base–base FRET and that are described here. Base–base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications.

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7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein

Abstract: 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine ((BF)dG) was synthesized and incorporated into an oligodeoxynucleotide (ODN). The single-stranded ODN containing (BF)dG shows 91-fold fluorescence enhancement upon binding of single-strand DNA binding protein.

Cited by 33 publications

References 43 publications

8-Furylimidazolo-2′-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence

8-Furylimidazolo-2′-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence

Acetophenyl‐thienyl‐aniline‐Linked Nucleotide for Construction of Solvatochromic Fluorescence Light‐Up DNA Probes Sensing Protein‐DNA Interactions

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

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