Synthesis, Photophysical Properties and Incorporation of a Highly Emissive and Environment‐Sensitive Uridine Analogue Based on the Lucifer Chromophore

Tanpure, Arun A.; Srivatsan, Seergazhi G.

doi:10.1002/cbic.201402052

Cited by 16 publications

(9 citation statements)

References 92 publications

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“…A similar increase in stability (2.7 °C) was observed for tC- and tC O -incorporation into DNA, and presumably reflects that the increased base stacking interactions act to stabilize the duplex structure 30, 31 . In the few reports on fluorescent base analogues in RNA, a slightly stabilizing effect was also reported for the emissive guanosine isomorph, th G 47 , whereas a negligible effect was reported for the uridine analogue U Dz 48 , and a destabilizing effect was reported for benzo [b] thiophene- 49 , benzofuran- 50 and naphthalimide-conjugated 51 uridine analogues.…”

Section: Resultsmentioning

confidence: 99%

Fluorescent RNA cytosine analogue – an internal probe for detailed structure and dynamics investigations

Füchtbauer

Preus

Börjesson

et al. 2017

Sci Rep

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The bright fluorescent cytosine analogue tCO stands out among fluorescent bases due to its virtually unquenched fluorescence emission in duplex DNA. However, like most reported base analogues, it has not been thoroughly characterized in RNA. We here report on the first synthesis and RNA-incorporation of tCO, and characterize its base-mimicking and fluorescence properties in RNA. As in DNA, we find a high quantum yield inside RNA duplexes (<ΦF> = 0.22) that is virtually unaffected by the neighbouring bases (ΦF = 0.20–0.25), resulting in an average brightness of 1900 M−1 cm−1. The average fluorescence lifetime in RNA duplexes is 4.3 ns and generally two lifetimes are required to fit the exponential decays. Fluorescence properties in ssRNA are defined by a small increase in average quantum yield (<ΦF > = 0.24) compared to dsRNA, with a broader distribution (ΦF = 0.17–0.34) and slightly shorter average lifetimes. Using circular dichroism, we find that the tCO-modified RNA duplexes form regular A-form helices and in UV-melting experiments the stability of the duplexes is only slightly higher than that of the corresponding natural RNA (<ΔT m> = + 2.3 °C). These properties make tCO a highly interesting fluorescent RNA base analogue for detailed FRET-based structural measurements, as a bright internal label in microscopy, and for fluorescence anisotropy measurements of RNA dynamics.

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Section: Resultsmentioning

confidence: 99%

Fluorescent RNA cytosine analogue – an internal probe for detailed structure and dynamics investigations

Füchtbauer

Preus

Börjesson

et al. 2017

Sci Rep

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“…Design and synthesis of ethynyl-extended regioisomersof HBT Various groups with different Hammett substituent constants (s)w ere introducedv ia Sonogashira cross-couplingr eactions between terminal alkynes and aryl halides. [27][28][29] The commercially available regioisomers of brominated salicylaldehyde could make further chemical modification feasible. Synthetic strategies of the 3'-, 4'-a nd 6-substituted regioisomers of HBT are outlinedi nS cheme 1.…”

Section: Resultsmentioning

confidence: 99%

Excited State Intramolecular Proton Transfer in Ethynyl‐Extended Regioisomers of 2‐(2′‐Hydroxyphenyl)benzothiazole: Effects of the Position and Electronic Nature of Substituent Groups

Wang

Niu

et al. 2016

Chemistry An Asian Journal

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Although the organic dyes based on excited state intramolecular proton transfer (ESIPT) mechanism have attracted significant attention, the structure-property relationship of ESIPT dyes needs to be further exploited. In this paper, three series of ethynyl-extended regioisomers of 2-(2'-hydroxyphenyl)benzothiazole (HBT), at the 3'-, 4'- and 6-positions, respectively, have been synthesized. Changes in the absorption and emission spectra were correlated with the position and electronic nature of the substituent groups. Although 4'- and 6-substituted HBT derivatives exhibited absorption bands at longer wavelengths, the keto-emission of 3'-substituted HBT derivatives was found at a substantially longer wavelength. The gradual red-shifted fluorescence emission was found for 3'-substituted HBT derivatives where the electron-donating nature of substituent group increased, which was opposite to what was observed for 4'- and 6-substituted HBT derivatives. The results derived from the theoretical calculations were in conformity with the experimental observations. Our study could potentially provide experimental and theoretical basis for designing novel ESIPT dyes that possess unique fluorescent properties.

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“…Our studies and literature reports indicated that responsive fluorescent nucleobase analogues can be generated by attaching heterocyclic moieties onto nucleobases . As part of our continuous efforts to develop responsive fluorescent probes, we identified the naphthalimide core of Lucifer dye as a promising heterocyclic moiety to build the fluorescent PNA building block for the following reasons . The Lucifer dye, based on a 1,8‐naphthalimide core, has an excitation and emission maximum in the visible region with a large Stokes shift and high quantum yield .…”

Section: Resultsmentioning

confidence: 99%

A Lucifer‐Based Environment‐Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs

2018

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Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore (1,8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them.

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Synthesis, Photophysical Properties and Incorporation of a Highly Emissive and Environment‐Sensitive Uridine Analogue Based on the Lucifer Chromophore

Cited by 16 publications

References 92 publications

Fluorescent RNA cytosine analogue – an internal probe for detailed structure and dynamics investigations

Fluorescent RNA cytosine analogue – an internal probe for detailed structure and dynamics investigations

Excited State Intramolecular Proton Transfer in Ethynyl‐Extended Regioisomers of 2‐(2′‐Hydroxyphenyl)benzothiazole: Effects of the Position and Electronic Nature of Substituent Groups

A Lucifer‐Based Environment‐Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs

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