Naphthalenyl‐ and Anthracenyl‐Ethynyl dT Analogues as Base Discriminating Fluorescent Nucleosides and Intramolecular Energy Transfer Donors in Oligonucleotide Probes.

Xiao, Qiang; Ranasinghe, Rohan T.; Tang, A.; Brown, Tom

doi:10.1002/chin.200726170

Cited by 3 publications

(3 citation statements)

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“…Briefly, anthracene ( 1 ) was converted to 9-bromoanthracene ( 2 ) in the presence of aqueous hydrohalic acid and hydrogen peroxide following the bromination methodology reported by Vyas et al . Subsequently, reaction of 9-bromoanthracene with 2-methylbut-3-yn-2-ol in a standard Sonogashira coupling produced the corresponding 4-(anthracen-10-yl)-2-methylbut-3-yn-2-ol ( 3 ), ,− which was converted to the 9-ethynylanthracene ( 4 ) , by treatment with potassium hydroxide in refluxing toluene. Finally, the resulting terminal acetylene ( 4 ) was coupled with 9-bromoanthracene formed in the same coupling procedure used before to obtain ( 3 ), to yield the desired 1,2-di(anthracen-9-yl)ethyne or 1,2-bis(9-anthryl)acetylene, BisAA ( 5 ), − in 68% in the last reaction step.…”

Section: Methodsmentioning

confidence: 99%

Dynamics of the Formation of a Charge Transfer State in 1,2-Bis(9-anthryl)acetylene in Polar Solvents: Symmetry Reduction with the Participation of an Intramolecular Torsional Coordinate

et al. 2013

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We have studied 1,2-bis(9-anthryl)acetylene as a model compound for the characterization of the process of solvent-mediated symmetry reduction in an excited state. Thanks to the acetylenic bridge that joins the two anthracenic moieties, this system maintains minimal steric hindrance between the end chromophores in comparison with the classic 9,9'-bianthryl model compound. The acetylenic bridge also allows for significant electronic coupling across the molecule, which permits a redistribution of electron density after light absorption. Femtosecond resolved fluorescence measurements were used to determine the spectral evolution in acetonitrile and cyclohexane solutions. We observed that, for 1,2-bis(9-anthryl)acetylene, the formation of a charge transfer state occurs in a clear bimodal fashion with well separated time scales. Specifically, the evolution of the emission spectrum involves a first solvent-response mediated subpicosecond stage where the fluorescence changes from that typical of nonpolar solvents (locally excited) to an intermediate, partial charge transfer state. The second stage of the evolution into a full charge transfer state occurs with a much longer time constant of 37.3 ps. Since in this system the steric hindrance is minimized, this molecule can undergo much larger amplitude motions for the torsion between the two anthracenic moieties associated with the charge redistribution in comparison with the typical model compound 9,9'-bianthryl. Clearly, the larger range of motions of 1,2-bis(9-anthryl)acetylene gives the opportunity to study the electron transfer process with a good separation of the time scales for the formation of a partial charge transfer state, determined by the speed of solvent response, and the intramolecular changes associated with the formation of the fully equilibrated charge transfer state.

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Section: Methodsmentioning

confidence: 99%

Dynamics of the Formation of a Charge Transfer State in 1,2-Bis(9-anthryl)acetylene in Polar Solvents: Symmetry Reduction with the Participation of an Intramolecular Torsional Coordinate

et al. 2013

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“…Nucleic acids carry out their functions by interacting with nucleic acids, proteins, and small-molecule metabolites, and during such processes, they often undergo significant conformational changes. Numerous biophysical tools have been developed to investigate these conformational changes and hence the dynamics and binding properties of nucleic acids in vitro. − Biophysical probes, in particular, fluorescent nucleoside analogues that closely resemble natural nucleosides and photophysically report conformational changes, have been instrumental in studying the dynamics and function of various nucleic acid motifs. − Some examples include (a) the detection of single nucleotide polymorphism (SNP) − and DNA and RNA lesions, − (b) monitoring of nucleic acid structural dynamics, − (c) the determination of binding affinities of therapeutically relevant nucleic acid–protein and nucleic acid–small molecule complexes, − and (d) the analysis of the electron-transfer process in nucleic acids. , However, the excitation maximum in the UV region and low quantum yields when incorporated into oligonucleotides have substantially limited the applications of the majority of fluorescent nucleoside analogues to in vitro systems only . Interestingly, comparative studies in aqueous buffers and in membrane models, mimicking the physical properties and crowding that exist in a cellular environment, indicate that the structure, dynamics, activity, and recognition properties of biological macromolecules depend on the environment in which they are present. − Therefore, a fundamental understanding of the behavior of oligonucleotides in a model cellular milieu could provide new insights into nucleic acid folding and recognition properties, which may have implications for the discovery of drugs and diagnostic tools.…”

Section: Introductionmentioning

confidence: 99%

Environment-Responsive Fluorescent Nucleoside Analogue Probe for Studying Oligonucleotide Dynamics in a Model Cell-like Compartment

Pawar

Srivatsan

2013

J. Phys. Chem. B

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The majority of fluorescent nucleoside analogue probes that have been used in the in vitro study of nucleic acids are not suitable for cell-based biophysical assays because they exhibit excitation maxima in the UV region and low quantum yields within oligonucleotides. Therefore, we propose that the photophysical characterization of oligonucleotides labeled with a fluorescent nucleoside analogue in reverse micelles (RM), which are good biological membrane models and UV-transparent, could provide an alternative approach to studying the properties of nucleic acids in a cell-like confined environment. In this context, we describe the photophysical properties of an environment-sensitive fluorescent uridine analogue (1), based on the 5-(benzo[b]thiophen-2-yl)pyrimidine core, in micelles and RM. The emissive nucleoside, which is polarity- and viscosity-sensitive, reports the environment of the surfactant assemblies via changes in its fluorescence properties. The nucleoside analogue, incorporated into an RNA oligonucleotide and hybridized to its complementary DNA and RNA oligonucleotides, exhibits a significantly higher fluorescence intensity, lifetime, and anisotropy in RM than in aqueous buffer, which is consistent with the environment of RM. Collectively, our results demonstrate that nucleoside 1 could be utilized as a fluorescent label to study the function of nucleic acids in a model cellular milieu.

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“…Synthesis of donor/acceptor system. Compounds 1 and 5 were synthesized according to published methods (15,16; Scheme 1).…”

mentioning

confidence: 99%

Manipulation of Förster Energy Transfer of Coupled Fluorophores Through Biotransformation by Pseudomonas resinovorans CA10

Daniele

Bandera

Foulger

2011

Photochem & Photobiology

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An alkyne-terminated anthracene and azide-terminated carbazole were joined through a copper-catalyzed cycloaddition to form a joined donor/acceptor pair. The photonic pair exhibited energy transfer when excited at the peak absorbance of carbazole and fluoresced with an anthracene spectral response. The fluorescent behavior was confirmed as Förster energy transfer (FRET). The lysate of Pseudomonas resinovorans CA10, a member of a predominant group of soil microorganisms that can metabolize a host of substrates, was employed to degrade the pair and alter the luminance spectral characteristics. The FRET was diminished and the corresponding, individual fluorescence of carbazole and anthracene returned. This general approach may find applications in single-cell metabolic studies and bioactivity assays.

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Naphthalenyl‐ and Anthracenyl‐Ethynyl dT Analogues as Base Discriminating Fluorescent Nucleosides and Intramolecular Energy Transfer Donors in Oligonucleotide Probes.

Abstract: ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Cited by 3 publications

References 1 publication

Dynamics of the Formation of a Charge Transfer State in 1,2-Bis(9-anthryl)acetylene in Polar Solvents: Symmetry Reduction with the Participation of an Intramolecular Torsional Coordinate

Dynamics of the Formation of a Charge Transfer State in 1,2-Bis(9-anthryl)acetylene in Polar Solvents: Symmetry Reduction with the Participation of an Intramolecular Torsional Coordinate

Environment-Responsive Fluorescent Nucleoside Analogue Probe for Studying Oligonucleotide Dynamics in a Model Cell-like Compartment

Manipulation of Förster Energy Transfer of Coupled Fluorophores Through Biotransformation by Pseudomonas resinovorans CA10

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