Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores

Barandun, Luzi Jakob; Kool, Eric T.

doi:10.1039/c6ob01199c

Cited by 13 publications

(6 citation statements)

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“…Non-nucleoside surrogates suitable for multiple incorporation into oligonucleotides usually contain a reactive group for functionalization and primary plus secondary (or two primary) hydroxyl groups on a backbone more or less mimicking nucleoside structure (Figure ). Pyrene reagents were reported on a number of backbones: 1,2-diols, 1-substituted 1,3-diols (including chiral 2,4-dihydroxybutyramides , ), 2-substituted 1,3-diols (including serinol and threoninol − ), 1,2-disubstituted 1,3-diols (including pyrrolidine and tetrahydrofurans ,− ,− ), 1,4-diol (hydroxyprolinol), 1,5-diols (diethanolamine , and 1,3-bis(hydroxymethyl)benzene), etc. 1,2-Diol reagents in 5′-terminal position usually suffer from partial cleavage during ammonia deprotection due to cyclophosphate formation.…”

Section: Resultsmentioning

confidence: 99%

Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure

et al. 2017

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Oligonucleotide probes labeled with pyrene pairs that form excimers have a number of applications in hybridization analysis of nucleic acids. A long excited state lifetime, large Stokes shift, and chemical stability make pyrene excimer an attractive fluorescent label. Here we report synthesis of chiral phosphoramidite building blocks based on (R)-4-amino-2,2-dimethylbutane-1,3-diol, easily available from an inexpensive d-(-)-pantolactone. 1-Pyreneacetamide, 1-pyrenecarboxamide, and DABCYL derivatives have been used in preparation of molecular beacon (MB) probes labeled with one or two pyrenes/quenchers. We observed significant difference in the excimer emission maxima (475-510 nm; Stokes shifts 125-160 nm or 7520-8960 cm) and excimer/monomer ratio (from 0.5 to 5.9) in fluorescence spectra depending on the structure and position of monomers in the pyrene pair. The pyrene excimer formed by two rigid 1-pyrenecarboxamide residues showed the brightest emission. This is consistent with molecular dynamics data on excimer stability. Increase of the excimer fluorescence for MBs after hybridization with DNA was up to 24-fold.

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Section: Resultsmentioning

confidence: 99%

Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure

et al. 2017

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“…This close association resulted in interesting and sometimes surprising changes in their fluorescence behavior (e.g., emission color and intensity), and in the ability to selectively detect molecules. The combinatorial chemical libraries on polymer beads were built and useful reporter molecules were selected by fluorescence microscopy [ 194 , 195 , 196 , 197 ].…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

et al. 2017

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In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

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“…8 Another approach for preparing fluorescent oligonucleotide probes involves the coupling of a fluorescently labeled nucleotide monomer into a sequence-specific probe during solid-phase oligonucleotide synthesis. 9 The efficiency of this method depends strongly on the size and geometry of the labeled nucleotide molecule. 9,10 Although this method is habitually used, it faces challenges such as low coupling efficiency.…”

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confidence: 99%

“…9 The efficiency of this method depends strongly on the size and geometry of the labeled nucleotide molecule. 9,10 Although this method is habitually used, it faces challenges such as low coupling efficiency. Alternatively, post-synthetic bioconjugation strategies have been proposed for introduction of a functional group into the oligonucleotide sequence that serves as a substrate for post-synthetic labeling.…”

mentioning

confidence: 99%

“…Another approach for preparing fluorescent oligonucleotide probes involves the coupling of a fluorescently labeled nucleotide monomer into a sequence-specific probe during solid-phase oligonucleotide synthesis . The efficiency of this method depends strongly on the size and geometry of the labeled nucleotide molecule. , Although this method is habitually used, it faces challenges such as low coupling efficiency. Alternatively, post-synthetic bioconjugation strategies have been proposed for introduction of a functional group into the oligonucleotide sequence that serves as a substrate for post-synthetic labeling. − Efficient coupling of the functionalized oligonucleotide with different molecules using standard reagents and achieving high product yields are major improvements of this method …”

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Fluorescent Oligonucleotides with Bis(prop-2-yn-1-yloxy)butane-1,3-diol Scaffold Rapidly Detect Disease-Associated Nucleic Acids

Taskova

Astakhova

2019

Bioconjugate Chem.

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Biomedical research and clinical work demand rapid and reliable detection of disease-associated nucleic acids. Fluorescent oligonucleotides that bind precisely, and sense target DNA or RNA, are useful tools for simple hybridization-based assays. Although a plethora of oligonucleotide modifications are reported in the literature, they often result in poor coupling yields and are very expensive. We describe the synthesis of a new bisalkyne butane-1,3-diol scaffold and its efficient coupling into oligonucleotide sequences. We hypothesized that covalent attachment of multiple (2/4) fluorescent groups to the scaffold within oncogene-specific oligonucleotides could lead to beneficial detection of target DNA. To test this, we post-synthetically conjugated the oligonucleotides with azide-derivative dyes (2/4 per sequence): perylene, 5JOE, and (phenylethynyl)pyrene. We investigated the biophysical and photophysical properties of the oligonucleotide–dye conjugates and confirmed a “light up” fluorescent sensing mechanism of the probes upon target binding. However, fluorescence of the probes was not sensitive to mismatches. Nevertheless, “clicked” probes showed a high specificity of binding to complementary target, with the difference in T m over 10 °C for matched vs mismatched duplex. When applied together, the mismatch-induced difference in temperature melting and fluorescence-based discrimination of the target-bound vs single-stranded probe state allowed us to apply the perylene conjugates to detect mutations in human oncogenes. Due to the beneficial target binding properties of the perylene labeled probes, along with the high fluorescence intensity of probe:target duplexes, human oncogenes could be detected in a convenient and fast (2.5 h) bead-based assay.

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Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores

Cited by 13 publications

References 51 publications

Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure

Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

Fluorescent Oligonucleotides with Bis(prop-2-yn-1-yloxy)butane-1,3-diol Scaffold Rapidly Detect Disease-Associated Nucleic Acids

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