Bodipy-Labeled Nucleoside Triphosphates for Polymerase Synthesis of Fluorescent DNA

Dziuba, Dmytro; Pohl, Radek; Hocek, Michal

doi:10.1021/bc5003554

Cited by 43 publications

(19 citation statements)

References 73 publications

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“…Regarding the methods of conjugation, a wide variety of them is again available (Fig. 17), the most utilized ones including Sonogashira coupling reactions, 186,187 O-alkylation, 188 amide formation, 189,190,197 isothiocyanate chemistry, 193 and axial substitutions. 194,195 For Por, there is a recent review by Stulz describing covalent strategies for their conjugation with DNA, 196 which can be easily extrapolated to the other PS types.…”

Section: Ps-nucleic Acid Biohybridsmentioning

confidence: 99%

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Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management

et al. 2018

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The development of photoactive and biocompatible nanomaterials is a current major challenge of materials science and nanotechnology, as they will contribute to promoting current and future biomedical applications. A growing strategy in this direction consists of using biologically inspired hybrid materials to maintain or even enhance the optical properties of chromophores and fluorophores in biological media. Within this area, porphyrinoids constitute the most important family of organic photosensitizers. The following extensive review will cover their incorporation into different kinds of photosensitizing biohybrid materials, as a fundamental research effort toward the management of light for biomedical use, including technologies such as photochemical internalization (PCI), photoimmunotherapy (PIT), and theranostic combinations of fluorescence imaging and photodynamic therapy (PDT) or photodynamic inactivation (PDI) of microorganisms.

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Section: Ps-nucleic Acid Biohybridsmentioning

confidence: 99%

“…Hocek and co-workers reported in 2014 the synthesis of deoxynucleoside triphosphate analogues labelled with a BODIPY unit, through a flexible and short linker. 186 The conjugates were used as nucleotide monomers by polymerases in the synthesis of DNA (Fig. 18).…”

Section: Ps Biohybrids With Nucleobases Nucleosides and Nucleotidesmentioning

confidence: 99%

Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management

et al. 2018

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“…Moreover, 2′-alkyne functionality can be attached to diverse fluorophores and nanoparticles under highly efficient azide-alkyne cycloaddition conditions. Attachment of ultra-bright BODIPY dyes and semiconductor nanocrystals called quantum dots (QDs) is especially promising for applications in fluorescent microscopy ( Figure 3D) [28,29]. In addition, fluorescent metal nanoclusters (for example, silver-or gold-based) have attractive optical qualities, which may increase the sensitivity of nucleic acid detection [30,31].…”

Section: Enzyme-free Hybridization Assays: Specificity In Focusmentioning

confidence: 99%

Novel Signal-Enhancing Approaches for Optical Detection of Nucleic Acids—Going beyond Target Amplification

Miotke

Barducci²,

Astakhova³

2015

Chemosensors

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Detection of low-abundance nucleic acids is a challenging task, which over the last two decades has been solved using enzymatic target amplification. Enzymatic synthesis enhances the signal so that diverse, scientifically and clinically relevant molecules can be identified and studied, including cancer DNA, viral nucleic acids, and regulatory RNAs. However, using enzymes increases the detection time and cost, not to mention the high risk of mistakes with amplification and data alignment. These limitations have stimulated a growing interest in enzyme-free methods within researchers and industry. In this review we discuss recent advances in signal-enhancing approaches aimed at nucleic acid diagnostics that do not require target amplification. Regardless of enzyme usage, signal enhancement is crucial for the reliable detection of nucleic acids at low concentrations. We pay special attention to novel nanomaterials, fluorescence microscopy, and technical advances in detectors for optical assessment. We summarize sensitivity parameters of the currently available assays and devices which makes this review relevant to the broad spectrum of researchers working in fields from biophysics, to engineering, to synthetic biology and bioorganic chemistry.

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“…The BODIPY dyes are readily amenable to structural modifications to tune their photophysical properties. Thus, a wide variety of BODIPYs have been synthesized and explored for their novel optical properties and energy‐harvesting applications . We recently reported a facile route for the synthesis of BF 2 complexes of meso ‐aryl pyrrolyldipyrrins (3‐pyrrolyl BODIPYs), which were not easily accessible before.…”

Section: Introductionmentioning

confidence: 99%

“…Thus, aw ide variety of BODIPYs have been synthesized ande xplored for their novel optical properties and energy-harvesting applications. [57][58][59][60][61][62][63][64][65][66][67][68][69] We recently reported af acile route for the synthesis of BF 2 complexes of meso-aryl pyrrolyldipyrrins [70][71][72][73] (3-pyrrolyl BODIPYs), which were not easily accessible before. The 3-pyrrolyl BODIPYsh ave better photophysical properties than mesoaryl BODIPYs.P erusal of the literature revealed interesting reports on covalently linked, strongly coupledB ODIPY oligomers, [21] but reports on multi-BODIPY systems based on 3-pyrrolyl BODIPYs are scarce because of the unavailability of appropriate functionalized 3-pyrrolyl BODIPYs.…”

Section: Introductionmentioning

confidence: 99%

Panchromatic Light Capture and Efficient Excitation Transfer Leading to Near‐IR Emission of BODIPY Oligomers

et al. 2016

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All-BODIPY-based (BODIPY=boron-dipyrromethene) donor-acceptor systems capable of wide-band absorbance leading to efficient energy transfer in the near-IR region are reported. A covalently linked 3-pyrrolyl BODIPY-BODIPY dimer building block bearing an ethynyl group at the meso-aryl position is synthesized and coupled with three different monomeric BODIPY/pyrrolyl BODIPY building blocks with a bromo/iodo group under Pd(0) coupling conditions to obtain three covalently linked 3-pyrrolyl-BODIPY-based donor-acceptor oligomers in 19-29 % yield. The oligomers are characterized in detail by 1D and 2D NMR spectroscopy, high-resolution mass spectrometry, and optical spectroscopy. Due to the presence of different functionalized BODIPY derivatives in the oligomers, panchromatic light capture (300-725 nm) is witnessed. Fluorescence studies reveal singlet-singlet energy transfer from BODIPY monomer to BODIPY dimer leading to emission in the 700-800 nm range. Theoretical modeling according to the Förster mechanism predicts ultrafast energy transfer due to good spectral overlap of the donor and acceptor entities. Femtosecond transient absorption studies confirm this to be the case and thus show the relevance of the currently developed all-BODIPY-based energy-funneling supramolecular sytems with near-IR emission to solar-energy harvesting applications.

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Bodipy-Labeled Nucleoside Triphosphates for Polymerase Synthesis of Fluorescent DNA

Cited by 43 publications

References 73 publications

Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management

Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management

Novel Signal-Enhancing Approaches for Optical Detection of Nucleic Acids—Going beyond Target Amplification

Panchromatic Light Capture and Efficient Excitation Transfer Leading to Near‐IR Emission of BODIPY Oligomers

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