Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• emission change upon binding to proteins, and a cyanine fluorescence that was selective for polynucleotides. Moreover, the FRET pair of chromophores was activated upon binding to biomolecules [18]. Continuing our previous work, two phenanthridine–pyrene conjugates Phen-Py-1 and Phen-Py-2 (Scheme 1

Thermally activated delayed fluorescence (TADF) emitters: sensing and boosting spin-flipping by aggregation

• Ashish Kumar Mazumdar,
• Gyana Prakash Nanda,
• Nisha Yadav,
• Upasana Deori,
• Upasha Acharyya,
• Bahadur Sk and
• Pachaiyappan Rajamalli

Beilstein J. Org. Chem. 2022, 18, 1177–1187, doi:10.3762/bjoc.18.122

• developed mainly by focusing on photophysical processes, such as photoinduced electron transfer (PET), excited-state intramolecular proton transfer (ESIPT), fluorescence resonance energy transfer (FRET), etc. [21][22][24][25]. Several literature reports have also demonstrated the switching of fluorescence

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• be performed. Supramolecular systems based on non-covalent interactions have drawn considerable attention in assembling efficient light harvesting systems (LHSs) in the last decade [60][61]. Significant attention has been centered to construct artificial LHSs via FRET (fluorescence resonance energy

• transfer) that include organic materials and supramolecular assemblies. Recently, FRET phenomena have been successfully demonstrated in supramolecular architectures based on metal organic frameworks and covalent organic frameworks [62][63][64]. However, poor solubility of such polymeric systems in common

• (26) was chosen as a FRET acceptor as there is a considerable overlap in energy of the donor emission and acceptor absorption. Then, artificial LHSs were constructed with aggregates from 24b or 25b at a donor/acceptor ratio of 5:1 (Figure 6). Finally, the light harvesting materials (24b + 26) and (25b

Tetraphenylethylene-embedded pillar[5]arene-based orthogonal self-assembly for efficient photocatalysis in water

• Zhihang Bai,
• Krishnasamy Velmurugan,
• Xueqi Tian,
• Minzan Zuo,
• Kaiya Wang and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2022, 18, 429–437, doi:10.3762/bjoc.18.45

• intramolecular phenyl-ring rotations and functioned as an ideal donor. After the loading of eosin Y (EsY) as acceptor on the surface of the assembly of m-TPEWP5 and G, the worm-like nanostructures changed into nanorods, which facilitates a Förster resonance energy transfer (FRET) from the m-TPEWP5 and G

• assembled donor to the EsY acceptor present in the nanorod assembly. The system comprising m-TPEWP5, G and EsY displayed moderate FRET efficiency (31%) at a 2:1 molar ratio of donor-to-acceptor. Moreover, the obtained supramolecular nanorod assembly could act as a nanoreactor mimicking natural

• power factories, containing many manufacturing units called chloroplasts. Briefly, the antenna molecules capture the light energy by using protein–pigment complexes and transfer it to the specialized reaction centers via the FRET process, where the excited state energy is transferred into useable

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• monitoring of the temperature-dependent Förster resonance energy transfer (FRET) between the dyes [46]. The particular oligonucleotide sequences were chosen because they are known to be involved in biologically relevant processes, namely in the transcription regulation of myc (FmycT) [47][48], kit (FkitT

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• labeled with environmentally sensitive/FRET fluorophores have allowed direct detection/monitoring of biomolecules in aqueous media and in live cells. In this review, key peptide-based approaches for different biological applications are presented. Keywords: fluorescent probe; fluorophores; molecular

• intensities of absorption or emission at two wavelengths minimizes the error from the physical or chemical fluctuations in the sample. Conventional peptide probes based on environment-sensitive fluorophores [20][21][22], fluorescence resonance energy transfer (FRET) pairs [13] and pyrene excimer/monomer [23

• ). Fluorescence resonance energy transfer (FRET) relies on the distance-dependent transfer of energy from a donor fluorophore to an acceptor fluorophore. Genetically encoded fluorophores, such as green fluorescent protein (GFP) and related blue, cyan, yellow and red fluorescent proteins have provided the ability

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• is desired, in order to introduce two or even more functionalities in a specific manner. For example, in earlier work we have used amine-NHS coupling reactions in combination with CuAAC to prepare double labeled RNA molecules for FRET analysis [19]. The conjugation of, sometimes rather large

• nucleic acids via Förster Resonance Energy Transfer (FRET) [20]. More recently, we started an effort to develop an efficient strategy for the preparation of a linker-modified adenosine building block, which in a future project is to be used for post synthetic conjugation of reporters or functional

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• experiments. For that purpose, the DNA melting temperature Tm of the dye-labeled oligonucleotides F21T and Fa2T (for sequence see caption of Figure 2) was monitored by fluorescence spectroscopy, as the thermally induced unfolding of the quadruplex disrupts the Förster resonance energy transfer (FRET) between

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• receptors is described. We show that the binding of DNA-based artificial receptors to E. coli expressing His-tagged outer membrane protein C (His-OmpC) induces a Förster resonance energy transfer (FRET) between the dyes, which results in the generation of a unique fluorescence fingerprint. Because the

• optical signatures owing to the FRET between the dyes (Figure 3A, step 1). In addition, we expected that a division of the labeled bacteria will increase the distance between the bacteria-bound receptors, which will lead to a decrease in the FRET efficiency and to a consequent change in the fluorescence

• excitation of the FRET donors (FAM or TAMRA) following 0, 12, and 24 hours of incubation. The spectra obtained by excitation of TAMRA (Figure 4A, 545 nm) at t = 0 indicate the manifestation FRET between the donor (TAMRA) and acceptor (Cy5), which results in a lower emission intensity of TAMRA. Over time

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• quenched in the absence of the analyte by Förster resonance energy transfer (FRET). In the latter case, the analyte binding either causes the chromophore to dissociate from the nanoparticle, if it is bound noncovalently (indicator displacement), or to move away from the metal surface as a consequence of a

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• , involves the exchanges of two electrons with different spin and energy between two molecules (Figure 4). Therefore, it can be termed a Dexter energy transfer mechanism, not a Forster resonance energy transfer (FRET) mechanism. The generated triplet state of the substrate then undergoes further chemical

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• therefore adaptable for the design of FRET pairs with other dyes along the peptide backbone. Such amino acid construct would bring a novel functional property into peptide–multichromophore systems targeting DNA/RNA. For the design of our new constructs we noticed that the majority of DNA/RNA targeting NDIs

• ]. That would allow in future research combining of the here studied NDI–AA derivatives with the above mentioned and other pH-sensitive fluorophore–AA, to prepare multicolour spectroscopic probes and eventually also FRET pairs. Also, the two NDI–AA conjugates 3a and 3b have protonatable amino groups at

• peptide-backbone constructed multichromophores targeting FRET-based sensing [14][26][58]. For the application of here presented results in bioanalytical sciences or biologically relevant studies it will be necessary to further modify the presented compounds and precisely collect information about their

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

Targeted photoswitchable imaging of intracellular glutathione by a photochromic glycosheet sensor

• Xianzhi Chai,
• Hai-Hao Han,
• Yi Zang,
• Jia Li,
• Xiao-Peng He,
• Junji Zhang and
• He Tian

Beilstein J. Org. Chem. 2019, 15, 2380–2389, doi:10.3762/bjoc.15.230

• remarkably quenched to ca. 30% (ΦF = 0.085, Table S1 in Supporting Information File 1) through an efficient intramolecular fluorescence resonance energy transfer (FRET) mechanism [29][30] after the photocyclization of Glyco-DTE. The fluorescence was fully recovered by irradiation with visible light and the

• broad and strong absorption makes the 2D MnO2 nanosheets a potential energy acceptor for the fluorophores which are stacked on the nanosheets plane, leading to the fluorescence quenching through FRET mechanism [32][34]. The transmission electron microscopy (TEM) image of the prepared product revealed

• effective FRET between the attached Glyco-DTE and 2D MnO2, which again suggested the close stacking of Glyco-DTE to the nanosheet surface. Aggregation-caused quenching might be another reason for the fluorescence quenching because of the close distance between fluorescence molecules when absorbed on the

Aggregation-induced emission effect on turn-off fluorescent switching of a photochromic diarylethene

• Luna Kono,
• Yuma Nakagawa,
• Ayako Fujimoto,
• Ryo Nishimura,
• Yohei Hattori,
• Toshiki Mutai,
• Nobuhiro Yasuda,
• Kenichi Koizumi,
• Satoshi Yokojima,
• Shinichiro Nakamura and
• Kingo Uchida

Beilstein J. Org. Chem. 2019, 15, 2204–2212, doi:10.3762/bjoc.15.217

• intermolecular Förster Resonance Energy Transfer (FRET) process between the fluorescent units and the photochromic moieties in their closed form within the aggregated state [29]. The crystal did not show any vapochromism, while a dramatic fluorescent color change from green to pink was observed when chloroform

Applications of organocatalysed visible-light photoredox reactions for medicinal chemistry

• Michael K. Bogdos,
• Emmanuel Pinard and
• John A. Murphy

Beilstein J. Org. Chem. 2018, 14, 2035–2064, doi:10.3762/bjoc.14.179

• , there are multiple pathways through which it can decay back to S0. The excited state can decay via non-radiative processes, such as vibrational relaxation. It can also return to S0 via fluorescence or non-radiative emission. While in S1 (or T1) Förster resonance electron transfer (FRET) can occur, a

Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• the macrocycle would be desirable. One possibility is the utilization of monofunctionalized CBs with outer cavity-attached fluorescent dyes [22][24]. This principally allows for the modular construction of various Förster resonance energy transfer (FRET) pairs as demonstrated with a Cy3-attached CB7

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• and its cytotoxicity was attributed to DNA minor groove binding ability [105]. Recently, Schmuck et al. have developed a first prototype of cationic oligopeptide-based molecular beacon (conjugate 43) coupled with a FRET pair, a naphthalene donor and a dansyl acceptor, for ratiometric detection of ds

• , thereby changing the efficiency of the FRET process between the two fluorophores and exhibiting a significant red shift in the emission spectrum. Moreover, the conjugate 43 could be used as an attractive tool for imaging of nuclear DNA in the cells due to its low cytotoxicity. A series of water-soluble

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• probes with nanomaterials as an external quencher. In addition, the uncharged backbone of PNA offers other unique designs, including the combination of PNA probes with cationic conjugated polymers that simultaneously act as a light harvesting antenna and fluorescent resonance energy transfer (FRET

• background and good response with DNA, as well as offering an excellent specificity [65]. In addition to fluorophore-quencher interactions, FRET [66] and pyrene monomer–excimer switching [67][68] have been employed as alternative mechanisms for inducing fluorescence changes in the DNA probes. The FRET and

• monomer–excimer switching approaches have some advantages over fluorescence quenching because of the large Stokes shifts and the ability to measure the signals at two different wavelengths, thereby providing a means for self-referencing. Furthermore, unlike the fluorophore-quencher beacons, the FRET and

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

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• , SE-412 96 Gothenburg, Sweden 10.3762/bjoc.14.7 Abstract 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, κ2, have a different

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• dyes which could be applied as FRET pair. In this case, labeling was achieved in two bioorthogonal reactions, an iEDDA and a SPAAC reaction. Furthermore, dual modification with an azido and an alkyne function enabled fluorophore/biotin labeling using a combination of SPAAC and CuAAC reaction. Efficient

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• (FRET). In the presence of the analyte (i.e., cholera toxin), galactose-AuNPs recognize the protein, avoiding the formation of QD complex and, consequently recovering the fluorescence. This method, although based on a monosaccharide, showed the impressive improvement obtained for using multivalent glyco

A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

• Heidi-Kristin Walter,
• Bettina Olshausen,
• Ute Schepers and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2017, 13, 127–137, doi:10.3762/bjoc.13.16

• -green contrast of 86). In order to test the functionality of the respective dyes as FRET pairs in DNA duplexes for imaging in cells, four representative duplexes, DNA2aD1–DNA3rD5, DNA2rD1–DNA3aD8, DNA2aD2–DNA3aD8 and DNA2rD4–DNA3aD8, were tested in HeLa cells. 5 × 104 HeLa cells were transiently

• /lysosomal vesicles. The fluorescence of the energy donors, D1, D2 and D4 (Figure 2, left column), as well as the fluorescence of the energy acceptors, D5 and D8 (Figure 2, middle column), could be detected showing that fluorescence energy was transferred from the donor to the acceptor in the respective FRET

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

• Vincent M. Rotello

Beilstein J. Org. Chem. 2016, 12, 1638–1646, doi:10.3762/bjoc.12.161

• undiluted serum [82] a project that we are currently testing in human studies. I should point out that we have managed to marry the strenths of the polymer and fluorescent protein systems [83] using polymer–protein FRET to provide modulated output [84]. You'll remember that I said that conjugated polymers