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Search for "probes" in Full Text gives 264 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response
Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223
- . One of the challenges in the bio-anion detection is that the sensory probes have to be effective under physiological conditions. The highly polar nature of the aqueous media considerably weakens supramolecular interactions such as H-bonding and electrostatic interactions and as a result, it is in
- general challenging to design high-affinity synthetic probes for anion sensing under such competitive conditions [7]. One of the strategies that has proven to be quite successful in this regard, not only for bio-anions, rather for a variety of several other analytes also, is multivalency [8][9][10][11
Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes
Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219
- development of optical probes [1][2][3][4][5][6]. They are accessible in different sizes and shapes, can be stabilized by immobilizing suitable ligands, and can easily be functionalized with ligands containing binding sites that mediate the interaction with the analyte. Different strategies allow analyte
- surface plasmon resonance of the individual AuNPs starts to couple when they approach each other [7][8][9]. Early examples of optical probes working in this way are the nanoparticles introduced by Mirkin et al., containing immobilized oligonucleotides that aggregated in the presence of single-stranded DNA
- with a complementary base sequence [10], the AuNPs with peripheral carboxylate groups introduced by the Hupp group [11] that responded to divalent transition metal ions, or Chen at al.’s crown ether-decorated AuNPs that allowed the sensing of potassium ions [12]. Numerous other such probes have been
Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties
Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189
- -pull dyes are promising candidate materials for optoelectronic device usages and various NLO applications and could be used for applications as water-soluble fluorescent probes for determination of pH. Experimental Materials, methods, and instrumentation Tetrabutylammonium hydroxide (TBAOH) was
Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator
Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185
- spectroscopy methods (FDCD, CPL), the sensitivity of response is approaching the classical fluorimetric probes [14]. Our systematic work on aryl-guanidiniocarbonyl-pyrrole (GCP) derivatives characterised the GCP moiety as very useful building block in the design of new small molecules targeting DNA/RNA. The
- recognition of various DNA/RNA sequences could be reversibly changed by adjusting the pH of the solution. The fine structural tuning of such aryl-GCP conjugates allowed us to prepare a wide variety of small molecules with different DNA or RNA sequence selectivity, many of them acting as multipurpose probes
Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA
Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170
- the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA. Keywords: amino acid–fluorophore conjugate; circular dichroism; DNA/RNA recognition; fluorescence; intercalation; naphthalene diimide
- ]. 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
- stronger quenching for GC-DNA and the weaker for AT(U)-polynucleotides (Figure 5a and b). Because guanine is the most electron-rich nucleobase, this behaviour points at a fluorescence quenching mechanism by charge transfer from the electron-rich purine bases to the electron-poor NDI molecular probes
Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines
Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151
- analogues in complex biological systems such as peptides and proteins, especially in 19F NMR labelling, where fluorinated prolines can serve as spectroscopic probes. Potential areas for the application of fluorinated prolines are numerous, and include the design of molecular recognition systems [101
Et3N/DMSO-supported one-pot synthesis of highly fluorescent β-carboline-linked benzothiophenones via sulfur insertion and estimation of the photophysical properties
Beilstein J. Org. Chem. 2020, 16, 1740–1753, doi:10.3762/bjoc.16.146
- abecarnil, tadalafil, cipargamin, yohimbine, etc. which are used in the treatment of various ailments [14][15]. Apart from their pharmaceutical properties, β-carboline derivatives also found various applications in fields such as organocatalysts, as ligands, and fluorescent probes [16][17][18]. Importantly
- chemosensors, ligands, and fluorescent probes. In order to investigate the fluorescence properties, compound 2bA was chosen as the model substrate for optimization of various parameters like time, concentration, and solvent. In order to obtain the maximum emission, various solvents were screened. The
Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies
Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145
- Bern, Switzerland Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, 10065 New York, United States of America 10.3762/bjoc.16.145 Abstract The chemical synthesis of molecular probes to identify and study membrane proteins involved in the biological pathway of protein
- glycosylation is described. Two short-chain glycolipid analogs that mimic the naturally occurring substrate mannosyl phosphoryl dolichol exhibit either photoreactive and clickable properties or allow the use of a fluorescence readout. Both probes consist of a hydrophilic mannose headgroup that is linked to a
- probes, previous studies relied on a chemoenzymatic approach to selectively incorporate the biologically relevant β-configured ᴅ-mannose headgroup as chemical approaches were deemed to be too challenging [10][13]. This method naturally has some limitations regarding the quantity of the obtained compound
The McKenna reaction – avoiding side reactions in phosphonate deprotection
Beilstein J. Org. Chem. 2020, 16, 1436–1446, doi:10.3762/bjoc.16.119
- as phosphorus acids and esters are prevailing in nature [3][4], and the compounds found wide applications as therapeutics [5][6], probes [7] or in materials science [8]. The McKenna reaction involves two steps: In the first step an alkyl ester is transformed into the corresponding trimethylsilyl
Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles
Beilstein J. Org. Chem. 2020, 16, 1411–1417, doi:10.3762/bjoc.16.117
- be visualized using fluorescent probes, the use of AIE fluorescent probes is being investigated as a tool for analyzing the causal relationship between prion diseases and prion proteins. The importance of fluorinated heterocyclic derivatives in the pharmaceutical and agrochemical industries continues
- , fluorescent probes having an isoxazole scaffold are rare and the limited examples that are available also contain other fluorophores such as styryl, anthranyl, or pyrenyl groups in the molecules. We recently reported the synthesis of 3,5-diaryl-4-fluoroisoxazoles 3 that were found to have planar structures
Development of fluorinated benzils and bisbenzils as room-temperature phosphorescent molecules
Beilstein J. Org. Chem. 2020, 16, 1154–1162, doi:10.3762/bjoc.16.102
- materials. Keywords: alkyne oxidation; benzils; bistolanes; fluorinated compounds; phosphorescence; Introduction The development of organic light-emitting molecules is recognized as one of the most important studies because of the broad application of these compounds as fluorescence probes, bio-imaging
A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA
Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100
- their binding capability [3] with sensitivities in the range from 1 mM for cocaine to 10 pM for Hg2+, but for many targets it averages in the 1–10 nM range [4]. Although the diversity of NAs is very large, they can be divided into DNA-based biosensors, for example, molecular beacon or TaqMan probes
Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates
Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82
- -binding properties to be used as DNA-sensitive fluorescent probes in cell imaging [60][61][62] or as photoswitchable DNA ligands [63]. Therefore, we were interested in a combination of the photochromic properties of the spirooxazine moiety with the advantageous photophysical and biological properties of
Synthesis of triphenylene-fused phosphole oxides via C–H functionalizations
Beilstein J. Org. Chem. 2020, 16, 524–529, doi:10.3762/bjoc.16.48
- -containing ladder molecules and their application as fluorescence probes for biological imaging [10][11]. Marinetti extensively studied the synthesis of phosphahelicenes with linear fusion of the phosphole and the carbohelicene units [12], and their applications in asymmetric catalysis [13] and organic light
Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0
Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40
- less as aforementioned molecular ovens. Recently development of light sources in the NIR based on LEDs brought new hope in this field [65]. Furthermore, the fact that still some fluorescence occurs makes them interesting as fluorescent probes for imaging applications. NIR radiation possesses a
Chemical tuning of photoswitchable azobenzenes: a photopharmacological case study using nicotinic transmission
Beilstein J. Org. Chem. 2019, 15, 2812–2821, doi:10.3762/bjoc.15.274
- Lorenzo Sansalone Jun Zhao Matthew T. Richers Graham C. R. Ellis-Davies Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA 10.3762/bjoc.15.274 Abstract We have developed photochromic probes for the nicotinic acetylcholine receptor that exploit the unique chemical
- maintains the near-ideal chemical properties of Hecht’s 4FAB chromophores [12][13] (see below). The final synthetic challenge was the installation of a maleimide onto chromophore 2. The original AB photoswitchable probes which were cross-linked to cysteine mutants had amides with a reverse orientation [19
- photochemical probes. JZ performed the biological experiments. MTR first made some model photoprobes. GCRE-D supervised the work and wrote the paper. All authors commented on the paper and approved the final submitted version.
Dyes in modern organic chemistry
Beilstein J. Org. Chem. 2019, 15, 2798–2800, doi:10.3762/bjoc.15.272
- properties. Traditionally, organic dyes are the basis of well-established color indicators for qualitative and quantitative analysis. Nowadays, we cannot imagine research in the life sciences or in medical diagnostics without the sophisticated applications of organic dyes as fluorescent probes, dye labels
- , two-photon absorption probes or chemosensors [24][25][26][27][28][29][30]. After all, dye chemistry is literally an "evergreen" in scientific research, and consequently, its significant contributions to scientific developments and breakthroughs is well-documented in several Nobel prizes that are
Iodine-mediated hydration of alkynes on keto-functionalized scaffolds: mechanistic insight and the regiospecific hydration of internal alkynes
Beilstein J. Org. Chem. 2019, 15, 2747–2752, doi:10.3762/bjoc.15.265
- through a 5-exo-dig neighboring group participation (NGP) cyclization and an α-iodo intermediate. The work described herein probes the existence of the intermediate through NMR investigations and explores the scope of the hydration process with internal alkynes. The NMR experiments confirm the existence
A photochemical determination of luminescence efficiency of upconverting nanoparticles
Beilstein J. Org. Chem. 2019, 15, 2671–2677, doi:10.3762/bjoc.15.260
- , France 10.3762/bjoc.15.260 Abstract Upconverting nanoparticles are a rising class of non-linear luminescent probes burgeoning since the beginning of the 2000’s, especially for their attractiveness in theranostics. However, the precise quantification of the light delivered remains a hot problem in order
Plasma membrane imaging with a fluorescent benzothiadiazole derivative
Beilstein J. Org. Chem. 2019, 15, 2644–2654, doi:10.3762/bjoc.15.257
- related to this component responsible for the boundaries of the cells [2][3][4]. Various details have emerged due to the development of new sensitive molecular probes capable of staining organelles and cell components selectively, however, many open questions remain. Plasma membranes are the natural
- design and synthesis of small organic fluorescence imaging probes capable of selectively stain plasma membranes has been proven, however, often as a challenging task. The development of small organic probes, in general, has been hindered by the requirement of multistep syntheses to obtain the fluorophore
- application of water-soluble plasma membrane probes [17][18]. We have been developing a new class of selective bioprobes based on the derivatization of the 2,1,3-benzothiadiazole (BTD) core (Figure 1) [19][20][21][22]. After we disclosed the use of these BTD derivatives as a new class of selective
A new approach to silicon rhodamines by Suzuki–Miyaura coupling – scope and limitations
Beilstein J. Org. Chem. 2019, 15, 2569–2576, doi:10.3762/bjoc.15.250
- in super-resolution microscopy [1][2][3][4][5][6][7][8] and as probes for targeting various biomolecules [9][10][11][12] or sensors for metal ions [13][14][15][16][17], pH [15], voltage [18] or metabolites [19][20][21][22]. Since our group is interested in synthesizing new tumor tracers for
In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization
Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243
- , artificial probes activated by visible-light irradiation are highly desired in biological applications. Here, we report two novel types of visible-light photoswitchable peptide nucleic acids (PNAs) based on the molecular transducers: hemithioindigo and tetra-ortho-fluoroazobenzene. Our study reveals that the
- and Discussion Initially, short 12-mer PNA probes (Table 1) complementary to the HDAC-1 mRNA sequence were synthesized since, in general, PNAs are active with shorter sequences than the canonical analogues due to the superior binding abilities [40]. Despite that target specificity may be compromised
- synthesized longer PNA conjugates (6–11, 18 and 19) with flanking lysines, which improved the solubility of the probes. In addition, we compared our probes with the ones that contained the classical unmodified azobenzene moiety (Azo) (PNA 12–17). The lower stability of the unmodified cis-Azo forced us to
Effect of ring size on photoisomerization properties of stiff stilbene macrocycles
Beilstein J. Org. Chem. 2019, 15, 2408–2418, doi:10.3762/bjoc.15.233
- ][9][10][11]. The interplay between the forces involved in the switching action and the pull from groups attached to the stiff stilbene has been investigated, e.g., as molecular force probes [12][13][14][15][16][17][18]. While these do incorporate other isomerizable units in addition to stiff stilbene
Targeted photoswitchable imaging of intracellular glutathione by a photochromic glycosheet sensor
Beilstein J. Org. Chem. 2019, 15, 2380–2389, doi:10.3762/bjoc.15.230
- state of the cells, e.g., causing false-positive/negative results. Generally, strategies like designing ratiometric [4][5] or near-infrared [6][7][8] fluorescence sensors are applied to overcome this obstacle. Recently, a novel category of photochromic probes with light-controlled dynamic fluorescence
- signals has been developed, aiming at reducing interferences and improving sensing precision in complex physiological environments [9][10][11][12][13][14][15][16][17]. This photoresponsive design presents several advantages over conventional probes: 1) The light-activation mode endows the probe with light
Synthesis of a dihalogenated pyridinyl silicon rhodamine for mitochondrial imaging by a halogen dance rearrangement
Beilstein J. Org. Chem. 2019, 15, 2333–2343, doi:10.3762/bjoc.15.226
- microscopy [2][3][4][5][6][7][8][9], as direct probes for various biomolecules [10][11][12][13] or as sensors for metal ions [14][15][16][17][18], pH [16], voltage [19] or metabolites [20][21][22][23]. Several attempts were made, partially supported by DFT calculations, to correlate the dyes’ structural
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