J. Sobek's research while affiliated with Hochschule für Technik Zürich and other places

... [1][2][3][4][5][6][7][8][9][10][11] Libraries containing billions of compounds from a relatively small number of building blocks (e.g., few thousand chemical compounds) can be constructed using a variety of different experimental approaches, such as pool-andsplit methodologies, [12] DNA-templated chemical reactions with preformed oligonucleotide derivatives [13][14][15] or the use of encoded self-assembling strategies. [16][17][18][19][20][21] The attractiveness of encoding chemical compounds with DNA fragments relate to the possibility of constructing and storing large libraries as a mixture, that can be interrogated by affinity capture procedures on immobilized proteins of interest, followed by decoding, using highthroughput DNA sequencing. [12,22,23] Indeed, the identity and relative frequency of each compound in the library (e.g., before and after a screening experiment) can be directly retrieved from the results of a DNA sequencing experiment, since each library member is encoded by a distinctive DNA fragment. ...

... Concerning the protein functionality, several solutions were investigated (adding different denaturants, adding imidazole, and using the binding buffer) in combination with adding 20% glycerol. Adding denaturants was recommended in the previous studies [165]. Therefore, in order to solve protein aggregation problem, several denaturants were investigated. ...

... The species A oligonucleotide probe (NLT499: 5′-ACA GAG TTA GCC GTG GCT-3′) was developed and designed to target the 16S rRNA genes from members of the classes Leptospirillia, Thermodesulfovibrionia, as well as other uncultivated classes within the phylum Nitrospirota 62 . Two oligonucleotide probes were used to target members of the order Betaproteobacteriales, including species B. Previously, a probe (BETA359 or Beta1: 5′-CCC ATT GTC CAA AAT TCC CC-3′) 63,64 had been reported, but the optimal hybridization conditions were not. A second probe was designed for this study (BETA867: 5′-AGG CGG TCA ACT TCA CGC-3′). ...

... Astraphloxin, better known under the name of CY3 (Figure 1), and its sulfonated derivatives linked to nucleosides and oligonucleotides are used in a large variety of analytical applications. The photophysical properties of the dyes are well investigated by static and time-resolved methods, including single-molecule applications [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20]. The main deactivation pathway of the first excited state of CY3 proceeds via a radiationless transition, the trans-cis isomerisation of an exocyclic double bond, which decreases the fluorescence quantum yield to less than 10% [3,5,7,9,[21][22][23][24]. Blocking the isomerisation by conjugation with nucleosides, oligonucleotides, and proteins, the chemical modification of the chromophore as in CY3B, or the use of a highly viscous solvent, increases the quantum yield up to 85% [3,9,[25][26][27]. ...

... Astraphloxin, better known under the name of CY3 (Figure 1), and its sulfonated derivatives linked to nucleosides and oligonucleotides are used in a large variety of analytical applications. The photophysical properties of the dyes are well investigated by static and time-resolved methods, including single-molecule applications [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20]. The main deactivation pathway of the first excited state of CY3 proceeds via a radiationless transition, the trans-cis isomerisation of an exocyclic double bond, which decreases the fluorescence quantum yield to less than 10% [3,5,7,9,[21][22][23][24]. Blocking the isomerisation by conjugation with nucleosides, oligonucleotides, and proteins, the chemical modification of the chromophore as in CY3B, or the use of a highly viscous solvent, increases the quantum yield up to 85% [3,9,[25][26][27]. ...

... Incubation times of more than 4 h are required for immobilizing the probe molecules (like oligonucleotides) under the particular chemical and humidity conditions [102]. Betaine may be used in the spotting mixture of PCR products or oligonucleotides to reduce evaporation during transferring PCR products to the array surface [103]. ...

... Stock solution of thiol-linked glycans 1-17 were solubilized in PBS (pH 7.4) containing an equimolar concentration of tris (2-carboxyethyl) phosphine hydrochloride (Thermo Fisher Scientific, USA) to 1 mM glycan concentration and were immobilized on sciCHIP EPOXY activated glass slides (Scienion AG, Berlin, Germany) with a piezoelectric spotting device (S3; Scienion AG, Berlin, Germany) as published earlier [43]. After spotting, microarray slides were incubated for 18 h in a humid chamber to complete the coupling reaction. ...

... [65,66] With high-performance focusing optics that are capable of low micrometer or submicrometer spot sizes,M ALDI-MS allows single-cell and subcellular analysis,r espectively. [67][68][69] This analysis can be conducted in the context of high-spatialresolution MS imaging for tissue-embedded cells [70,71] or local MS analysis for unicellular organisms [72][73][74] and cells dissociated from tissues. [75][76][77] In some cases,i ti sp ossible to use native cellular constituents as the matrix. ...

... At the same time, imaging MS can be used to profile cells in situ, thus not only minimizing the cell perturbation required in conventional metabolomics but also allowing the association of molecular information with the spatial context, such as cell morphometric information or cell-cell interactions. Various single-cell metabolomics and lipidomics imaging MS approaches have been proposed and have demonstrated the potential of obtaining rich metabolic and lipidomics profiles that can predict cell types and associated molecular changes with perturbations (152)(153)(154)(155). We have recently demonstrated that single-cell metabolomics can discover molecularly distinct cell subpopulations even in cell cultures (155). ...

... Very recently, random mutagenesis of the macrodomain Af1521 was used to develop an engineered Af1521 (eAf1521) with 1000-fold increased affinity towards ADP-ribose compared to wildtype Af1521 [164]. Its use for the proteomic ADP-ribosylome MS workflow increased the ADP-ribosylated protein identification rates and yielded greater ADPribosylome coverage. ...