Journal: Nature Communications

Article Title: A comprehensive synthetic library of poly- N -acetyl glucosamines enabled vaccine against lethal challenges of Staphylococcus aureus

doi: 10.1038/s41467-024-47457-4

Figure Lengend Snippet: A Relative fluorescence unit (RFU) of F598 mAb binding with the library of 32 PNAG pentasaccharides. The glycans are grouped according to the number of NHAc units in the molecule. Each PNAG sequence is printed five times on the glycan microarray. The error bars represent the standard deviations of five individual spots. Data are presented as mean values ± standard deviation. F598 generally prefers highly acetylated PNAG sequences. Both the location and the number of NHAc units are important determinants of F598 binding. B Quantification of the preference of F598 for acetylation at each site of the PNAG pentasaccharide. The mean values are calculated from the values of the binding intensities of all 32 PNAG sequences to F598. Each PNAG sequence is printed five times on the glycan microarray. Data are presented as mean values ± standard deviation. Source data are provided as a file.

Article Snippet: Glycan microarray slides were produced as previously described , on SuperEpoxy 2 slides (SME2; ArrayIt Corp, Sunnyvale, CA) and stored vacuum sealed at −20 °C.

Techniques: Fluorescence, Binding Assay, Sequencing, Glycoproteomics, Microarray, Standard Deviation

Journal: Nature Communications

Article Title: A comprehensive synthetic library of poly- N -acetyl glucosamines enabled vaccine against lethal challenges of Staphylococcus aureus

doi: 10.1038/s41467-024-47457-4

Figure Lengend Snippet: A IgG antibody titers to the immunizing PNAG oligosaccharide in rabbit ( n = 2 per group) sera on day 35 after prime vaccination. B IgG antibody titers in pooled rabbit sera from mQβ-conjugate or 5GlcNH 2 –TT conjugate immunized animals ( n = 2 per group) as well as titer of natural human IgG in pooled human serum against native PNAG polysaccharide purified from Acinetobacter baumannii . The numbers above symbols are the average titer numbers. Titers and 95% confidence intervals (CI) were determined by linear regression using log 10 values of the average of replicate serum dilutions to determine the X intercept and 95% CI when Y = 0.5 (OD 405 nm of ELISA plate reading). C Stacked bar graphs depicting the IgG signals at the serum dilution of 1:50,000 for each rabbit ( n = 2) immunized with mQβ–PNAG0, mQβ–PNAG10, and mQβ–PNAG26 as well as pre-immune sera, respectively, on the array. The complete microarray results are provided in the file; D Normalized binding of the comprehensive library of PNAG pentasaccharides by IgG antibodies from post-immune sera of rabbits immunized with mQβ–PNAG0, mQβ–PNAG10, and mQβ–PNAG26, respectively, as well as pre-immune sera. PNAG sequences are grouped together according to the total number of acetamides in the molecules. The color scale bar is shown on the right with 100% indicating the strongest binding to a PNAG component and 0% indicating the weakest binder. For each antigen, the two rows represent sera from two rabbits per group immunized with the specific construct. Source data are provided as a file.

Article Snippet: Glycan microarray slides were produced as previously described , on SuperEpoxy 2 slides (SME2; ArrayIt Corp, Sunnyvale, CA) and stored vacuum sealed at −20 °C.

Techniques: Purification, Enzyme-linked Immunosorbent Assay, Microarray, Binding Assay, Construct

Journal: Analytical Chemistry

Article Title: Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates

doi: 10.1021/acs.analchem.3c04166

Figure Lengend Snippet: (top) Resistance of gold- and ITO-coated microscope slides before and after DNA synthesis under iodine or CSO-mediated oxidation conditions. Measurements were taken with an ohmmeter at three diagonally opposed locations (bottom): slide corners (green), within the reaction chamber (red), and within the MAS synthesis area (blue). Sheet resistance (in Ω/square) was estimated by dividing the resistance with the length/width ratio of the rectangle encasing the two measurement points. The ratio was ∼3:1 for the slide dimensions, 2:1 for the reaction chamber, and 1.4:1 for the synthesis area. The sheet resistance and electrical resistance should be understood as approximate values only with an error margin of at least ±10% across three independent measurements.

Article Snippet: Microarray synthesis was carried out on glass microscope slides (Schott Nexterion D) silane-functionalized with N -(3-triethoxysilylpropyl)-4-hydroxybutyramide (Gelest SIT8189.5), gold-coated microscope slides with a 3D-amine layer (PolyAn 109 10008), or ITO-coated SuperEpoxy 2 microscope slides (ArrayIt).

Techniques: Microscopy, DNA Synthesis

Journal: Analytical Chemistry

Article Title: Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates

doi: 10.1021/acs.analchem.3c04166

Figure Lengend Snippet: (A) Fluorescence signals with a Cy3-labeled complementary sequence hybridized onto 25mer DNA microarrays decorated with ∼2000 replicates of the same sequence. Synthesis was performed using either iodine/water (yellow bars) or CSO (blue bars) as the oxidizer and otherwise standard photolithographic conditions on gold- or ITO-coated microscope slides. The glass copy (gold/ITO) labeling refers to the signal from the glass slide when synthesized alongside a gold- or ITO-coated substrate. (B) The background signal is recorded from features that only contain a dT 5 linker. (C) The signal/background corresponds to the ratio between hybridization signal and background fluorescence. (D) The dual array ratio is the ratio between fluorescence signals on the conductive substrate and those of the glass microscope slide. Error bars are the SD. (E) In the dual-array MAS procedure, a second microarray is produced simultaneously on a common silanized glass slide (“glass copy”). (F) Excerpts of microarray scans after hybridization with a Cy3-labeled complementary 25mer DNA strand. Hybridization was performed on gold and ITO-coated microscope slides and their duplicate on silanized glass. Each feature is a matrix of 5 × 5 micromirrors with a one-mirror wide gap between adjacent features. Features are randomly distributed across the entire microarray, and all contain the same 25mer DNA sequence. Excerpts are ∼0.5% of the total synthesis area. The scale bar is ∼100 μm.

Article Snippet: Microarray synthesis was carried out on glass microscope slides (Schott Nexterion D) silane-functionalized with N -(3-triethoxysilylpropyl)-4-hydroxybutyramide (Gelest SIT8189.5), gold-coated microscope slides with a 3D-amine layer (PolyAn 109 10008), or ITO-coated SuperEpoxy 2 microscope slides (ArrayIt).

Techniques: Fluorescence, Labeling, Sequencing, Microscopy, Synthesized, Hybridization, Microarray, Produced