Journal: Nature Communications

Article Title: Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors

doi: 10.1038/s41467-018-07116-x

Figure Lengend Snippet: Characterization of the hybrid pore formation. a Typical current profile over time recorded through a 5.5 nm diameter SS pore at +100 mV. After injection of 0.1 nmol of portal protein, short current drops are detected, interpreted as portal collisions with the solid-state nanopore. b A representative current vs time trace recorded for a 5.4 nm SS nanopore at +80 mV, showing stable insertion of a portal protein. c Current as a function of the applied voltage for a 5.7 nm diameter SS pore recorded before (red markers) and after insertion of a portal protein (purple). d Current noise analysis of a 5.5 nm diameter solid-state nanopore before (red) and after insertion of a portal protein (purple). e Conductance of solid-state nanopore vs conductance of hybrid SS-portal pores formed after electrokinetic corking of the portal protein within the SS nanopore ( n = 32 for CD/N hybrids and n = 15 for CGG hybrids). Experiments were performed in 0.5 M NaCl, 20 mM Tris, pH 7.5

Article Snippet: Protein was exchanged into 20 mM Tris pH 7.5, 0.5 M NaCl buffer (Zeba Spin Columns, Thermofisher) for use in hybrid nanopore formation.

Techniques: Injection

Journal: Nature Communications

Article Title: Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors

doi: 10.1038/s41467-018-07116-x

Figure Lengend Snippet: Sensing different biopolymers using a hybrid nanopore. Current vs time trace recorded through the hybrid pore at +60 mV in the presence of a 36.0 μM insulin, b 7.7 μM DNA hairpin, c 10.3 μM TPX2 peptide and d 16.6 μM ssDNA. The data in a were filtered at 10 kHz (gray) or 0.5 kHz (green). e Scatter plot of Δ I vs dwell time for the DNA hairpin (red, n = 5883 events), the peptide (purple, n = 3368 events) and the ssDNA (orange, n = 18,812 events)). Experiments were performed in 0.5 M NaCl, 20 mM Tris, pH 7.5

Article Snippet: Protein was exchanged into 20 mM Tris pH 7.5, 0.5 M NaCl buffer (Zeba Spin Columns, Thermofisher) for use in hybrid nanopore formation.

Techniques:

Journal: Nature Communications

Article Title: Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors

doi: 10.1038/s41467-018-07116-x

Figure Lengend Snippet: Dynamics of TPX2 peptide transport. a Current vs time trace recorded through a hybrid pore at +30, +40 and +55 mV in the presence of 10.3 μM TPX2 peptide. b Semi-log plot of the event frequency as a function of the applied voltage. c Semi-log plot of the peptide dwell time as a function of the applied voltage. The lines in ( b , c ) are exponential fits to the data. Experiments were performed in 0.5 M NaCl, 20 mM Tris, pH 7.5. Data shown in semi-log plots are mean and s.d. of 23,516 events (total for all points) from one hybrid nanopore

Article Snippet: Protein was exchanged into 20 mM Tris pH 7.5, 0.5 M NaCl buffer (Zeba Spin Columns, Thermofisher) for use in hybrid nanopore formation.

Techniques:

Journal: Nature Communications

Article Title: Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors

doi: 10.1038/s41467-018-07116-x

Figure Lengend Snippet: Design of a bio-inspired lipid-free hybrid nanopore. a Cartoon of the DNA packaging machine of a dsDNA virus. Viral genomic DNA (red) is translocated into the preformed virus capsid by the packaging ATPase (yellow) through the portal protein (aqua) embedded in viral capsid (gray). b Left, electrostatic properties of the tunnel in wild-type and mutant portal proteins. Slice through the middle of molecular surface colored according to charge from red (−1 kT e −1 ) to blue (+1 kT e −1 ). b Right (gray box), dimensions of the portal protein (teal, L) and the SS nanopore (pink, R). c Insertion of the purified portal protein into a nanopore fabricated in a thin solid-state (SS) membrane. Portal protein is applied to the trans chamber of a SS nanopore device containing an electrolyte solution of 20 mM Tris pH 7.5, 0.5 M NaCl. The protein electrokinetically inserts into the SS pore during application of a positive voltage. d Cartoon image of the hybrid pore, in which application of voltage results in ion current through the pore (blue arrows), as well as leakage current that is peripheral to the pore (red arrows)

Article Snippet: Protein was exchanged into 20 mM Tris pH 7.5, 0.5 M NaCl buffer (Zeba Spin Columns, Thermofisher) for use in hybrid nanopore formation.

Techniques: Mutagenesis, Purification

Journal: Journal of inorganic biochemistry

Article Title: Binding of ?-Synuclein with Fe(III) and with Fe(II) and Biological Implications of the Resultant Complexes

doi: 10.1016/j.jinorgbio.2009.11.005

Figure Lengend Snippet: Fluorescence spectra of 10 μM α-syn only (solid) and mixture of 10 μM α-syn and 500 μM Fe(II) before (dashed) and after (dotted) aeration in Tris buffer at pH 7.4.

Article Snippet: Sodium dihydrogen phosphate, sodium hydroxide, sodium sulfate, ammonium sulfate, trifluoroacetic acid, ferrous ammonium sulfate (Fe(NH4 )2 (SO4 )2 ), Trizma base (Tris), isopropyl β-D-thiogalactopyranoside (IPTG), and acetonitrile were purchased from Thermo Fisher Scientific Inc. (Pittsburgh, PA).

Techniques: Fluorescence

Journal: Journal of inorganic biochemistry

Article Title: Binding of ?-Synuclein with Fe(III) and with Fe(II) and Biological Implications of the Resultant Complexes

doi: 10.1016/j.jinorgbio.2009.11.005

Figure Lengend Snippet: (A) Cyclic voltammograms of Tris buffer (pH 7.4) containing 200 μM α-syn (dotted line curve) in ambient atmosphere, 200 μM α-syn and 200 μM Fe(II) (solid line curve) in a N 2 -purged glovebox, and 200 μM α-syn and 200 μM Fe(II) after exposure to air for 2 h (dashed line curve). The scan rate was 20 mV/s and the solid arrow indicates the initial scan direction. The dashed arrow indicates a shoulder peak at −0.075 V. Inset: a CV of Fe(NH 4 ) 2 (SO 4 ) 2 . (B) Differential pulse votammograms of 200 μM α-syn in the presence of various concentration of Fe(NH 4 ) 2 (SO 4 ) 2 : 200 μM (solid line curve), 400 μM (dotted line curve), 800 μM (dashed line curve), and 1000 μM (dash-dotted line curve).

Article Snippet: Sodium dihydrogen phosphate, sodium hydroxide, sodium sulfate, ammonium sulfate, trifluoroacetic acid, ferrous ammonium sulfate (Fe(NH4 )2 (SO4 )2 ), Trizma base (Tris), isopropyl β-D-thiogalactopyranoside (IPTG), and acetonitrile were purchased from Thermo Fisher Scientific Inc. (Pittsburgh, PA).

Techniques: Concentration Assay

Journal: Journal of neuroscience research

Article Title: Bacterially Expressed F1-20/AP-3 Assembles Clathrin Into Cages With a Narrow Size Distribution: Implications for the Regulation of Quantal Size During Neurotransmission

doi: 10.1002/jnr.490410104

Figure Lengend Snippet: The bacterially expressed 33 kD NH 2 -terminus of F1-20/AP-3 binds specifically to clathrin triskelia; 15 µg of the bacterially expressed 33 kD NH 2 -terminus of F1-20/AP-3 was incubated with 0.5 ml clathrin-Sepharose in 0.5 ml isolation buffer at 4°C for 2 hr ( A ), and binding was monitored by batch analysis, as described in Methods. Fraction 1 is the flow-through; fractions 2,3,4 are washes with isolation buffer; and fractions 5,6,7 are eluates with 0.5 M Tris (pH 7.0). All samples were analyzed by SDS-PAGE, followed by silver staining. Negative controls were carried out by incubating 15 µg bacterially expressed 33 kD NH 2 -terminus of F1-20/AP-3 with 0.5 ml underivatized Sepharose ( B ), and by incubating 15 µg E. coli GST protein with 0.5 ml clathrin-Sepharose ( C ).

Article Snippet: The Sepharose was then eluted three times with 0.5 ml 0.5 M Tris, 0.1 mM PMSF (pH 7.0) at 37°C for 15 min. Flow-through, washes, and eluates were all concentrated using Millipore quick concentrator-10s, and each sample was brought to 20 µl in IX SDS sample buffer.

Techniques: Incubation, Isolation, Binding Assay, Flow Cytometry, SDS Page, Silver Staining

Journal: The Scientific World Journal

Article Title: Identification of Proteins with Potential Osteogenic Activity Present in the Water-Soluble Matrix Proteins from Crassostrea gigas Nacre Using a Proteomic Approach

doi: 10.1100/2012/765909

Figure Lengend Snippet: 2DE gel (11 cm, pH 4–7, Bis-Tris 12%) showing all the protein spots detected in nacre WSM from Crassostrea gigas . Numbered spots represent proteins identified by mass spectrometry.

Article Snippet: After the alkylation step, each strip was quickly washed with MOPS running buffer pH 7,7 (50 mM MOPS, 50 mM Tris, 0,1% (w/v), and 1 mM EDTA) and loaded on 13,3 × 8,7 cm Criterion XT gels (Bio-Rad) with the wells previously filled with an agarose solution for 2DE, composed of 0,5% (w/v) low melting point agarose, 25 mM Tris, 192 mM glycine, 0,1% (w/v) SDS, and vestigial quantities of bromophenol blue (Bio-Rad).

Techniques: Two-Dimensional Gel Electrophoresis, Mass Spectrometry

Journal: Journal of bioenergetics and biomembranes

Article Title: Minocycline chelates Ca2+, binds to membranes, and depolarizes mitochondria by formation of Ca2+-dependent ion channels

doi: 10.1007/s10863-010-9271-1

Figure Lengend Snippet: (Panel A ) Minocycline (20 µM) in the presence of 3 mM Ca 2+ induces an electrical current in BLM made from DPhPC. The experimental buffer was 10 mM Tris, 10 mM MES, 100 mM KCl, pH 8.5; the voltage was 30 mV. (Panels B, C ) Ion channel activity induced by minocycline (8 µM) in the presence of Ca 2+ (3 mM in panel B and 20 µM in panel C) at 50 mV in BLM made from DPhPC. The experimental buffer was 10 mM Tris, 10 mM MES, 1 M KCl, pH 9.0. (A current of 0.7 pA at 50 mV corresponds to a conductance of 14 pS)

Article Snippet: β-Alanine, micro Biuret protein assay kit, bovine serum albumin (fatty acid free grade Sigma A-6003), CaCl2 , EGTA, gramicidin A, Hepes (ultra grade), minocycline, KCl, KOH, KH2 PO4 , MES, Ruthenium 360 (Ru360), succinate, sucrose (ultra grade), PBS-Tween buffer, and Tris-base were obtained from Sigma (St. Louis, MO, USA).

Techniques: Activity Assay

Journal: Scientific Reports

Article Title: GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1

doi: 10.1038/srep18097

Figure Lengend Snippet: ( A ) ChIP experiment to determine the occupancy of hras -1, hras -2 and control sequence (870 bp downstream from TSS) by hnRNP A1. Histograms shows the relative occupancy of hras -1 and hras -2 by hnRNP A1, RNA Pol II (positive control) and IgG (negative control). Data have been normalized by IgG signal; ( B ) EMSA of 32 P-labelled hras -1 Y and hras -2 Y in 50 mM Tris-acetate pH 5.5, 50 mM KCl, incubated 40 min at room temperature with increasing amounts of recombinant hnRNP A1 (0–12 μg). Lane (Δ,A1) indicates the i M incubated 40 min at room temperature, with denatured hnRNPA1 in binding buffer (see Methods); ( C ) EMSA at pH 5.5 of hras -1 Y with BSA or denatured hnRNP A1 and EMSA of hras -1 Y (m) with hnRNP A1; ss = single-stranded oligonucleotide; 1:1 and 1:2 DNA-protein complexes.

Article Snippet: Radiolabelled oligonucleotides (10 nM) were incubated for 30 min at 20 °C with increasing amounts of hnRNP A1 (0–12 μg) as specified in , in 50 mM Tris–acetate, pH 5.5, 50 mM KCl, 1 mM DTT, 8% glycerol, 1% Phosphatase Inhibitor Cocktail I (Sigma, Milan, Italy), 5 mM NaF, 1 mM Na3 VO4 , 2.5 ng/μl salmon sperm DNA (binding buffer).

Techniques: Chromatin Immunoprecipitation, Sequencing, Positive Control, Negative Control, Incubation, Recombinant, Binding Assay

Journal: Scientific Reports

Article Title: GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1

doi: 10.1038/srep18097

Figure Lengend Snippet: Circular dichroism analysis of 3 μM (0.5 cm pathlength cell) hras -1 Y and hras -2 Y at pH 5.5, 50 mM Tris-acetate, 50 mM KCl, after incubation with increasing amounts of hnRNP A1 (r = 0–4). Spectra of DNA-protein complex have been subtracted of protein spectrum.

Article Snippet: Radiolabelled oligonucleotides (10 nM) were incubated for 30 min at 20 °C with increasing amounts of hnRNP A1 (0–12 μg) as specified in , in 50 mM Tris–acetate, pH 5.5, 50 mM KCl, 1 mM DTT, 8% glycerol, 1% Phosphatase Inhibitor Cocktail I (Sigma, Milan, Italy), 5 mM NaF, 1 mM Na3 VO4 , 2.5 ng/μl salmon sperm DNA (binding buffer).

Techniques: Incubation

Journal: Scientific Reports

Article Title: GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1

doi: 10.1038/srep18097

Figure Lengend Snippet: ( A ) Sequences of the GC-rich elements located in the HRAS promoter upstream of major TSS’s; ( B,C ) Circular dichroism titrations of hras -1 Y and hras -2 Y (3 μM, 1 cm pathlength cell) in 50 mM Tris-acetate, 50 mM KCl, 40% PEG-300 and pH from 4.5 to 8; ( D ) Ellipticity (287 nm) versus pH curves for hras -1 Y and hras -2 Y in the presence and absence of PEG-300; ( E ) Determination of number of protons picked up by hras -1 Y and hras -2 Y upon folding into the i M.

Article Snippet: Radiolabelled oligonucleotides (10 nM) were incubated for 30 min at 20 °C with increasing amounts of hnRNP A1 (0–12 μg) as specified in , in 50 mM Tris–acetate, pH 5.5, 50 mM KCl, 1 mM DTT, 8% glycerol, 1% Phosphatase Inhibitor Cocktail I (Sigma, Milan, Italy), 5 mM NaF, 1 mM Na3 VO4 , 2.5 ng/μl salmon sperm DNA (binding buffer).

Techniques: