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1

Affinity Purification and Validation of Anti-TSEN Antibodies

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Rabbit polyclonal antibodies raised against TSEN2 (N-NGDSGKSGGVGDPREPLG-C), TSEN34 (N-QASGEQEEAGPSSSQAGPSNG-C), and TSEN54 (N-RSRSQKLPQRSHGPKDFLPD-C)23 (link) (Gramsch Laboratories, Schwabhausen, Germany) were affinity-purified from rabbit sera and eluted sequentially by addition of 1.5 M MgCl2 and 0.1 M glycine, pH 2.5. Eluates were dialyzed against HEPES-buffered saline (HBS, pH 7.9) overnight, supplemented with 10% (v/v) glycerol, and stored at −80 °C. Small-scale pilot experiments were set up to assess the suitability of the affinity-purified antibodies for immunoprecipitation experiments using total cell lysate from HEK 293 cells. Antibodies used in western blotting (WB) and immunoprecipitation (IP) were: anti-TSEN15 (rabbit polyclonal, Atlas Antibodies, HPA029237; WB dilution 1:1000), anti-TSEN34 (IP, WB dilution 1:5000), anti-TSEN54 (WB dilution 1:5000), anti-TSEN2 (IP, WB dilution 1:5000), anti-GAPDH (rabbit monoclonal, 14C10, Cell Signaling Technology, #2118; WB dilution 1:1000), anti-β-actin (mouse monoclonal, clone AC-74, Sigma-Aldrich, A2228; WB dilution 1:3000), anti-mouse IgG–peroxidase conjugate (secondary goat polyclonal, Sigma-Aldrich, A2554; WB dilution 1:20.000), anti-rabbit IgG–peroxidase conjugate (secondary goat polyclonal, Sigma-Aldrich, AP307P; WB dilution 1:20.000), anti-polyHistidine (mouse monoclonal, clone HIS-1, Sigma-Aldrich, H1029; IP).
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2

Optimized Western Blot Protocol

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7.5% or 10% SDS-PAGE gels or 4–15% mini-PROTEAN TGX gels (Bio-Rad Laboratories) were transferred onto nitrocellulose. Antibodies were used at the following concentrations: rabbit anti-CKA, 1:2,000 (a gift from W. Du); mouse anti–α-tubulin, 1:2,000 (DM1A; Sigma-Aldrich); goat anti-GST, 1:1,000 (Pharmacia); mouse anti-polyHis, 1:3,000 (HIS-1; Sigma-Aldrich); rabbit anti-GFP, 1:2,000 (Molecular Probes); rat anti-Strip, 1:500 (a gift from T. Chihara, University of Tokyo, Tokyo, Japan); mouse anti-dynein intermediate chain, 1:2,000; mouse anti-Flag, 1:20,000 (M2; Sigma-Aldrich); and rabbit anti-tRFP, 1:1,667 (recognizes TagBFP; Evrogen). Fluorescently labeled secondary antibodies IR800CW and IR680RD (LI-COR Biosciences) were used at 1:5,000. Images of blots were obtained using Image Studio software (version 3.1; LI-COR Biosciences).
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3

Purification and Binding of Recombinant HIS-Tagged Proteins

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Recombinant HIS-tagged proteins were produced by IPTG induction (0.4 mM) of T7 Express lysY/Iq Competent E.coli (New England Biolabs C3013I) transformed with HIS-tag expressing control vector, pET-30a+ (Novagen) or HIS-tagged KRT76 domains in pDEST17 gateway backbone (Life Technologies), grown for 6–8 hours at 37°C in low salt LB, supplemented with 100 µg/ml ampicillin or 50 µg/mL kanamycin (as required). Recombinant protein was purified using 0.1 ml per 1 ml of culture of PopCulture lysis reagent (Novagen), 1 µl per mL of culture of 40 U/ml of Lysonase bioprocessing reagent (Novagen), protease inhibitors (Sigma P8849), and His-Mag beads (Novagen) according to manufacturer's protocols. Bound recombinant HIS and HIS-KRT76 protein were washed and stored at 4°C as a 1∶2 resin slurry in Tris-saline pH 7.4 containing protease inhibitors. Paw pad skin of adult was collected in RIPA lysis buffer and incubated with HIS or HIS-KRT76 overnight at 4°C. HisMag bead-bound HIS and HIS-KRT76 + lysates were then washed four times in Tris-saline pH 7.4 including 1% Triton X-100 and immunoblotted for mCLDN1 (Santa Cruz Biotechnology, SC-81796) and the HIS tag (Sigma-Aldrich, clone HIS-1).
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4

Construction of M. smegmatis MSMEG_5447 Complementation Strain

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The M. smegmatis mutant with MSMEG_5447 disruption, ΔM5447, was constructed by using DNA homologous recombination in our previous studies (Deng et al., 2016 (link)). For constructing MSMEG_5447 gene-complemented strain (Comp), the MSMEG_5447 gene (1551 bp) was amplified by PCR from M. smegmatis mc2155 genomic DNA using a forward primer (5′AGCATATGACCGCCCTCGACACCGATAC3′, underlined is the NdeI site) and a reverse primer (5′GTACTAGTCTAGTGATGATGGTGATGGTGGCGCCA-GCTCGGCAACC3′, underlined is the SpeI site). The PCR product of the MSMEG_5447 gene was cloned to the pJET1.2/blunt vector, yielding a pJET-MSMEG_5447 plasmid. After confirmation by DNA sequencing, the MSMEG_5447 gene was inserted into expression vector pMind, thereby generating pMind-MSMEG_5447 plasmid. The pMind-MSMEG_5447 plasmid was transformed into ΔM5447 electro-competent cells, generating a MSMEG_5447 gene complementary strain, Comp. The expression of His-tagged MSMEG_5447 protein was induced by tetracycline (20 ng/ml) for 24 h and detected by Western blot with α(anti)-polyhistidine clone HIS-1 (Sigma) followed by AP-conjugated goat anti-mouse IgG (Proteintech, Rosemont, IL, United States) and finally visualized by using NBT/BCIP solution.
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5

Immunofluorescence and Western Blot Antibodies

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Primary antibodies used were rabbit anti‐p65 from Santa Cruz (clone C‐20, ref. sc‐372) at 1/250, mouse anti‐myc9E10 (developed by Bishop, J.M. was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH and maintained at the University of Iowa), mouse anti‐HA (Eurogentec, clone 16B12, ref. MMS‐101R), rabbit anti‐HA (Sigma, ref. H6908), rabbit anti‐GFP (Amsbio, ref. TP401), rabbit anti‐UBAP1 (Proteintech, ref. 12385‐1‐AP), mouse anti‐His (Sigma, clone HIS‐1, ref. H1029), mouse anti‐FLAG (Sigma, clone M2, ref. F1804) all at 1/1000 and mouse anti‐TNFR1 (Santa Cruz, clone H‐5, ref. sc‐8436) and rabbit anti‐TSG101 (Atlas Antibodies, ref. HPA006161) both at 1/200. Rabbit polyclonal anti‐PumA serum was obtained by repeated immunization of rabbits with purified PumA (Eurogentec) and was used at 1/1,000 for Western blot and for immunofluorescence microscopy. Purified BtpA was used to obtain chicken anti‐BtpA (Eurogentec). Anti‐EF‐Tu antibody (kind gift from R. Voulhoux) was used at 1/10,000.
Secondary antibodies used were anti‐rabbit, mouse, chicken or rat conjugated with Alexas‐488, ‐555 or ‐647 all from Jackson ImmunoResearch. When necessary, phalloidin‐568 (1/1,000) was used to label the actin cytoskeleton and DAPI nuclear dye (1/1,000) for the host cell nucleus. For Western blots, anti‐mouse or rabbit‐HRP antibodies were used at 1/5,000.
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