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Typhoon 9500 imager

Manufactured by GE Healthcare
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The Typhoon 9500 imager is a versatile and high-performance imaging system designed for a wide range of applications in molecular biology and biochemistry. The core function of the Typhoon 9500 is to capture and analyze fluorescent signals from various types of biological samples, such as gels, blots, and microplates. The system utilizes advanced optics and detection technologies to provide high-sensitivity and high-resolution imaging capabilities.

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Lab products found in correlation

Rnasin, by Promega (3 mentions) Bovine serum albumin (bsa), by Merck Group (2 mentions) Rnase h2, by New England Biolabs (1 mentions) Quantity one, by Bio-Rad (1 mentions) Sapphire biomolecular imager, by Azure Biosystems (1 mentions) Criterion xt bis tris gel, by Bio-Rad (1 mentions)

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Typhoon FLA 9500 Variable Mode Imager Amersham Typhoon FLA 9500 Phospor Imager Typhoon FLA 9500 gel imager Typhoon FLA 9500 imager Typhoon FLA 9500 Fluorescence Imager Typhoon Phosphor Imager FLA 9500 Typhoon 9500 fluorescence imager Typhoon FLA 9500 Molecular Imager Typhoon FLA 9500 biomolecular imager Typhoon 9500

14 protocols using typhoon 9500 imager

1

Helix Destabilization Assay Protocol

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The standard helix destabilizing assay was performed as previously described (Shu et al.2019 (link)). Briefly, the indicated recombinant protein and 0.1 pmol/L of HEX-labeled helix substrate were added to the standard reaction mix containing 50 mmol/L HEPES-KOH (pH 8.0), 50 mmol/L NaCl, 2 mmol/L MgCl2, 5 mmol/L ATP and 20 U RNasin (Promega). After incubation at 37 °C, the reaction was terminated by adding 10 × loading buffer [100 mmol/L Tris-HCl, 1% SDS, 50% glycerol, and bromophenol blue (pH 7.5)]. The mixtures were then electrophoresed on 15% native-PAGE gels, followed by scanning with a Typhoon 9500 imager (GE Healthcare, Piscataway, NJ).
Shu T., Huang M., Wu D., Ren Y., Zhang X., Han Y., Mu J., Wang R., Qiu Y., Zhang D.Y, & Zhou X. (2020). SARS-Coronavirus-2 Nsp13 Possesses NTPase and RNA Helicase Activities That Can Be Inhibited by Bismuth Salts. Virologica Sinica, 35(3), 321-329.
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2

Nuclease Assays with 6-FAM Labeled DNA

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For nuclease assays involving 6-FAM labeled DNA substrates, purified Apn2FL or Apn2FL mutants in storage buffer (10 mM Tris pH 8.0, 75mM NaCl, 1 MgCl2, 1 mM TCEP, 50% glycerol) were diluted in 1X reaction buffer (10 mM Tris pH 8.0, 1 MgCl2, 1 mM TCEP) and combined with PCNA, for a final concentration of 250 nM each. To begin reaction, 50 nM DNA substrate, in 1X reaction buffer, was added to the Apn2FL/PCNA complex in a final reaction volume of 30 μL. Samples were incubated at 37°C for an hour and 10 μL aliquots were removed at indicated time points. For testing effect of salt on Apn2FL activity, 1X reaction buffers were prepared containing additional 10 mM NaCl, and reactions were carried out as described above. For the 3′-phosphorothioate experiments, BSA (Sigma) was added to the 1X reaction buffer to a final concentration of 0.1 mg/mL. All reactions were quenched with 2-fold gel loading buffer (98% formamide, 10 mM EDTA), denatured at 95°C for 10 min, and cooled at 4°C for 2 min prior to sample loading. Samples were loaded and resolved on a 20% TBE-Urea gel. Gels were imaged using a Typhoon 9500 imager (GE Healthcare) and viewed using ImageJ.
Williams J.S., Wojtaszek J.L., Appel D.C., Krahn J., Wallace B.D., Walsh E., Kunkel T.A, & Williams R.S. (2022). Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Cell reports, 41(1), 111448.
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3

Helix Unwinding Assay for Recombinant Proteins

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The standard helix unwinding assay was performed as previously described (27 (link)) with minor modifications. Briefly, 20 pmol of recombinant protein and 0.1 pmol of HEX-labeled helix substrate were added to a mixture containing 50 mM HEPES–KOH (pH 8.0), 2 mM MgCl2, 100 mM NaCl2 and 20 U RNasin (Promega). After incubation at 37°C for 60 min, the reaction was terminated by adding 5× loading buffer [100 mM Tris–HCl, 1% SDS, 50% glycerol, and bromophenol blue (pH 7.5)]. The mixtures were then electrophoresed on 15% native-PAGE gels, followed by scanning with a Typhoon 9500 imager (GE Healthcare, Piscataway, NJ, USA).
Shu T., Gan T., Bai P., Wang X., Qian Q., Zhou H., Cheng Q., Qiu Y., Yin L., Zhong J, & Zhou X. (2019). Ebola virus VP35 has novel NTPase and helicase-like activities. Nucleic Acids Research, 47(11), 5837-5851.
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4

Mutant c-JMJD5 and JMJD7 Activity Assay

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Overall, all activity assays of mutated versions of c-JMJD5 and JMJD7 follow the similar procedures as reported8 . Briefly, bulk histone treated with PRMTs were used as substrates for mutated c-JMJD5 and JMJD7. After the reaction, the sample was separated by SDS-PAGE gel, which was then dried using a vacuum pump. The 14C radioactive signal was detected using a Typhoon 9500 imager (GE Healthcare).
Liu H., Wang C., Lee S., Ning F., Wang Y., Zhang Q., Chen Z., Zang J., Nix J., Dai S., Marrack P., Hagman J., Kappler J, & Zhang G. (2018). Specific Recognition of Arginine Methylated Histone Tails by JMJD5 and JMJD7. Scientific Reports, 8, 3275.
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5

Nuclease Assays with 6-FAM Labeled DNA

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For nuclease assays involving 6-FAM labeled DNA substrates, purified Apn2FL or Apn2FL mutants in storage buffer (10 mM Tris pH 8.0, 75mM NaCl, 1 MgCl2, 1 mM TCEP, 50% glycerol) were diluted in 1X reaction buffer (10 mM Tris pH 8.0, 1 MgCl2, 1 mM TCEP) and combined with PCNA, for a final concentration of 250 nM each. To begin reaction, 50 nM DNA substrate, in 1X reaction buffer, was added to the Apn2FL/PCNA complex in a final reaction volume of 30 μL. Samples were incubated at 37°C for an hour and 10 μL aliquots were removed at indicated time points. For testing effect of salt on Apn2FL activity, 1X reaction buffers were prepared containing additional 10 mM NaCl, and reactions were carried out as described above. For the 3′-phosphorothioate experiments, BSA (Sigma) was added to the 1X reaction buffer to a final concentration of 0.1 mg/mL. All reactions were quenched with 2-fold gel loading buffer (98% formamide, 10 mM EDTA), denatured at 95°C for 10 min, and cooled at 4°C for 2 min prior to sample loading. Samples were loaded and resolved on a 20% TBE-Urea gel. Gels were imaged using a Typhoon 9500 imager (GE Healthcare) and viewed using ImageJ.
Williams J.S., Wojtaszek J.L., Appel D.C., Krahn J., Wallace B.D., Walsh E., Kunkel T.A, & Williams R.S. (2022). Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Cell reports, 41(1), 111448.
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6

Chromatin Immunoprecipitation of mESCs

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The method refers to the study of Liu [39 (link)]. mESCs were cross-linked in 1% formaldehyde for 60 min and then added to 1 ml of SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM tris- HCl and 1 mM PMSF). Ultrasonically-induced cell lysis was used to obtain chromatin fragments <1 kB. The supernatant was added to 1 ml of IP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris, 167 mM NaCl and 1 mM PMSF), and then incubated with antibodies at 4°C overnight. Eluting buffer (10 mM Tris, 5 mM EDTA, 1% Triton X-100 and 0.1% SDS) was added at 65°C for 30 min and then de-crosslinked at 65°C. The protease K with a final concentration of 100 μg/ml was added and incubated at 50°C for 2 h. The immunoprecipitated DNA was purified through QIAEX II System. DNA was denatured and hybridized to a GeneScreen plus hybrid membrane, which was hybridized with a 32P-labelled-telomere repeats (4× TTAGGG) probe overnight at 42°C. The exposure and scanning were performed with a typhoon 9500 imager (GE Healthcare Life Sciences, USA). The anti-GFP (No. D191040), anti-Myc (No. D110006) and anti-Flag (No. D110005) antibodies were purchased from Sangon Biotech, Shanghai, China. This experiment was repeated for 3 times independently.
Liu Z., Wei X., Gao Y., Gao X., Li X., Zhong Y., Wang X., Liu C., Shi T., Lv J, & Liu T. (2022). Zbtb34 promotes embryonic stem cell proliferation by elongating telomere length. Aging (Albany NY), 14(17), 7126-7136.
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7

RNA Hybridization Assay for Protein-RNA Interactions

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The RNA hybridization assay was conducted as described (Gebhard et al., 2012 (link)). The reaction mixture was prepared containing 50 ​mmol/L HEPES-KOH (pH 8.0), 40 ​mmol/L KCl, 20 U of RNasin and 2 ​mmol/L dithiothreitol. Subsequently, 0.1 ​pmol HEX-labeled stem-loop-structured RNA strand, 0.1 ​pmol unlabeled stem-loop-structured RNA strand and the indicated amount of protein were added to the reaction mixture, followed by an incubation at 37 ​°C for 30 ​min. Annealing reactions were terminated by adding 10× ​ending buffer (1.2 ​mg/mL proteinase K, 1.0% sodium dodecyl sulphate) to the mixture. The reaction products adding 10× ​loading buffer were resolved on 15% native PAGE gels, followed by scanning with a Typhoon 9500 imager (GE Healthcare, Piscataway, NJ, USA).
Chen Z., Xiong X., Li Y., Huang M., Ren Y., Wu D., Qiu Y., Chen M., Shu T, & Zhou X. (2022). The nonstructural protein 2C of Coxsackie B virus has RNA helicase and chaperoning activities. Virologica Sinica, 37(5), 656-663.
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8

Helix-Unwinding Assay of Recombinant Proteins

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The standard helix-unwinding assay was as according to a previous research (Shu et al., 2019 (link)) with minor modifications. Briefly, unless mentioned elsewise, 20 ​pmol of recombinant protein and 0.1 ​pmol of HEX-labeled helix substrates were added to the standard reaction mixture containing 50 ​mmol/L HEPES-KOH (pH 8.0), 2 ​mmol/L MgCl2, 5 ​mmol/L ATP, 50 ​mmol/L NaCl and 20 U RNasin (Promega, Madison, WI, USA). After a 60 ​min incubation at 37 ​°C, the reaction was terminated with 10× ​loading buffer [100 ​mmol/L Tris-HCl, 50% glycerol, 1% SDS, and bromophenol blue (pH 7.5)]. The mixtures were separated by electrophoresis on 15% native-PAGE gels, and the gels were scanned with a Typhoon 9500 imager (GE Healthcare, Piscataway, NJ, USA).
Chen Z., Xiong X., Li Y., Huang M., Ren Y., Wu D., Qiu Y., Chen M., Shu T, & Zhou X. (2022). The nonstructural protein 2C of Coxsackie B virus has RNA helicase and chaperoning activities. Virologica Sinica, 37(5), 656-663.
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9

Multiple-Round Transcription Assay

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DNA template (50 ng) was mixed with either RNAP only (250 nM) or RNAP plus SigN (1,000 nM) per reaction. Each reaction mixture was incubated for 15 min at 37°C in a 25-μl total reaction volume including the transcription buffer (18 mM Tris-HCl [pH 8.0], 10 mM MgCl2, 30 mM NaCl, 1 mM DTT, 250 μM GTP, 100 μM ATP, 100 μM CTP, 5 μM UTP, and ∼2 μCi [α-32P]UTP) to produce multiple-round transcription. To stop the reaction, 25 μl of 2× Stop/Gel loading solution (7 M urea, 10 mM EDTA, 1% SDS, 2× TBE, 0.05% bromophenol blue) was used. Samples were run on a 5% denaturing acrylamide gel (5% acrylamide [19:1 acryl:bis], 7 M urea, 1× TBE) for 3 h at 200 V. Gels were imaged with a Typhoon 9500 imager (GE Life Sciences).
Burton A.T., DeLoughery A., Li G.W, & Kearns D.B. (2019). Transcriptional Regulation and Mechanism of SigN (ZpdN), a pBS32-Encoded Sigma Factor in Bacillus subtilis. mBio, 10(5), e01899-19.
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10

Nuclease Assay with PCNA Regulation

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2.5 μL of XlAPE2, as a 200 nM stock in storage buffer (5
mM Tris pH 8.0, 75 mM NaCl, 0.5 mM TCEP, 0.5 mM MgCl2, 50% glycerol), or
2.5 μL of 1 U/μL APE1 (NEB) was added to 2.5 μL 200
nM substrate, 1 uL 10x reaction buffer (100 mM Tris pH 8.0, 10 mM TCEP,
10 mM MnCl2, 1 mg/mL BSA) and 4 μL ddH2O at
37°C to initiate a reaction with final concentrations of 50 nM
XlAPE2 and 50 nM substrate. For nuclease assays in the presence of PCNA,
reactions were supplemented with 50 nM PCNA (Figure S4B). At noted
timepoints, 10 μL reactions were stopped by the addition of 20
μL of formamide buffer (98% formamide, 10 mM EDTA) and immediate
denaturation at 95°C for 5 minutes. Samples were resolved on 20%
polyacrylamide TBE-Urea gels, imaged on a Typhoon 9500 imager (GE
Healthcare), and viewed using ImageJ. For RNase H2 (NEB) reactions, 2
U/μL enzyme was used with NEB-supplied 10x ThermoPol reaction
buffer (200 mM Tris-HCl pH 8.8, 100 mM
(NH4)2SO4, 100 mM KCl, 20 mM MgSO4,
1% Triton X-100).
Álvarez-Quilón A., Wojtaszek J.L., Mathieu M.C., Patel T., Appel C.D., Hustedt N., Rossi S.E., Wallace B.D., Setiaputra D., Adam S., Ohashi Y., Melo H., Cho T., Gervais C., Muñoz I.M., Grazzini E., Young J.T., Rouse J., Zinda M., Williams R.S, & Durocher D. (2020). Endogenous DNA 3′ blocks are vulnerabilities for BRCA1 and BRCA2 deficiency and are reversed by the APE2 nuclease. Molecular cell, 78(6), 1152-1165.e8.
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