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2 protocols using dynabeads his tag isolation and pulldown beads

1

Quantifying m6A in RNA-Protein Complexes

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Purified recombinant His-SRSF3-AA1-85 was diluted to a final concentration of 500 nM in IPP buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% NP-40, 0.5 mM DTT and 20 U/uL SUPERase-In RNase Inhibitor along with 800 ng HeLa mRNA fragmented with RNA fragmentation reagents [ThermoFIsher]). Protein and RNA were mixed at 4°C for 2 hr. Dynabeads His-Tag Isolation and Pulldown beads (ThermoFisher, 20 uL) were added after being washed four times and resuspended in 40 uL IPP buffer. The mixture was rotated for an additional two hours. The beads were immobilized and the aqueous phase (flow through) precipitated by ethanol precipitation. The beads were washed four times in 500 uL IPP buffer and homogenized in TriZol reagent. RNA was collected and digested for LC-MS/MS to quantify m6A in each sample.
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2

Protein Expression and Purification Protocol

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Biotinylated human IgG, goat-anti-chicken DyLight®633 (GAC633), goat-anti-chicken DyLight®487 (GAC487), donkey-anti-rabbit DyLight®633 (DAC633), goat-anti-human IgG DyLight®633, and goat-anti-chicken HRP conjugate were purchased from Immunoreagents (Raleigh, NC). Chicken anti-c-myc antibody, rabbit-anti-HA antibody, streptavidin R-phycoerythrin conjugate (SA-PE), Dynabeads Biotin Binder (streptavidin-coated beads), Dynabeads His-Tag Isolation and Pulldown beads, High-fidelity Phusion polymerase, and CloneJET PCR cloning kit (K1231) were purchased from Thermo-Fisher (Waltham, MA). Mouse anti-penta-His antibody-Alexa Fluor 647 conjugate and Ni-NTA agarose were obtained from Qiagen (Valencia, CA). Frozen-EZ Yeast Transformation Kit, Zymoprep Yeast plasmid Miniprep II kit, Quick-DNA Miniprep Plus Kit were purchased from Zymo Research (Irvine, CA). All restriction enzymes were purchased from New England BioLabs (Ipswich, MA). Gene fragments were purchased from Integrated DNA Technologies (IDT; Coralville, IA). Oligonucleotide primers were purchased from IDT or Eton Biosciences (Raleigh, NC). Sequences of all primers and G-blocks are included in Table S1 (primers) and Table S2 (gene fragments). The composition of yeast culture media used was as previously described31 (link).
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