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16 protocols using site directed mutagenesis kit

1

Cloning and Mutagenesis of DOT1L

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Full-length DOT1L or various fragments (N-terminal domain, 1-416aa; N-terminal central region domain, 417-579aa; STAT1 binding domain, 580-1138aa; C-terminal domain, 1139-1537aa) were cloned into pGEX-4T-3 vectors (Addgene, USA). Site-specific DOT1L mutations (K358Q, K358R, K1228R) were generated using a site-directed mutagenesis kit (Vazyme, China). The pHBLV-luci control vector was purchased from Hanbio Biotechnology, China. DOT1L(WT), DOT1L(K358Q) and DOT1L(K358R) were cloned into a pHBLV-luci control vector. Transient and stable transfections of these plasmids were performed using Lipofectamine 2000 (Invitrogen, USA), according to the manufacturer's protocol.
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2

ALDH1L2 and SIRT3 Cloning and Knockdown

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5-Fu was purchased from Selleck (S1209). The complementary DNA encoding full-length human ALDH1L2 and SIRT3 were cloned into Flag- or HA-tagged vectors (pRK7-Flag and pcDNA-3HA). ALDH1L2 point mutations were generated by Site-Directed Mutagenesis kit (C215–01, Vazyme). The siRNAs of ALDH1L2 and SIRT3 were purchased from RiboBio and the siRNA sequences are as follows: siSIRT3#1:5ʹ-GCTTGATGGACCAGACAAA-3ʹ; siSIRT3#2: 5ʹ-AAAGGTGGAAGAAGGTCCATATCTT-3ʹ; siALDH1L2#1:5ʹ-CTGTGTTCAAG CTTCCTAAATGG-3ʹ; siALDH1L2#2:5ʹ -CCCATGGATATAATTGAT AGTCC-3ʹ.
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3

Molecular Mechanisms of Kindlin-2 and IKK Regulation

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Full length kindlin-2 expression constructs were amplified and cloned into the p3×FLAG-CMV-10, pGEX-4T3 vector (Addgene). GFP-tagged IKKε and Myc-DDK-tagged IKKε were purchased from OriGene. Site-specific mutations in kindlin-2 (S159A and S159D) and IKKε (K38A) were generated using a site-directed mutagenesis kit (Vazyme). The following siRNAs were used to silence target genes by transient transfection with UltraFection 3.0 (4A Biotech) reagent, according to the manufacturer's instructions: IKKα-1: 5'-GCCUUACACAGCCACUGUUTT-3';
IKKα-2: 5'-GCAGCCAUUUACCUGGCAUTT-3';
IKKβ-1: 5'-GGAAAUGAAAGAGCGCCUUTT-3';
IKKβ-2: 5'-GGAAGUACCUGAACCAGUUTT-3';
IKKε-1: 5'-CCACUGCCAGUGUGUACAATT-3';
IKKε-2: 5'-CCUGCAUCCCGACAUGUAUTT-3';
TBK1-1: 5'-CCAUGUGGGAGUUUAUACATT-3';
TBK1-2: 5'-GCCUUCUGGUGCAAUAUCUTT-3'.
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4

Investigating ATM Kinase-Histone H1 Interactions

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All plasmids were transfected with Lipofectamine 2000 (Life Technologies-Invitrogen, USA) according to the manufacturer’s instructions. H1.2, H1.3 and H1.4 cDNAs were amplified and cloned into the p3× FLAG-CMV-10 vector (Addgene, USA). Full-length H1.2 and various fragments (N-terminal domain, 1–35 aa; globular domain, 36–112 aa; C-terminal domain, 113–213 aa; ΔC1, 1–179 aa; ΔC2, 1–112+180–213 aa; ΔC, 1–112 aa) were cloned into the pEGFP-C2, pGEX-4T3 or pET28a vectors (Addgene, USA). The full-length FLAG-ATM expression construct was purchased from Addgene, USA. GST-ATM fragments (F1, 1–247 aa; F2, 250–522 aa; F3, 523–769 aa; F4, 722–1102 aa; F5, 1098–1371 aa; F6, 1245–1435 aa; F7, 1239–1770 aa; F8, 1764–2138 aa; F9, 2141–2428 aa; F10, 2427–2841 aa; F11, 2842–3056 aa; F12, 2682–3012 aa) were provided by Dr. Fabrizio d’Adda di Fagagna (FIRC Institute of Molecular Oncology Foundation, Italy). Site-specific mutations of H1.2 (T126/146/165A, T126/146/165E, E115A, S173A, S188A) were generated using a site-directed mutagenesis kit (Vazyme, China).
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5

Transfection of Human Lens Epithelial Cells

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Control human lens epithelia cells (HLEpiCs) from an unaffected subject were obtained from American Type Culture Collection (ATCC) and cultivated in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, USA). The cells were cultured at 37 °C in a humidified 5% CO2 atmosphere.
Recombinant human GJA8 was amplified from genomic DNA and inserted into the pEGFP-N1 vector. The mutant GJA8 gene was obtained using a Site-Directed Mutagenesis Kit (Vazyme, China). Recombinant plasmids containing the normal or mutant gene were transfected into HLEpiCs using Lipofectamine 2000 (Invitrogen, USA) according to the manufacturer’s protocols.
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6

Molecular Cloning and Gene Silencing

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SIRT7 and PCAF cDNAs were cloned into p3×FLAG-CMV-10, pET-28a, and pGEX-4T1 plasmids. All indicated mutations were generated using a site-directed mutagenesis kit (Vazyme). All expression constructs were verified by DNA sequencing (Shanghai Sangon Biotech Company). siRNAs (Shanghai GenePharma Company) were used to silence target genes by transient transfection with lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. The RNAi oligonucleotide sequences were as follows:
NC siRNA: 5′-UUCUCCGAACGUGUCACGU-3′;
SIRT7 siRNA 1#: 5′-TAGCCATTTGTCCTTGAGGAA-3′;
SIRT7 siRNA 2#: 5′-GAACGGAACTCGGGTTATT-3′.
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7

Lentiviral Plasmid Constructs and Knockdown

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All plasmids were transfected with polyethylenimine (Polysciences, USA) according to the manufacturer’s instructions. The packaging plasmids pMD2.G (Addgene plasmid, 12259), psPAX2 (Addgene plasmid, 12260), and HEK293FT were used for producing lentivirus. The lentivirus was generated by transfecting HEK293FT cells with packaging plasmids pMD2.G and psPAX2 and targeting shRNAs or plasmids with polyethylenimine. The medium containing lentivirus was harvested with a 0.45-μm filter at 72 hours after transfection. SMYD2, Ku70, and Ku80 cDNAs were amplified, at full length, and various fragments were cloned into pLVX-Puro, pGEX4T1, pET-28b, or pEGFP-C2 vectors (Addgene, USA). Site-specific mutations were generated using a site-directed mutagenesis kit (Vazyme, China). The shRNA sequences targeted human SMYD2 (sequence 1, CGGCAAAGATCATCCATATAT; sequence 2, ACTTAGTTCAGAAACCTTAAA). The shRNA sequences targeted mouse SMYD2 (sequence 1, CCATTTGGGATCGGCGATATT; sequence 2, CCGGCTAAGAGACTCCTATTT).
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8

FLT3 Mutant Cell Line Development

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LT-171-861 was originally designed and synthesized by China Pharmaceutical University. Sorafenib (Cat. #3009) and AC220 (Cat. #5793) were purchased from ApexBio Company (Houston, TX). The human leukemia cell lines MV4-11, MOLM13, and murine pro-B cell line BaF3 were purchased from Cobioer company (Nanjing, China). Human leukemia cell line THP-1, U937 and human marrow stromal cell line HS-5 were originally obtained from the Cell Bank of Shanghai Institute of Cell Biology (Shanghai, China). MV4-11 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM) (Grand Island, NY) containing 10% FBS (Grand Island, NY). MOLM13, THP-1, and U937 cells were cultured in RPMI 1640 medium (Grand Island, NY) with 10% FBS. Murine pre-B cell line BaF3 was cultured in RPMI 1640 (Grand Island, NY) containing 10% FBS and 3 ng/mL interleukin (IL)-3 (R&D, MN, USA). HEK‑293T and HS-5 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) (Grand Island, NY) supplemented with 10% FBS. Plasmids for construction of transformed BaF3-FLT3-wt and BaF3-FLT3-ITD were obtained from Dr. Bailiang He from The University of Hong Kong. A site-directed mutagenesis kit (Vazyme Biotech Co., Ltd, Nanjing, China) was used to generate plasmids for the construction of transformed BaF3-FLT3-ITD-F691L, BaF3-FLT3-ITD-N676D, BaF3‑FLT3-ITD-Y842C and BaF3-FLT3-D835Y.
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9

Purification and Analysis of Ran-Mog1 Complex

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The DNA fragments encoding full-length Ran and Mog1 were amplified by PCR from a human brain cDNA library and cloned into pET22b (+) (Novagen) vectors (for NMR and SPR) or pGEX-4T1 vectors (for GST pull-down).
To obtain a stable complex of Ran–Mog1 for NMR experiments, we co-expressed the proteins in a pRSFDuet-1 plasmid, which contained Mog1 without a tag and Ran with a His6 tag at the N-terminus. To investigate the role of Mog1 interacting with the Ran C-terminus (residue 181–216), which is disordered in complex with other cofactors, the Ran C-terminus was deleted by mutation in the pRSFDuet-1 and pGEX-4T1 plasmids.
For immunofluorescence and living cell imaging, the cDNA encoding fluorescent proteins (mCerulean and GFP) and Mog1 were cloned into pcDNA3.1(+)/myc/his B (Novagen) vector at the N- and C-terminus, respectively. All of Mog1 mutants were generated by the MutanBESTkit (TaKaRa). EGFP-tagged siRNA-resistant Ran wild-type and site-specific mutants were generated by PCR-based, site-directed mutagenesis kit from Vazyme (C212) according to the manufacturer’s instructions.
All plasmids were verified by DNA sequencing (Invitrogen).
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10

T7-based Heterologous Protein Expression

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The pQE-30 plasmid and Escherichia coli BL21(DE3) were purchased from Novagen Inc. (Madison, WI, USA) for T7 RNAP heterologous expression. The site-directed mutagenesis kit and dsRNA quantitative kit were supplied by Vazyme Co., Ltd. (Nanjing, China). ATP, GTP, CTP, UTP, pyrophosphatase, and murine RNase inhibitor were purchased from Vazyme Co., Ltd. (Nanjing, China). MgCl2, glycerol, dithiothreitol (DTT), and other chemicals were purchased from Aladdin Industrial Inc. (Shanghai, China) and other commercial sources.
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