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12 protocols using ligation kit

1

Constructing NIR-BRET Probes for Mammalian Expression

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Six different plasmids encoding near infrared (NIR)-BRET probes were constructed for the mammalian expression (Figure 3A).
The cDNA templates encoding fluorescent proteins (FPs), i.e., LSSmCherry, LSSmKate2 (S159T), LSSmNep (i.e., mNeptune with C162D mutation), and mCherry, were custom-synthesized by Eurofins Genetics (Tokyo, Japan) according to the precedent sequence information [30 (link),31 (link)].
First, a series of cDNA segments encoding three different fluorescent proteins (FP) were generated by PCR using corresponding primers to introduce unique restriction sites, HindIII/BamHI. Similarly, cDNA segments encoding ALuc47 (19–193 AA) and NanoLuc were synthesized by PCR using corresponding primers to introduce BamHI (KpnI)/XhoI at the 5′ and 3′ ends, respectively. The cDNA segments were double digested by the corresponding restriction enzymes (NEB, Ipswich, MA, USA), ligated using a ligation kit (Takara Bio), and subcloned into a respective enzyme-digested pcDNA3.1(+) vector (Invitrogen, Carlsbad, CA, USA) as illustrated in Figure 3A. After expression, the probes were named LSSmChe_A47, LSSmKate2_A47, LSSmNep_A47, mChe_NLuc, LSSmKate2_NLuc, and LSSmNep_NLuc for highlighting the components.
We used N-terminal secretion peptide (SP: 1–18 AA)–eliminated ALuc47 (i.e., 19–193 AA) in this study for excluding spontaneous secretion of the expressed fusion proteins from cells.
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2

Cloning Ins1/2 Promoter Variants

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Wild-type or mutated Ins1/2 promoter cDNAs containing approximately 1000 bp of the 5′-flanking sequences of the Ins1/2 promoter regions were amplified using PCR with appropriate linker-containing primers, which were then used to replace the promoter region of the Rat Ins2 promoter–reporter (luciferase) plasmid37 (link) using a ligation kit (TaKaRa, Tokyo, Japan) (Supplementary Fig. 3).
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3

Cloning of hDRD1-3HA fusion construct

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hDRD1 gene (GeneBank N0. NC000005.9) fused with 3HA-tag at the N-terminus of hDRD1 was amplified by PCR with primers (5′ AAG GTA CCA TGT ACC CAT ACG ATG TTC C 3′, 5′ AAC TCG AGG GTT GGG TGC TGA CC 3′) using pcDNA3.1 containing hDRD1 cDNA and 3HA-tag. Amplified PCR product was inserted into in-frame between the KpnI and XhoI of restriction sites of a multiple cloning site in a mammalian expression vector pDsRed-N1 using ligation kit (Takara).
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4

Ligation of DNA Fragments

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Two ligation systems were adopted. The first one combined all the N + 2 fragments with the same molar concentration into one test tube, followed by the ligation process using the commercial Takara ligation kit. The second one is called “grouped ligation”, in which the linear ligation process was divided into several runs. Taking the group of ligation fragments FR, F1, F2, F3 and FK as an example (Figure 5), FR and F1 were ligated into FR1, F2 and F3into F23 in the first run, and FK was left for the next run. During the second run of ligation, FR1 and F23 were ligated to form FR123, and FK was left for the next round. In the final round, FR123 and FK were ligated to become the final product FR123K. In each run, an equal mole of every two adjacent fragments was assigned in one group and ligated at 16°C for 2 h. This method could reduce unspecific ligation between non-adjacent fragments. After the in vitro ligation process, the circular DNA products that could replicate in E. coli directly were formed in circular ligation system, and E. coli S17-1λpir was transformed with these circular DNA products.
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5

Insulin Promoter Mutagenesis and Reporter Assay

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Wild-type or mutated insulin promoter cDNAs containing ~1000 bp of the 5′-flanking sequences of the Ins1/2 promoter regions were amplified using PCR with appropriate linker-containing primers, which were then used to replace the promoter region of the Rat Ins2 promoter-reporter (luciferase) plasmid35 (link) using a ligation kit (TaKaRa, Tokyo, Japan).
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6

Expression Vector Construction for HA-tagged CA-AKT

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To construct an expression vector for HA‐tagged CA‐AKT, the insert sequence of pLNCX‐Myr‐HA‐Akt (Addgene) was amplified using KOD FX polymerase (Toyobo, Osaka, Japan) following the manufacturer's recommendation, with primers 5′‐CTGAATTCCACCATGGGGTCTTCAAAATCTAAAC‐3′ and 5′‐CTGAATTCTCAGGCCGTGCCGCTGGCCGAGT‐3′ and subcloned into the EcoRI site of the pRetroX‐Tight‐Pur retrovirus vector (Clontech, Palo Alto, CA, USA) using a ligation kit (TaKaRa Bio, Ohtsu, Japan).
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7

CRISPR/Cas9 Plasmid Construction

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The plasmid used, pX330-U6-Chimeric_BB-CBh-hSpCas9, was gifted from Feng Zhang (Cong et al., 2013), through Addgene (https://www.addgene.org/42230/). The single guided RNAs (sgRNAs) were designed (Table), using the Benchling database website (https://www.benchling.com), authenticated using BLAST tool of the NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and annealed according to the previously described methods (Ran et al., 2013). Briefly, the forward and reverse sgRNAs were annealed in a buffer containing 150 mM NaCl and heated for 2 min at 94 °C and then gradually cooled down to 25 °C at the rate of 5 degrees per minute using BioRad thermocycler. The annealed oligos were then ligated to BbsI-digested and gel-purified plasmid vector pX330-U6-Chimeric-B-CBhSpCas9, using a ligation kit from Takara (Takara, Dalian, China). The E. coli strain DH5a was used for the transformation of the ligation product. Large prep of plasmid was obtained using alkaline lysis plasmid prep method. The final plasmids, psgRNA-Bex2-1 and psgRNA-Bex2-2, were confirmed by Sanger sequencing (https://www.genewiz.com.cn) using U6 promoter primers (Table).
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8

Preparation of MBP-FGF2 Fusion Protein Surfaces

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MBP-FGF2 surfaces were prepared using our previously described method [38 (link)]. Briefly, MBP-FGF2 fusion proteins were obtained from Escherichia coli carrying pMAL-FGF2 plasmids that were generated by inserting human FGF2 cDNA (Bioneer, Korea) into pMAL vectors (New England Biolabs, U.K.). human FGF2 cDNA was cloned from human fibroblasts via polymerase chain reaction (PCR) using oligonucleotide pairs (5′-CCG AAT TCC CCG CCT TGC CCG AGG ATG GC-3′ and 5′-CAA AGC TTT CAG CTC TTA GCA GAC ATT GGA AG-3′; Bioneer) with EcoRI and HindIII restriction sites, respectively. The PCR products were cloned into pGEM-T plasmids (Promega, Madison, WI, USA) to generate pGEM-FGF2. pGEM-FGF2 and pMAL plasmids were digested using EcoRI-HindIII, recovered from an agarose gel, and ligated using a ligation kit (TaKaRa, Shiga, Japan) to generate pMAL-FGF2. MBP-FGF2 (20 μg/mL) spontaneously adsorbed onto polystyrene (PS) surface plates (non-tissue culture-treated 96 or 384 well plates; Falcon, Fisher Scientific, Forest Lawn, NJ, USA) at 37 °C for 4 h.
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9

Chemical Reagents for Molecular Biology

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Daidzin, daidzein and (S)-equol were purchased from Daicel Chiral Technologies Co., Ltd. (Shanghai, China). The antibiotics and isopropyl-D-thiogalatopyranoside (IPTG) were ordered from Sangon Biotech Bio (Shanghai, China). The restriction enzymes and ligation kit were purchased from TaKaRa Bio (Dalian, China).
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10

Cloning Mouse Leptin Promoter

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A fragment of the mouse leptin promoter between -154 and +60 bp was amplified by PCR using mouse genomic DNA and primer pairs with sequence 5′-cagctagccgcctagaatggagcactagg-3′ and 5′-ttagatctaagactggtggaggagaaagtagg-3′ containing NheI and BglII restriction sites (underlined). The PCR product was inserted into pGL 4.19 (Promega, WI, USA) using a ligation kit (TaKaRa, Tokyo, Japan), andconfirmed by DNA sequencing.
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