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5 protocols using dna gel extraction kit

1

Whole Mitochondrial Genome Amplification

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LG-PCR was conducted as described by Zhang et al. [18 (link)]. Briefly, a set of back-to-back primers (designated as PM primers; Table 1) were designed based on the NC_001323.1 sequence for amplifying the whole mitochondrial genome. The product comprised approximately 16.8 kb. We performed PCR amplification with about 15–50 ng tissue/blood DNA as the template in a 50-μL PCR system, using LampTM DNA Polymerase with Mg2+ plus buffer (Vazyme Biotech Co. Ltd) under the following conditions: initial incubation at 94°C for 2 min, followed by 30 PCR cycles with denaturation at 94°C for 30s, and annealing and extension at 68°C for 10 min, before one final extension cycle at 72°C for 7 min and holding at 4°C. Next, 3 μL of the PCR products were subjected to electrophoresis on 1.5% agarose gels. The LG-PCR products were purified by DNA gel extraction kit (Generay, Shanghai, China) and then conducted Illumina HiSeq Sequencing.
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2

Biotin-labeled circPTEN1 Synthesis

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The DNA template used for the in vitro synthesis of biotinylated circPTEN1 or the flaking sequences of the circPTEN1 transcript was generated by PCR. As shown in Table S2, the forward primer contained the T7 RNA polymerase promoter sequence to allow for subsequent in vitro transcription. PCR products were purified using the DNA Gel Extraction Kit (GENERAY BIOTECH), and in vitro transcription was performed using the T7-Flash Biotin RNA Transcription Kit (Epicenter, biotin labeling) or Transcript Aid T7 High Yield Transcription Kit (Thermo Scientific, without biotin). RNA was purified by phenol-chloroform extraction and then used for in vitro cyclization or biotin RNA pull-down.
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3

Chemicals and Reagents for Molecular Biology

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Standard substances such as L-rhamnulose and L-rhamnose were purchased from Sigma-Aldrich (USA). Electrophoresis reagents, the genomic DNA minipreparation kit with a spin column, the polymerase chain reaction (PCR) kit, and isopropyl β-D-1thiogalactopyranoside (IPTG) were purchased from Beyotime Institute of Biotechnology (China). Restriction enzymes and T4 DNA ligase were purchased from New England Biolabs (USA). A DNA gel extraction kit was purchased from Generay Biotech (China). A universal DNA purification kit was obtained from Tiangen Biotech Co., Ltd. (China). All other reagents (analytical grade) were purchased from Sinopharm Chemical Reagent Co., Ltd. (China).
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Full-length cDNAs of HcToll6 and HcToll7

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The partial cDNA sequences of HcToll6 and HcToll7 were retrieved from our previous hepatopancreas transcriptome database (unpublished). In this experiment, 3′ and 5′ RACE were performed by using a Clontech Advantage® 2 PCR kit from Takara (Japan) with two pairs of specific primers (HcToll6-F:5′-TGGATAAACGATGTGCTAAGCGACCCC-3′, HcToll6-R: 5′-CTGTGAAGACCACGCAAATAGAGACGGAAC-3′; HcToll7-F: 5′-GAGAGAACTTGGACAGGAAAGGGGGCT-3′, HcToll7-R: 5′-CGTATCGGCAGGTCGCCAAGGGTAAC-3′) to obtain the full-length cDNAs of HcToll6 and HcToll7. The amplification products were purified using a DNA gel extraction kit (Shanghai Generay Biotech Co., Ltd., Shanghai, China), inserted into the pEasy-T3 vector, and transformed into Escherichia coli Trans1-T1 cells (TransGen Biotech, Beijing, China). The putative clones were identified by PCR with M13F and M13R primers. The selected clones were sequenced by a commercial company (Springen, China).
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5

Identification and Characterization of SsMT2 Gene

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We have identified some candidate salt-responsive genes in S. salsa using the full-length cDNA over-expressing gene (FOX)-hunting system53 (link). The SsMT2 gene was one of those genes identified. Seeds of S. salsa plants were collected from an alkaline soil area in Northeast China and germinated on MS medium54 (link) at 28 °C under 2000 Lux irradiation with a 16 h light/8 h dark photoperiod in an illuminated incubator. Total RNA was isolated from 4-week old seedlings using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). cDNA was synthesized from l µg of the total RNA with Prime-Script Reverse Transcriptase (Takara, Tokyo, Japan) using an oligo (dT) primer. MT cDNA sequence from FOX-hunting system was obtained and open reading frame (ORF) was found by blasting in the NCBI database. A transcript fragment was amplified by PCR from the cDNA with the forward primer (5′-ATGTCTTGCTGTGGTGGTAACTGTGG-3′) and reverse primer (5′-TCATTTGCAGGTGCATGGGTTG-3′), which were designed from the MT ORF sequence. The PCR product was purified from agarose gel using the DNA Gel Extraction Kit (Generay, Shanghai, China) and cloned into plasmid pMD18-T (Takara, Tokyo, Japan) and sequenced. A new gene was designated as SsMT2 and its ORF nucleotide sequence and protein sequence was deposited to GenBank database (MF447531).
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