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Pcr blunt 2

Manufactured by Thermo Fisher Scientific
Sourced in Germany

The PCR-Blunt-II is a high-fidelity DNA polymerase designed for use in PCR applications. It features blunt-end cloning capabilities and is known for its ability to generate PCR products with minimal errors.

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5 protocols using pcr blunt 2

1

Cloning and Expression of CD28 Isoforms

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cDNAs containing the entire coding region of full-length CD28, CD28i, and CD28Δex2, which do not contain nucleotides for the stop codon, were obtained by RT-PCR analysis of Jurkat cells using the specific primer pairs shown in Additional file 6. cDNAs encoding each CD28 splicing isoform were inserted into pCR-blunt II (Thermo-Fisher Scientific) and subcloned into pAcGFP1-Hyg-N1 (Takara-bio) using XhoI.
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2

Bimolecular Fluorescence Complementation Assay

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BiFC analysis was performed in leaf cells of 3–4-week-old N. benthamiana as described in earlier studies8 . Coding sequences of XPO1a and XPO1b were first cloned into pCR BLUNT II (Thermo Scientific). DNA fragments were then digested and fused to the full-length eGFP (aa1-241), the N-terminal fragment of eGFP (N-eGFP; aa1-aa155), or the C-terminal fragment of eGFP (C-eGFP; aa156-aa241) and then cloned into pENTR. LR recombination with the pMDC32 destination vector was then performed. Generation of full-length eGFP, N-terminal eGFP, and C-terminal eGFP fused WUS in pMDC32 destination vector was previously described8 . Mutations for EAR-like domain were introduced with primers from Supplementary Table 5. Empty N-terminal eGFP and C-terminal GFP were used as negative controls. Agrobacterium tumefaciens GV3101 was transformed with the BiFC constructs and infiltrated into leaves of 3–4-week-old N. benthamiana plants using agroinfiltration buffer solution (10 mM MES pH 5.7, 10 mM MgCl2, 20 uM Acetosyringone). Infiltration of corresponding BiFC plasmids along with the p19 suppressor of gene silencing plasmid was introduced as a 1:1:1 cocktail. Fluorescence of eGFP was monitored using a Leica SP5 Confocal microscope. eGFP fluorescence was detected with 488 nm excitation and emission was collected between 500–525nm. Plastid autofluorescence emission was collected between 631–700 nm.
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3

Cloning and Comparison of Cas9 Variants

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FnCas9 was amplified using the primers found in Table S1 and cloned into the XbaI and PmeI sites of pcDNA3.3 (Invitrogen). FnCas9 point mutants were amplified from strains published previously (8 (link)). SpCas9, StCas9, and NmCas9 were amplified from Addgene vectors 48669, 41815, and 47872, respectively. To create rgRNA vectors, F. novicida CRISPR repeat sequences and the indicated targeting sequence were cloned into the gRNA-encoding plasmid from the Church Lab (Addgene 41824) (9 (link)), within the pCR-Blunt-II (Invitrogen) backbone, using overlapping PCR and the primers indicated in Table S1.
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4

Determining dsRNA Genome Terminal Sequence

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To determine the terminal sequence of the dsRNA ChNSV1 genome, a RNA ligase mediated RACE (RLM-RACE) protocol was followed [59 (link)]. or dsRNA enrichment, total RNA was extracted using Trizol reagent (Life Technologies), followed by precipitation with 2M LiCl to remove single stranded (ss) RNA. Supernatant was collected and dsRNAs were precipitated with 4 M LiCl. dsRNAs were fractionated by 1% (wt/vol) agarose gel electrophoresis, gel-purified (PureLink Quick Gel Extraction Kit—Life Technologies) and denatured at 95°C for 5 min. The miRNA Cloning Linker 1 (IDT) (5'App/CTGTAGGCACCATCAAT/3'ddC/) was ligated to the 3’end of each strand of the denatured RNA using AIR Ligase (Bioscientific) in the presence of RNAseOUT (Invitrogen). The ligated products were used as templates for cDNA synthesis using Superscript III Reverse Transcriptase (Invitrogen) following the manufacturer’s instructions but with a denaturation step of 98°C for 10 min. The resulting cDNAs were amplified with the primers ORF1-reverse/P7-modban and ORF2-forward/P7-Modban to amplify the 3’ end from each strand. A total of 12 PCR reaction products for both strands were cloned into pCR-BluntII (Invitrogen) for sequence analysis.
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5

cDNA PCR Amplification and Sequencing

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cDNA was subjected to PCR using DreamTaq polymerase (Thermo Scientific) for 30 cycles under the following conditions: 1 min at 98°C, 30 s at 60°C, 30 s at 72°C. Primers for this analysis are provided in Table 1. PCR products were analyzed on 2.5% agarose gel and bands of interest were eluted, cloned to pCR-Blunt II (Invitrogen) and sequenced (GATC Biotech sequencing service, Germany).
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