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Gblocks gene fragment

Manufactured by Integrated DNA Technologies
Sourced in United States, Belgium, Singapore

GBlocks Gene Fragments are synthetic, double-stranded DNA sequences designed for a variety of applications in molecular biology and genetic engineering. They serve as building blocks for constructing larger DNA molecules, such as plasmids, gene expression cassettes, and pathways.

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133 protocols using gblocks gene fragment

1

Cloning and Mutagenesis of miRNA Targets

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Primary miRNAs were ordered as gBlocks® gene fragments from Integrated DNA Technologies (IDT), and cloned downstream of a U6 promoter by restriction digestion. Perfect targets and non-targeting controls for each miRNA were designed based on the mature miRNA sequence. Sequences were ordered as gBlocks® gene fragments from Integrated DNA Technologies (IDT), and cloned into a psiCHECK-2 vector by Gibson assembly. Complete 3’UTR and CDS of candidate genes were amplified by PCR from cDNA, generated from total RNA harvested from donor human brain samples. This was done to ensure brain expressed isoforms were being studied. The 3’UTR gene products were cloned into psiCHECK-2 vectors by Gibson assembly. The CDS genes were cloned downstream of a CMV promotor in a mammalian expression construct by Gibson assembly, along with a Flag and 6XHis tag on the C-terminal end. We used site-directed mutagenesis by overlap-extension PCR to generate altSNPs and Scr variants of each gene.
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2

Teneurin4 Protein Expression Protocols

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The plasmid encoding the full ECD of human Teneurin4 (residues 375–2,769) was created by subcloning a gBlocks Gene Fragment (residues 375–662, Integrated DNA Technologies) with the partial coding region of human Teneurin4 (residues 663–2,769, BC172403, Biocat) into the pUPE106.03 vector containing a N‐terminal cystatin secretion signal and N‐terminal His6 tag (U‐Protein Express) using BamH1, SfiI and NotI cloning sites. The plasmid encoding full‐length human Teneurin4 was created by subcloning a gBlocks Gene Fragment (residues 1–374, Integrated DNA Technologies) with the full ECD segment of Teneurin4 into the pUPE3620 vector containing a N‐terminal GFP tag using BamH1, Stu1, and NotI cloning sites. The plasmid encoding the C‐rich domain of human Teneurin4 (residues 834–871) was created from a template including restriction sites ordered from GeneArt (Thermo Fisher Scientific), which was subcloned into the pUPE106.03 vector containing a N‐terminal cystatin secretion signal and N‐terminal His6 tag (U‐Protein Express) using BamH1 and NotI cloning sites.
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3

Cloning and Verification of Mutant FOs

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All FOs were Escherichia coli codon-optimized and synthesized using Integrated DNA Technologies’ gBlocks Gene Fragments. Fragments and the destination vector (CL20) were cut with Not1 and Xba1 restriction enzymes and ligated together New England BioLabs’ Quick Ligation Kit per the manufacturer instructions. All plasmid sequences were confirmed by whole plasmid sequencing. Mutant FOs (Fig. 6) were synthesized in the same manner.
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4

Cloning and Validating 3' UTR Constructs

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The wild-type (WT) sequences of DUSP16 3′ UTR (NCBI acc. no. NM_030640.3) and CDK13 3′ UTR (NCBI acc. no. NM_003718.5) were designed using gBlocks® gene fragments (Integrated DNA Technologies, Inc., Coralville, IA, USA). Given the length of their 3′ UTRs (3551 and 4000 nt, respectively) and the difficulty of cloning such long fragments, we opted for shorter segments which carried potential binding sites for EBOV-derived miRNAs. Thus, 727 nt of the DUSP16 3′ UTR and 403 nt of the CDK13 3′ UTR were introduced downstream of the Renilla luciferase (Rluc) reporter gene in the XhoI/NotI cloning sites of the psiCHECK2 vector (Promega, Madison, WI, USA). Reporter constructs bearing the mutated versions of these 3′ UTRs were also engineered. The details of the construction strategy are summarized in Supplementary File S4. All the constructs were independently confirmed by DNA sequencing at the Plateforme de Séquençage et Génotypage des Génomes (Centre de Recherche du CHU de Québec—CHUL, QC, Canada).
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5

C. albicans CRISPR-Cas9 Plasmid Toolkit

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The plasmid backbone used in this study was adapted from the C. albicans-optimized CRISPR-Cas9 plasmid (also known as pRS252) used in our previous study (33 (link)), containing the NEUT5L homology site and CAS9 (79 (link)). To create a sgRNA cloning locus in this plasmid, the SNR52 promoter, SapI cloning locus, and sgRNA tail were synthesized in vitro as gBlocks gene fragments from Integrated DNA Technologies (IDT) and were cloned into the CRISPR-Cas9 plasmid (pRS252) at the NgoMIV restriction enzyme site, using Gibson assembly, as previously described (33 (link), 79 (link)). We have made the relevant CRISPRi (dCas9 and dCas9-Mxi1) plasmids available via Addgene (reference numbers 122377, 122378, 122379, and 122380).
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6

GFP Reporter Plasmid Construction

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The GFP reporter plasmids were cloned with the MultiSite Gateway Technology (Thermo Fisher Scientific) and the destination vector pCFJ15047 (link). Modified 5′-UTRs and 3′-UTR fragments were ordered as gBlocks® Gene Fragments (Integrated DNA Technologies) and cloned into Entry clones using Gibson assembly48 (link). Supplementary Data 1 lists gBlock sequences and resulting entry plasmids. For every final reporter plasmid, three entry plasmids and the pCFJ150 vector backbone were recombined (Gateway LR Clonase II Enzyme mix, Thermo Fisher Scientific; 11791020) resulting in a plasmid containing a promoter, 5′-UTR, GFP(PEST)-H2B coding sequence and a 3′-UTR. Transgenic animals were obtained by single-copy integration into the ttTi5605 locus on chromosome II, using the protocol for injection with low DNA concentration49 (link).
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7

Construction and Validation of Pif1 Mutants

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The PIF1 promoter was excised from plasmid pVS102 (16 (link)) by digestion with PspXI and AgeI (New England Biolabs, NEB) and then cloned into plasmid pMB282 (CEN ARS TRP1) containing PIF1 with a C-terminal 3xFLAG tag (32 (link)). The resulting plasmid referred to as pCG17 was verified by restriction enzyme digestion and DNA sequencing and used as the target plasmid for mutagenesis. Mutations within the conserved Pif1-family SM were generated in pCG17 using QuikChange Lightning Site-directed Mutagenesis (Agilent Technologies), Q5® Site-directed Mutagenesis (NEB) or cloned in using gBlocks® gene fragments (Integrated DNA Technologies) and the Gibson Assembly® method (NEB). Mutations were verified by NotI and AvaI restriction enzyme digestion (NEB) and DNA sequencing. The SM mutations analyzed in this study are listed in Figure 2C.
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8

Quantifying Amphibian Pathogen Loads

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DNA was extracted and quantified using standardized protocols (Boyle et al. 2004 (link); Hyatt et al. 2007 (link)) and swabs were run in triplicate with an internal positive control (IPC) to test for DNA inhibition. Samples were declared ‘positive’ only if they amplified at least twice across runs. Total B. dendrobatidis zoospore-equivalents (ZE) per swab were averaged across swabs and rounded to the nearest whole number. Ranaviral DNA was extracted from liver and kidney tissue samples and infection was determined using standard quantitative PCR protocols (Forson and Storfer 2006 (link)). Viral load (i.e. viral copies ng-1 of DNA) was estimated based on a known standard curve. We used a synthetic double-stranded DNA standard by synthesizing a 250bp fragment of the major capsid protein (MCP) gene (gBlocks Gene Fragments; Integrated DNA Technologies), which is conserved among ranaviruses. Viral equivalents (VE) were rounded to the nearest whole number.
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9

Cloning and Manipulation of Ion Channel Genes

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cDNAs encoding full-length mouse TWIK-1 (NM_008430) and mouse TASK-3 (NM_001033876) were obtained by using the Gateway cloning method (Invitrogen, Carlsbad, CA, USA). cDNAs encoding full-length human NTSR-1 (NM_002531) and human NTSR-2 (NM_012344) were synthesized by designing gene blocks (gBlocks® Gene Fragments; Integrated DNA Technologies, Coralville, IA, USA) and constructing entry clones using the Gateway BP cloning method (Invitrogen). The constructs were cloned into several vectors, including pDEST-HA-N, pDEST-FLAG-N, pDEST-IRES2-GFP, and pDEST-IRES2-mCherry by using Gateway LR cloning (Invitrogen). To construct the concatenated TWIK-1 and TASK-3, TASK-3 and TWIK-1 were recloned into the pDONR207 P1P5R and pDONR207 P5P2 vectors, respectively, via two independent BP reactions (Invitrogen), followed by a MultiSite Gateway LR recombination reaction (Invitrogen) according to the manufacturer’s guidelines to produce pDEST-IRES2-GFP. The target regions of the shRNA (mouse TWIK-1: 5′-GCATCATCTACTCTGTCATCG-3′; mouse TASK-3: 5′-GCTGGTGTCCAGTGGAAATTC-3′) were obtained by oligonucleotide-directed mutagenesis using an EZchange site-directed mutagenesis kit (Enzynomics, Daejeon, Korea).
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10

Constructs for Optogenetic Manipulation

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Constructs for stable transduction in mammalian cells were cloned into the pHR lentiviral backbone with an SFFV promoter driving the gene of interest. The pHR backbone was linearized using MluI and NotI restriction sites. BcLOV4, iLID, BFP, SOScat, and iSH coding DNA fragments were generated via PCR and inserted into the pHR backbone via HiFi cloning mix (New England Biolabs). For expression in Drosophila S2 cells, BcLOV-mCherry, BcLOV-iSH, and BcLOV-SOScat were amplified and inserted into the pbphi-nanos promoter-αTubulin 3’UTR vector44 between the NheI and BamHI restriction sites. The resulting vectors were digested with NotI and XhoI to replace the nanos protomer with the metallothionein promoter (pMt)45 , which was synthesized by gBlocks gene fragments (Integrated DNA Technologies). The pMt promoter permits inducible expression in the presence of heavy metals, e.g. copper. For zebrafish mRNA expression experiments, BcLOV-mCherry, BcLOV-SOScat and ERK-KTR-BFP (adapted from Regot et al32 (link)) were amplified with primers containing att sites for Gateway cloning. PCR amplicons were transferred into pDONR221 plasmids and sequence verified. Gateway cloning was used to transfer each insert into pCSDest plasmids 46 .
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