...dCas9VP64 and sgRNA from separate promoters. Table 2. pmax dCas9 Activator Expression Plasmids ID Plasmid...plasmids are described in: Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional...

... of 2 components: 1) an SB transposase, the enzyme required for catalysis of transposition; and 2) a transposon... gene (red) for expressing the transposase enzyme.2.) The transposase enzyme is expressed (red stars) ... 2015 Feb 4. doi: 10.1002/biot.201400821. PubMed. 2. Mates L, et al. Molecular evolution of a novel hyperactive...organism’s genome (see figure) and to disrupt endogenous genes at the site of insertion. In both of these...and binds the inverted repeats (green); and an endonuclease reaction occurs which cuts the DNA.3.) The released...

.... Diagnostic restriction digests are comprised of 2 separate steps: 1) incubating your DNA with restriction...which cleave the DNA molecules at specific sites and 2) running the reaction on an agarose gel to determine...including a 1.2 kb insert. The plasmid was digested with 2 unique enzymes (HindIII and BamHI) and run on an agarose...to serve as a reference band. The uncut DNA (lane 2) shows 3 possible plasmid conformations, with relaxed... JM110 or INV110. Avoid star activity. Some endonucleases (for example BamHI) are capable of cleaving ...manufacturers make High Fidelity versions of the endonucleases and/or supply custom buffers as means to avoid...

...illustrated in the schematic below.   Figure 2: gRNA target sequences (colored rectangles) are cloned... plasmids: This plasmid set allows you to express 2-4 gRNAs, with four being the ideal number. First you...the total number of gRNAs you wish to clone, from 2-7. For example, if you’re expressing 4 gRNAs, you’...gRNAs into spectinomycin-resistant plasmids pX330S-2 to pX330S-(last gRNA number). The 5’ most gRNA is ...Multiplexing Plasmids: These plasmids allow you to assemble 2-4 gRNAs through Golden Gate or Gibson Assembly. gRNAs...Multiplex Plasmids: These plasmids allow expression of 2-5 gRNAs in zebrafish. Custom destination vectors are...and a subsequent curing protocol that requires only 2-3 hours incubation. Kondo Lab multiplexed base editing...

...repeated multiple times (2-4 rounds) at increasing scale over the course of 1-2 weeks. Each round of amplification...creating adenoviral vector constructs. It consists of 2 plasmids: a shuttle vector (in which the transgene...Addgene’s Adenoviral Guide webpage, and references 1, 2.*Pro-Tip*: once the correct recombinant pAdV plasmid...confirm its integrity. Initial production (2-3 weeks) - Here you’ll produce the primary recombinant adenoviral...media will turn yellow. Do NOT change the media (add 2-3 mL of fresh media once a week), and do NOT harvest...it will result in very low titer. Amplification (1-2 weeks) - The rAdV-S is used to infect more HEK293 ...in a 10-100-fold increase in virus. Purification (2 days) - Purification is required if rAdV is to be ...

...difficult-to-manipulate primary cells, achieving knockdown within 1-2 hr of reagent delivery. TRIM-Away is suitable for ...factor 1 controls expression of transcription factor 2, which directly controls expression of a reporter ...modulating the induction of transcription factors 1 and 2. See Aranda-Díaz et al. for more information. The ...our Hot Plasmids Podcast! TRIM-Away: Targeted endogenous protein degradation Article contributed by Mary... hr of treatment. In some primary cell lines, endogenous TRIM21 is sufficient for TRIM-Away, and you only... et al. Cell. 2017. PubMed PMID: 29153837. Endosomal pH sensors for STED nanoscopy Article contributed...contributed by Eric J. Perkins Listen to Endosomal pH Sensors podcast segment The first Addgene plasmid deposit...

... to the lysosome where they are finally degraded (2, 3). Once you've created your fusion protein, it's...examples include the ImageJ plugins JACoP and Coloc 2, BioImageXD, and customized CellProfiler pipelines...colocalization analysis example is given in Figure 2 (adapted from 4) - Dunn et al. 2011 provides an in-depth...Since colocalization relies upon the detection of 2 independent fluorescent signals and their potential...here! References 1. Allen Institute Plasmid Pages 2. Cooper GM. 2000. The Cell: A Molecular Approach. ..., most secreted proteins are produced in the endoplasmid reticulum, modified in the golgi and then transported...the Addgene Blog Learn More about Plasmids for Endogenous Gene Tagging in Human Cells Check Out the Michael...

...safely. Recently, many SARS-CoV-2 researchers began pseudotyping the SARS-CoV-2 spike protein into a lower ...SARS-CoV-2 virus. Scientists have been using similar pseudotyping methods with other viruses in a BSL-2 lab... et a., 2018).   Figure 2: To pseudotype with the SARS-CoV-2 spike protein, scientists encode...production uses three plasmids: (1) The transfer plasmid, (2) the envelope plasmid, and (3) the packaging plasmid...example, production of vesicular stomatitis virus, HIV-2, and human foamy virus in cell lines expressing galactosyl...for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays. Viruses 12...Are Inactivated by Human Serum. Molecular Therapy 2:218–222 . https://doi.org/10.1006/mthe.2000.0116 Gutierrez-Guerrero...

...plasmid-based expression requires serial transfection of 1 or 2 plasmids that express the reprogramming factors of...for generating iPSCs by plasmid transfection where 2 of 11 clones tested had plasmid integration. Another...understanding the mechanisms of reprogramming, and 2) studies with clinical endpoints. In the first scenario...PubMed PMID: 27764162. PubMed Central PMCID: 5072705. 2. Sommer, Cesar A., and Gustavo Mostoslavsky. "The ...challenges." Journal of Cellular Physiology 228, no. 2 (2012): 267-75. PubMed PMID: 22767332.  3. Kim, Dohoon...PubMed PMID: 23546745. PubMed Central PMCID: 4176696. 2. Yusa, Kosuke, Roland Rad, Junji Takeda, and Allan...generation. Expert opinion on biological therapy, 10 2, 231-42. PubMed PMID: 20088717. PubMed Central PMCID...

... necessarily suitable for combining endogenous sequences. Table 2: High Throughput Cloning Strategies ... TagBFP 399nm/ 456nm histone 2B (H2B) Chromatin 2 Cerulean 433nm/ 475nm Lyn-tag (derived from the tyrosine-protein...based (chaining-based) cloning. The modules (Figure 2) are contained in individual plasmids and are each...between various cloning methods are listed in Table 2. For example,  chaining-based cloning methods require...PMID: 20205762. PubMed Central PMCID: PMC2822740. 2. Engler C, Kandzia R, Marillonnet S. A one pot, one...modules themselves (so may not be suitable for endogenous coding sequences), so enzyme choice is critical...

...for retrograde transport has been found for AAV1, -2, -5, -7, -8 (Taymans et al., 2007), AAV1 (Hollis et... tropism and axonal transport of AAV serotypes 1, 2, 5, 6, 8 and 9 in the mouse brain. PLoS One 8:e76310...reveal novel hippocampal CA2 circuits. Nat Neurosci 17(2), 269–279. PubMed PMID: 24336151. PubMed Central PMCID... Mechanisms of Motility and Regulation. Neuron 84(2), 292–309. PubMed PMID: 25374356. PubMed Central PMCID...transduction efficiency of recombinant AAV serotypes 1, 2, 5 and 8 in the rat nigrostriatal system. J Neurochem...analysis of adeno-associated viral vector serotypes 1, 2, 5, 7 and 8 in mouse brain. Hum Gene Ther 18, 195–...retrograde access to projection neurons. Neuron 92(2), 372–382. PubMed PMID: 27720486. PubMed Central PMCID...

...the light-inducible heterodimerizing cryptochrome 2 (CRY2) and calcium and integrin-binding protein 1 ...inactive, dead Cas9 protein (dCas9) fused to CIB1; and 2) the activator - the CRY2 photolyase homology region... fused to both the N- and C-termini of dCas9; and 2) CRY2FL-VP64, a fusion of full-length CRY2 and the...researchers saw an 11-fold increase in mRNA levels after 2 hr and a 400-fold increase after 30 hr. The system...authors fragmented Cas9 into N-terminal (residues 2-713, N713) and C-terminal (residues 714-1368, C714...nMagC714 instead of nMagHigh1-C714, generating paCas9-2. This change did not significantly alter the system...prior work, the Sato lab also showed that the paCas9-2 system could be spatially controlled and reversibly...

...recognize Fab fragments from the same species and 2) these fragments will be more likely to bind (and ...epitopes recognized by the secondary.   Figure 2: There are a few common solutions to avoid background...(IHC) applications an issue? The culprits are endogenous IgGs in your tissue sample. Most common IHC protocols...and a second against the first antibody. When endogenous IgGs of the same species as your primary antibody..., your secondary antibody recognizes both the endogenous IgGs and your primary antibody, resulting in ... Not all tissues will have the same levels of endogenous IgGs, so some researchers can get away with species...to be sure that your secondary is not binding endogenous IgGs, you should include no primary antibody ...

...purify IVT sgRNA in the lab. Figure 2: Cas9 RNP complexed with 2-part cr:tracrRNA tags genes more effectively...into stem cells. Cells are allowed to recover for 2-5 days and then analyzed for tagging efficiency using...IVT sgRNA) approach (Dewari et al. 2018 and Figure 2). Not only is the cr:tracrRNA approach highly efficient...cell suspension, transfect and let cells recover for 2-5 days.Note: We use the Nucleofection method for delivery...success was ~%50. If you get low knock-in efficiency (<2% positive by ICC for the tag) or do not see any cells...PMID: 28096221. PubMed Central PMCID: PMC5312033. 2. Dewari PS, Southgate B, Mccarten K, Monogarov G, ...Additional Resources on the Addgene Blog Plasmids for endogenous gene tagging in human cells Plasmids 101: Protein...

... analogs such as 2-fluoroadenine (2-FA), organisms with functional APT will convert 2-FA to cytotoxic ...selection of plants undergoing RNAi, and LIIbeta F 1-2 RNAi, which allows assembly of intron-spliced hpRNAs...nucleotides, resulting in death. In the presence of 2-FA, potent gene silencing of APT is required for survival...resulting in processing by the endogenous RNAi machinery. Alternatively, endogenous miRNA precursors can be ...Although similar, amiRNAs are engineered from endogenous precursors of microRNAs found in the genome, ...

...3 plates at different densities for selection). A 2% agarose solution is then melted (and thereby sterilized...96-well assay plate. We generally freeze at least 2 ampules each of 4 clones with different levels of ...of agarose, which is then overlaid with the firmer 2% agarose gel solution discussed above for picking....Additionally, many cell lines, especially the endocrine cell lines we most commonly work with, require...do not seem to require this, while nearly all endocrine cells do. While not all of the wells in the 48...Western blotting and PCR, depending on the level of endogenous expression. We highly recommend the use of an...cell lines, from HEK to CHO cells to neural and endocrine cells such as AtT-20, PC12, Rin5F, Neuro2A and...

...properly exiting the ER and fluorescing (see Figure 2) [5].  When using FPs containing two cysteine residues...compartments including the secretory pathway (Figure 2), the inner membrane space of mitochondria and chloroplasts...PMID: 18228466. Pubmed Central PMCID: PMC2875081. 2. Snapp, Erik Lee. "Fluorescent proteins: a cell biologist's...rewarding. But, what if an FP fusion with a resident endoplasmic reticulum (ER) protein instead localizes to the...organelles that compose the secretory pathway, endocytic vesicles, mitochondria, lysosomes or they are ...gram negative bacteria periplasm. Efforts to tag endogenous genes for proteins in these compartments using...quality control of secretory proteins in the Endoplasmic Reticulum and live cell imaging approaches. Erik...

...for shipping stability by incubating at 37 °C for 2 weeks, freezing at -80 °C, thawing on ice, and then... been retained. If the target antigen is not endogenously-expressed (e.g., using an anti-GFP antibody)...

...transient mammalian expression 101126 pACP-tag (m)- 2 Vector ACP/MCP-tag Empty backbone for stable and transient...pSNAP-CaaX Control Plasmid SNAP-tag Control for endomembrane (CaaX box) localization 101129 pSNAPf-Cox8A ...

...them in Regenerative Medicine. Acta Naturae, 2010. 2(2): p. 18-28. PubMed PMID: 22649638. PubMed Central...capability to differentiate into specialized cell types [2]. We general speak of 4 levels of stem cell potency...zygote through to the morula stage are totipotent [2-4]. Pluripotency: When a cell has the ability to differentiate...stem cells (ESCs), which I discuss in detail below [2]. Multipotency: When a cell can differentiate into...PMID: 26726264. PubMed Central PMCID: PMC4686367. 2. Jaenisch, R. and R. Young, Stem cells, the molecular...differentiate into cells of any of the three germ layers: endoderm, ectoderm, and mesoderm. In essence, pluripotent...