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We narrowed to 634 results for: des.2

Showing: 161 - 180 of 634 results

  1. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    ...Cas9 from Streptococcus pyogenes.   Figure 2:  Crystal structure of S. pyogenes Cas9 in the apo...NUC and REC lobes laying open like a book (Figure 2). The portion of the CTD that recognizes the PAM is...it doesn’t appear in the crystal structure (Figure 2) at all. When this crucial recognition region is disordered...regions, so crystal structures like those in Figures 2 and 3 don’t show these regions, even if they are present...itself at the bottom of the image. Stem loops 1 and 2 extend horizontally across both lobes. The guide RNA...is required for Cas9 nuclease function. Stem loops 2 and 3 are not strictly necessary for in vitro cleavage...open conformation, but highly flexible, as in Figure 2. The guide RNA is bound primarily by the REC lobe,...

  2. How-to: 5 Steps to a Great Panel Discussion

    Type
    Blog Post
    ... let the panelists introduce themselves. I do a 1-2 minute introduction. If you chose good panelists, ...take 5 minutes to introduce themselves and, voila, 1/2 of your time is gone with no interesting discussion...introductions. The moderator asks questions, calling on 1-2 panelist for each question in a way that elicits those...shift, they are checking out. If you can, plant 1-2 good questions with trusted audience members. A good... asking the panelists not to use any slides for the event. Slides are for presentations, not discussions...discussions. I will rarely work with a panel if slides are allowed. Don't put your panelists behind a table. ...organizations, I asked audience members to stand and describe unique nonprofit models that differed from the...

  3. HA Frankenbody, a New Imaging Tool to Visualize Single Molecules and Nascent Peptides

    Type
    Blog Post
    ...structure-based framework engineering. Methods, 34(2), 184–199. PubMed PMID: 15312672. Inbar, D., Hochman...epitopes (Ewert et al., 2004). This scFv hybrid provides the probe structure and stability from the scaffold...translated quickly by the ribosome. This feature provides HA frankenbody the ability to bind nascent HA ...

  4. Mouse Modeling, Part 2: Breeding and Crossing Mice

    Type
    Blog Post
    ...detect your targeting vector or gene of interest. 2. Breed your parental mice to generate F1 Once you’... allele decreases. Crossing mice to generate a desired phenotype Instead, genetic engineering should be...in the journey towards producing mice with your desired combination of mutations. Assuming your parental...generate mice that are homozygous for all of your desired genes. Remember Punnett squares from high school... are homozygous (or hemizygous) at all of your desired alleles to conduct your experiments. You should...

  5. 15 Hot Plasmids from 2017

    Type
    Blog Post
    ...NGG)  Editing window ~2 nt  85175  pBK-EE-BE3  SpCas9 (NGG)  Editing window ~2 nt  85176  pBK-YE2-... editors with editing windows as small as 1-2 nucleotides! To reduce off-target effects associated with...quantum yield of 0.54) and mScarlet-H with M164H (2-fold improvement in photostability compared to mScarlet...pBK-YE2-BE3  SpCas9 (NGG)  Editing window ~2 nt  85177  pBK-YEE-BE3  SpCas9 (NGG)  Lower on-target activity...activity than BE3; editing window ~1-2 nt  87438  pET42b-HF-BE3  HF-Cas9 (NGG)  Very low off-target activity...Ladders Are Awesome Tools: They are comprised of 2 plasmids, pPSU1 and pPSU2, that can be amplified affordably...libraries The Gross Lab at UCSF recently deposited 2 Bacillus subtilis libraries with Addgene – the B. ...

  6. CRISPR-mediated Plant Base Editors

    Type
    Blog Post
    ...satisfactorily accepts DNA as its substrate (see figure 2).          The artificially evolved adenosine deaminase...editing platforms for plant systems.  Figure 2: Plant base editor platforms and their molecular components...available for plant systems. Target-AID based (CBE-2)-  and rAPOBEC based (CBE-1)-  CBEs are successful...based CBEs are known to deaminate cytosine placed in 2-6 bp and 4-8 bp, respectively, of the protospacer....PMID: 27096365. PubMed Central PMCID: PMC4873371.  2. Nishida, Keiji, et al. "Targeted nucleotide editing...second outcome and increases the generation of the desired T-A base pair. Figure 1: Transition mutation...by base editors. Pathways that compete with the desired outcome are not pictured. Adenine base editors...

  7. Bricking Science: Portraying Scientific Reality Through LEGO

    Type
    Blog Post
    ...thanks to our guest blogger, Dalila Cunha de Oliveira. Dalila Cunha de Oliveira is a PhD student in Hematology...post was contributed by guest blogger, Dalila Cunha de Oliveira. Bricking Science is an idea built, literally...motion videos is very time consuming; producing a 1-2 minute video takes an entire week of our free time...with my husband, I thought about how the limitless design possibilities of the LEGOs were mirrored by the...made, colorful laboratory. When we started, the hardest part of the process was to embed personality in...

  8. 9 Tips to Achieve Success in Academia

    Type
    Blog Post
    ...favorite journals. “If you don't read, you're doomed.” 2. Always be sure to include various positive and negative...will be periods when opportunities arise. “Grab it!” 2. Don’t get caught up in the hype. 3. “Passion gives...sustained motivation is a huge component of success.” 2. “Enjoy Teamwork.” Be friendly, open, sharing, rather...entertainment, politics, K-12, etc.” Addgene's team includes many PhD scientists who have stepped away from...

  9. Truncated gRNAs for Regulating Gene Expression

    Type
    Blog Post
    ...the absence of genome editing (Fig. 2 and 3) (5, 3). Figure 2: Gene activation with nuclease-competent...shown to exhibit more limited activity than SpCas9 (2). In many cases this is due both to lower relative...PMID: 24076762. PubMed Central PMCID: PMC3844869. 2. Chari, Raj, et al. "Unraveling CRISPR-Cas9 genome...genetic locus when complexed with an appropriately designed small RNA, or guide RNA (gRNA). The gRNA conventionally...exploited to either inactivate a gene or introduce a desired genetic alteration. Listen to Our Podcast Interview... truncated such that it exhibits 15 or fewer nucleotides of complementarity to a target site, Cas9’s DNA...truncated gRNAs Importantly, the use of truncated guides has largely been demonstrated to result in decreased...

  10. Year of the Camelid: Antibody Style

    Type
    Blog Post
    ...and a source of sdAbs (Figure 2) (Xu, et al., 2021).      Figure 2: Genetically modified mice offer... from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature 595:278–282. https://doi.org/10.1038...camelids too, though not just for the reasons the UN describes. In honor of the Camelid family, I wanted to take...of times on this blog over the years and have described how they compare to other antibodies and affinity...

  11. Optogenetics + CRISPR, Using Light to Control Genome Editing

    Type
    Blog Post
    ...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...

  12. Plasmids 101: Gateway Cloning

    Type
    Blog Post
    ...is excised from the donor vector.   Figure 2: The Gateway system adopts phage integration into ...our website to search for your favorite gene! STEP 2: Generate an Expression Clone When making the expression...expression construct in only 1 day, as opposed to 2+ days with traditional restriction and ligation cloning...Clon Transgen 4:138. doi:10.4172/2168-9849.1000138 2. Hartley JL. Use of the Gateway System for Protein...clone in their desired DNA sequences. Gateway technology relies on the two reactions described below: The ...pLenti CMV Puro DEST (w118-1) or the doxycycline-inducible pLIX_403. The chosen attR destination vector will...between the entry clone and destination vector creates two products: the desires expression clone and a byproduct...

  13. Plasmids 101: Restriction Cloning

    Type
    Blog Post
    ... used. Follow the manufacturer’s instructions.   2. Isolate Your Insert and Vector by Gel Purification...DNA concentration alone. One method is to conduct 2 ligations for each plasmid you are trying to create...containing the ligation mixture with backbone alone; 2. Transformation containing ligation mixture with insert...colonies than the vector + insert plate (unsuccessful 2), or roughly equivalent numbers of colonies on each... or equivalent to backbone + insert, unsuccessful 2 and 3 above), you can try ligating the recipient plasmid...single enzyme if your insert is flanked on both sides by that enzyme’s restriction sites, but the insert...the orientation of your insert. You may want to design a diagnostic digest for this purpose. Ideally, ...

  14. Simplify Cloning with in vivo Assembly

    Type
    Blog Post
    ...(109 CFU/μg) cells. Primer design Using specific primer design (Figure 2), IVA cloning can be used to...multiple genes. Primer design for each type of modification is shown in Figure 2, and is discussed in more...procedure to be performed using a simple two-step, 2 hr protocol prior to transformation (Figure 1). As...Biotechniques 10.1 (1991): 62-66. PubMed PMID: 2003926. 2. Bubeck, Peter, Monica Winkler, and Wilfried Bautsch...primers that bind at either side of the undesired portion, designed to amplify the rest of the vector sequence...primary method to produce the linear fragments, as desired modifications and homologous regions can be encoded...specifically cuts methylated DNA, so it will selectively destroy the template, but not newly synthesized sequences...

  15. Optimizing Donor DNA for Enhanced CRISPR Genome Editing

    Type
    Blog Post
    ...mechanism of action are presented in Figure 2. Figure 2: Single-stranded donor DNA interaction with...Nature biotechnology (2016). PubMed PMID: 26789497.  2. Lin, Steven, et al. "Enhanced homology-directed human...DNA post-cut. Using substrate DNA labeled on both sides of the break, we determined that Cas9 held tightly... single or double stranded donor DNA with other design parameters. Example single stranded donor DNA and...approaches. Moreover, the cost of reagents is relatively modest, requiring expressed Cas9 protein, transcribed ... Blog Brush Up on Your HDR Basics Learn How to Design Your gRNA Find the Ideal CRISPR Software for Your...Plasmids for Your Research Check out Our List of gRNA Design Tools ...

  16. Simple CRISPR-based Epigenetic Editing: dCas9-directed DNA Demethylation

    Type
    Blog Post
    ...Hrit et al. 2018, Kaas et al. 2013). Figure 2: CRISPR TET-based epigenetic editing. In reality, ...doi.org/10.7554/eLife.34870.  Kaas GA, Zhong C, Eason DE, Ross DL, Vachhani RV, Ming G-L, King JR, Song H,...approach for targeted DNA demethylation. Cell Discov 2, 16009. https://doi.org/10.1038/celldisc.2016.9.  ...Recently, however, a particular tool has gained widespread popularity – and notoriety – as a tool of choice...leave you with a few practical considerations: Design your gRNA to overlap the CpG of interest. Having..., too), but if this is not possible due to gRNA design restrictions, anything within 5 base pairs should...

  18. Fluorescent Proteins 101: Aptamer Fluorophores

    Type
    Blog Post
    ... to DFHBI in the presence of that metabolite (Fig.2). Spinach eventually evolved into Spinach2, a more...PMID: 25713381. PubMed Central PMCID: PMC4364232. 2. Baker, Monya. “RNA imaging in situ”. Nature Methods...emerging environmental pollutants.” Front Chem. 2014; 2: 41. PubMed PMID: 25019067. PubMed Central PMCID: ...biosensors.” TrAC Trends in Analytical Chemistry 27(2):108-117 · February 2008. 11. Svensen, Nina and Jaffrey...Researchers have used oligonucleotides in fluorescent visualization techniques for decades, most notably for... exponential enrichment (SELEX), some 1010 oligonucleotides could be screened for their affinity to a ...aptamers as well, and over the course of the next two decades, these nucleotide-based ligand binders would prove...

  19. CRISPR 101: Making a Knock-In Cell Line

    Type
    Blog Post
    ...200 bp – 2 kb), a dsDNA donor will need to be used due to synthesis limits of oligonucleotides. These donors... mechanisms Mammalian cells have 2 primary repair mechanisms besides HR - Non-homologous end-joining (...accidentally change your protein of interest.   Fig. 2: Stop re-cutting with PAM and guide RNA disrupting.... Com., 8(2024), (2017). 10.1038/s41467-017-01836-2 Charpentier, M., Khedher, A. H. Y., Menerot, S., Brion...harnessing the homology-directed repair pathway, designing the best donor DNA, and avoiding common mishaps...knock-in. Then choose which Cas enzyme to use and design a gRNA to where you would like to introduce the...sequence to introduce, which is done through the design and use of a donor DNA molecule. Your donor molecule...

  20. Hot Plasmids and Viral Preps - January 2021

    Type
    Blog Post
    ...by Leopold Parts. This library delivers 2 randomly paired guides per construct and allows a reduced scale... Opto-Cre-Vvd is fast and can cut in as little as 2 hours.  Sheets, MB, et al., ACS Synth Biol. 2020....they investigated three Casɸ orthologs, Casɸ-1, Casɸ-2, and Casɸ-3. This system is notable for several reasons...a minimal PAM requirement. For instance, for Casɸ-2 the PAM sequence is 5’-TBN-3’ (where B is G, T, or...
Showing: 161 - 180 of 634 results