...systems work using a multi-Cas complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade...compositions of the Cascade complex. Created with BioRender.com.   The Cascade complex Cascade is an important... Cascade complex from CRISPR type I-E. Created with BioRender.com. Thanks to this complex, developing...Cascade-Cas3 plasmids in Addgene's collection! A “complex” system Cas3 is part of the Class 1 CRISPR family... settings — mostly a consequence of Cascade's complexity. Figure 1: Schematic of Class 1 CRISPR...component of the CRISPR Cas3 system. Most Cascade complexes are comprised of a combination of Cas5, Cas6, ...Cutting both strands ensures that there isn’t a template strand left behind that the cell can use to repair...

...adeno-associated viral vector (AAV) samples and created a simplified process, termed viral genome sequencing...platform that allows us to provide scientists with complete plasmid sequences. After launching our viral service...parallel, there is a very real risk of mixing up samples, serotypes, or both. Unfortunately, the standard...present SMRT sequencing only works for self-complementary AAVs and the TA-based ligation and tagmentation...ligation and tagmentation require a double-stranded template.  Using viral genome sequencing to verify the ...double-stranded species that could be used as a template for downstream applications (Berns, 1972). Using...molecules in the DNA extract associate with complementary strands, enough double-stranded species exist...

...CRISPR guide. Some examples include: TwinPE: two prime editors make complementary edits to opposite strands...without double-strand breaks (DSBs) or donor DNA templates.  Figure 1: An overview of prime editing...edited strand. The first iteration of prime editor simply fused the wild-type Moloney Murine Leukemia Virus...editing is also more precise. Base editors, for example, typically edit all the target bases within the...increase activity, enhance binding between the template and primer binding site, increase processivity...remake that strand using the edited strand as the template. The PE3 system does just this by including an...component of the MutSα–MutLα mismatch repair (MMR) complex, to temporarily inhibit this process and promote...

...detecting the target-of-interest in your assay and sample-of-interest. The approaches available broadly map...determining the selectivity of antibodies for other sample types and for non-surface (intracellular) antigens...protocol used and the abundance of the epitope in the sample, relative to cross-reactive antigens – that is,...approaches used will be different depending on the sample and target type. To start the validation process...the target at a robust level, similar to that in samples of interest. If you are working with cells that... be necessary to try multiple techniques. For example, we have found that some antibodies perform well...antibodies, using the knockout approach. You can see an example of their work on their synaptotagmin 1 page. The...

...experiment is targeted amplicon sequencing. The information from targeted amplicon sequencing is highly ...detection isn’t as sensitive as targeted amplicon sequencing. For example, GUIDE-seq seems to have a minimum...have been widely adopted due to their relative simplicity and low cost. The problem with these assays is...techniques differ in important ways, but can also complement one another by providing both broad and specific...Mismatch Cleavage Assay Not Provided 5% Inexpensive, simple Low-throughput, low sensitivity Sanger Sequencing...heterogenous populations, low sensitivity Targeted Amplicon Sequencing Provided 0.01% (variable) Sequence-...investigator can be relatively certain that their samples don’t have off-target mutations if they remain ...

...beyond discussion in the abstract and follow an example of a plasmid-based experiment, delineate its requisite...transfected into human cells. From this result one could simply conclude that the shRNA didn’t work, as the expression...the results. Typically, plasmid-based experiments employ transfection, negative, positive, and replicate...transfected successfully and expressing the protein. For example, fluorescence microscopy images resulting from ...provide the baseline/standard against which other samples can be compared. The Empty Vector Control (mentioned...expression in your target cells. In experiments employing gene targeting or genome editing technologies,...endogenous gene in your experimental cells. For example, in the experiment above, Plasmid A contains an...

...The Golden GATEway cloning kit simplifies the cloning process for complex DNA constructs, particular for...recombination template vectors, to perform multiple site mutagenesis and create complex fusion or recombination...cloning. Amplify the pCoofy vector and the sequence of gene of interest in separate PCR amplication reactions...outer mitochondrial membrane. Sequestration is accomplished by knocking down your endogenous protein of ...via Golden GATEway Cloning Frustrated by the complexity of assembling recombination of transgenesis constructs...to classical cloning methods, particularly for complex transgenesis constructs. Kirchmaier et al., PLOS... a critical role in development and are often implicated in disease progression. One of the major challenges...

...protein expression varies from sample to sample. To compare one sample to another, you’ll need to normalize...curve, your standard, and your sample(s), as you can only compare samples to a standard curve generated...multiple sites on an antigen, are cheap and can help amplify a weak signal. However, they have high cross-reactivity...conjugated to primary antibodies). Direct westerns are simpler and faster than indirect ones and can be used in...protein, and can require more antibody or loading sample, which may not be practical. Conjugated primary...Bradford assay or BCA assay. Be sure to aliquot your sample(s) before adding in your denaturing and/or loading...visualize proteins on a PVDF membrane without staining; simply wet your membrane with 20% methanol and place it...

...clones for complete functional knockout of your target gene. Mismatch nuclease assays are completely “blind... PCR Digital PCR (dPCR) involves splitting up a sample into thousands of physically isolated partitions...Conventional thermal cycling is then performed to amplify the target using PCR. Instead of tracking the reaction...of target DNA molecules present in the original sample with a great deal of precision. This means digital...theoretically detect a single target molecule in a sample. Digital PCR assays for mutation screening Now...assays include a forward and reverse primer to amplify the target locus, as well as a reference probe .... The drop-off probe is designed to perfectly complement the wild type sequence and is not capable of ...

... antibody complexes before applying them to samples, such as when performing IHC in a sample where your...gives you a better chance of getting the complex into the sample. Alternatively, Fab fragments can be used...constant region of the heavy chain. As the name implies, these Fabs are the regions of the antibody that...proteolytic approaches. This comes in handy when, for example, you want to swap out one isotype for another. ...antibody in isolation from another portion. For example, Fab fragments are molecules composed of just the...antibodies. Their smaller size allows them to get into samples more efficiently and can also improve localization...the lack of an Fc region. The lack of Fc also simplifies analyses when used in structural studies and ...

... that consistently receives around 200 new DNA samples every week. Here we will provide an inside look...own plasmids. Staying organized With hundreds of samples coming through our doors, the first step to ensuring...our deposit process, and then we carefully track samples through our lab using barcoded tubes and plates...assemble your expected full plasmid sequences (examples include Benchling, Serial Cloner, and Snapgene...process. Always sequence verify Once the physical sample and its associated information are at Addgene, ... will catch any errors made during the cloning, sample handling, or sequence assembly steps. All of our...protein fusions, and multiple cloning sites. In the simplest case we have a standard backbone with one insert...

...generally known as Bimolecular Fluorescence Complementation (BiFC). It can provide a qualitative or quantitative... or even single-particle tracking of the bound complex. There are so many FPs available, with many ways... fragments, even from a different base FP (for example, EBFP2(1-10) can be used with GFP(11)). Some of...because they are used with an already-available complementary fragment. Next, let's look at a round-up of...protein fragments for bimolecular fluorescence complementation analysis under physiological conditions. Shyu...fluorescent proteins for protein labeling and signal amplification. Zhou S, Feng S, Brown D, Huang B. PLoS One....

...with increasingly complex experimental conditions. The ability to construct more complex, multi-fragment...fragments in a single “one-pot” reaction to form complex, multi-insert modular assemblies that enable biosynthetic...T4 DNA ligase. Inserts, either precloned or in amplicon form (shown above) are flanked by BsaI sites in...enzyme cutting results in 5’ four base overhangs complementary to the overhangs of the assembled inserts. After...assembly Intermediate 5- or 12-fragment assembly More complex 24-fragment assembly Single insert cloning efficiencies...efficiency measurements using similarly sized Lambda amplicon inserts to control for any suppression of background...Sequencing of blue colonies showed the expected complete sequence for the lacI/lacZ genes (1), while sequencing...

... Their trust in the quality of the content is implicitly defined by their trust in the piñata builders...deals in post-experiment quality control, a good example is CRISPR-GA. These tools assess repair events ...published 1 Jan 2013, no longer available), is a simple catalogue of reported sgRNA designs. The second...similar to EENdb than CrisprGE, but is also a good example of how database tools can be used to aid design...this category are the most common between tools. Examples: “single-target design”, “multi-target design”...considered extremely useful, depending on design goals. Examples:  “feature aware”, “SNP aware”, “secondary structure...post-design process such as primer and plasmid design. Examples:  “multiplex design”, “multi-method design”, and...

... Many of these examples we’ve done annually - they are fan favorites! 6. Keep it simple This may be an...fun into the mix. Thus, our founders and early employees spent this remaining time by elaborately pranking...University Park at MIT.  I’m sure at some companies, employees wouldn’t be caught dead coming into the work vicinity...their teammates and project collaborators have completed their work thoroughly. It’s kind of a chicken ...seems to be a balance of productive and happy employees. The teambuilding culture helps us build relationships...continue the tradition and plan enjoyable events for employees. We now have a team of three (myself included)... best events have been at the suggestion of an employee, or have come to fruition from a lunchroom conversation...

... (5,12,13). For example, in the Ligase Detection Reaction (LDR), probes complementary to the sequence ...with a different complement strand covering all 16 possible NN pairs in the template. The probes were ...ligation of fully base-paired nicks with no gaps. For example, DNA assembly methods, such as Gibson Assembly®...without the exo/polymerase generation of annealed complementary regions. Why use a high fidelity ligase? Numerous... annealed to target DNA (genomic DNA or a PCR amplified fragment) and treated with a high fidelity thermostable...rounds of melting and annealing allows linear amplification of the probe ligation product. With the right...uses two sets of probes to achieve exponential amplification. What does fidelity mean for a ligase? DNA ligases...

...you are shuttling between. For example, if you are using E. coli simply for easy cloning and quick DNA...function in unrelated host species, even from completely different kingdoms of life. That’s convenient... for researchers who want to do experiments in complex eukaryotic cells, but would prefer to grow, clone...into plant genomes. Eukaryotes are a bit more complicated. Yeast vectors may contain an autonomously replicating...episomal vectors is to include viral oris to drive amplification, which helps increase cellular uptake, but this...systems don’t always translate to eukaryotes. For example, beta-lactam antibiotics like penicillin and ampicillin...pathways shared by bacteria and eukaryotes. For example, puromycin inhibits protein synthesis across kingdoms...

...people outside the department to accomplish a variety of goals. For example, I worked with some microscopy...experts that complement your (scientific) skill set and is therefore very useful for complex projects. It...collaborations are becoming increasingly important as more complex approaches to scientific questions become popular...mutual benefit.  Our partnership with SnapGene, for example, allows us to display high-quality maps and annotations...partner, connect the relevant teams, coordinate implementation, and now must focus on managing the established... in teamwork and collaboration management. For example, you may already be part of a scientific collaboration...common interest so naturally this may be easier to accomplish with people at your organization. You can meet...

... encode which amino acids (see example to the right). With such simple rules, you might think it’s easy...express proteins in heterologous hosts. If you simply amplify a gene of interest from the human genome, for...varied codon preferences among organisms aren’t completely understood, but some possible reasons include...resources for the entire translation process. For example, during high growth rate conditions, E. coli preferentially...encoded by highly abundant, charged tRNAs. For example Tuller et al. found that translation efficiency...translated regions a chance to fold properly. For example Pechmann and Frydman found that tracts of non-optimal...producing and charging specific tRNA pools. For example, tRNAs used in genes encoding amino acid biosynthetic...

...fully summarized in a short blog post, but some examples I’m personally interested in include: intracranial... preference.   Historically, ICSS was done by implanting an electrode and non-specifically electrically... also models reinforcement but is considerably simpler than ICSS. The test chamber is divided into two...expression of the early response gene c-fos. For example, using Chr2 stimulation should result in robust...Inhibition of neuronal activation is a little more complicated since basal neuronal activity in your brain region...c-fos expression to get the evidence you need. For example, as shown in this study [3], hippocampal neurons...but before you do any type of behavior analysis, simply take a few animals and stimulate them for 30min...