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...cutting at mismatched guide sites, but not necessarily binding to these sites. Thus, these enzyme swaps ... ChIP-Seq, where only DNA sites bound by Cas are sequenced, has been tested with some success. The major... sequencing Sites with high sequence similarity to the gRNA can be sequenced. These sites can be selectively... this often means DNA cleavage at unanticipated sites. While off-target effects are nearly impossible ...or is engineered not to cleave DNA and instead activates/represses gene expression by various mechanisms...words, they can sometimes localize to unintended sites with sequence similarity to the on-target site. ...When a CRISPR-Cas system localizes to unintended sites and performs its programmed function there, this...

...behavioral tests.    Forced swim test The forced swim test has been used since the 1970s to test the efficacy...general considerations for performing behavioral tests, but now we’ll focus on how viral vectors have changed...locomotion, anxiety, and depression.  Locomotion tests To study and quantify locomotion, scientists monitor...Such a behavior can be monitored in an open field test (Alpar et al., 2018). Locomotion can also be used...therapeutic approach against drug addiction. Anxiety tests Rodents have a natural preference to stay in dark...neurons turns on overexpression of IL-1 beta. They tested the mice in a series of behavioral tasks. One of... of antidepressant treatment in rodents. In this test, an animal is placed into a tank of water with no...

...the effect of the independent variable you are testing. Importantly, they demonstrate the functionality...associated with the independent variable you are testing and not some other unintended factor. Control plasmids...luciferase) that is either co-transfected with the test plasmid or transfected into a separate well of your...Regardless, the amount of reporter protein activity correlates to both the amount of DNA transfected into the... Plasmid B (as internal control) This result indicates that the transfection was not successful due to... and from different preparations of the purified test plasmid expressing the independent variable. There...technical and biological. In general, technical replicates can be thought of as "plate controls". They are...

...generated by the nickases; D10A creates 5’ overhangs and H840A creates 3’ overhangs in a PAM-out design...problem. D10A nickase outperformed both WT Cas9 sites tested by a wide margin, exhibiting >20% repair efficiency...Optimize your spacing D10A: nick sites separated by 37-68 bp H840A: nick sites separated by 51-68 bp Use...CRISPR nickases improve homology directed repair rates, and share their design rules for your next CRISPR...as examples for this post. The D10A mutation inactivates the RuvC domain, so this nickase cleaves only...Conversely, the H840A mutation in the HNH domain creates a non-target strand-cleaving nickase. Instead of...Mollie Schubert and Shuqi Yan designed experiments to test nickase preferences using HEK293 cells. They started...

...widespread testing is crucial in controlling this pandemic. Currently, the CDC uses RT-qPCR tests to diagnose...100% negative prediction rate. It is also the fastest test that has been developed so far.  A similar method... Highly similar to the SHERLOCK diagnostic test, this test varies in the sequence of steps and the Cas...and to do so, the WHO recommends one strategy: testing, tracking, and social distancing. With countries...diagnose COVID-19 and some serological tests to determine past exposure. However, the limited availability...general schematic of CRISPR/Cas based COVID-19 testing methods.   Rapid detection of 2019 novel coronavirus...:10-100 copies of RNA per microliter Time: ~40 minutes Equipment required: 37°C heat block and 62°C heat...

...expression piggyBac Excisible Medium Medium Generates transgene-free and vector-free cells Genome integration...mutations Adenovirus Non-integrating Low Medium Generates transgene-free and vector-free cells No genomic... Sendai Virus Non-integrating Medium Medium Generates transgene-free and vector-free cells No genomic...Plasmid Non-integrating, usually Medium Medium Generates transgene-free and vector-free cells Limited genomic... EBNA1 episome Non-integrating Medium Medium Generates transgene-free and vector-free cells No genomic... Minicircle Non-integrating Medium Medium Generates transgene-free and vector-free cells No genomic..., criteria used, etc.) can effect reprogramming rates and such a number maybe misleading. Integrating ...

...Subscribe to the Addgene blog to get all the latest hot plasmid updates!     Tol2 Gateway-compatiable toolbox...vectors that have standard cloning sites or gateway compatible cloning sites for easy cloning of your genes...variations in gene expression from these polycistronic cassettes could lead to comparable experimental results....compared different variants of the polycistronic cassettes and discovered reprogramming discrepancies, which... Klf4 isoform (KLF4s or KLF4L). Polycistronic cassettes that contained KLF4s had overall diminished KLF4...global gene expression patterns. Polycistronic cassettes that contained the KLF4L isoform had more robust.... The polycistronic piggyBac transposon vectors tested in this work are available at Addgene. Kim, et...

...higher mutation rates than they’d previously reported in protoplasts (15% and 9% of target sites.) How many...efficient tRNA processing is common to prokaryotes and eukaryotes. Though the plasmids made by Xie et. ...RNAs (gRNAs) are commonly packaged in 400-500 bp cassettes containing the RNA pol III promoter, gRNA and ...and pol III terminator. These relatively large cassettes (considering the gRNA itself is ~100 bases) limit...cleave 4 gRNAs separated by 28 base Csy4 recognition sites from a polycistronic transcript. Although this method... or pre-tRNAs are cleaved by RNase P and Z in eukaryotes (E in bacteria), and only a few elements of tRNAs...recognition and cleavage. This sequence flexibility indicates that gRNAs could be incorporated into these constructs...

...availability of enhancer sequences in different chromatin states. Alexander Stark and colleagues at the Research...self-transcribing active regulatory region sequencing) that tests enhancer sequences outside of their endogenous chromatin...Synthetic and basic biologists alike often need to test multiple expression systems before they achieve ...bacteria, the process of cloning, combining, and testing these different parts can be quite arduous. The... lab generated 5 common 30bp overlap sequences (Sites #1-5). Each overlap site encodes a unique restriction...restriction enzyme site and unique primer sites for more rapid screening by restriction digest and Sanger ...allows scientists to easily design, generate, and test constructs composed of complex genetic elements....

...Demonstration of PILATeS. Cell adhesion to a PILATeS-functionalized coverslip creates mechanical tension...reversible, making PILATeS suitable for live imaging with a time resolution of minutes.  Find PILATeS plasmids ...background signal when tested in more highly autofluorescent tissues like the intestine. Figure 3: ...antigenic differences between human, canine and simian isolates. J Gen Virol., 68 (Pt 11), 2769–2780. https://... happen within a few hours. In order to use the latest mScarlet tags, mScarlet3 and mScarlet-I3, Oliver...CRISPR/Cas9 workflow in M. abscessus. A) Sth1Cas9 mediates double strand break at the target site, which ...Bioluminescent reporting of mechanical forces with PILATeS By Emily P. Bentley Time to get flexible! Alex ...

...go over some of the common conjugates you may encounter and how conjugates and antibodies come together...enzyme conjugates are Horseradish Peroxidase (HRP) and Alkaline Phosphatase (AP). Various substrates for ...together. Common conjugates in the lab Fluorophores Fluorophores allow you to detect your antibodies using.... We also touched on fluorophores as antibody conjugates in an earlier post, where you can find some additional...biotin and its use in molecular biology. Other Conjugates to Know It would be overwhelming to try to cover...cover all of the possible antibody conjugates (especially if you start to consider clinical applications...potential. You will find antibody-oligonucleotide conjugates used in assays like proximity ligation, immuno-PCR...

...transfection into plates containing selection agent at different densities, then dispose of the plates that do ...to cloning rings, dilution cloning into 96-well plates, is extremely time- and resource-consumptive, since...cell can give rise to single clones, and thus many plates must be examined for single clones and then handled...can pick 48 clones from a 10 cm dish in 15- 20 minutes- a far more rapid pace than using cloning rings...12-48 individual colonies by (carefully) holding plates up to the light, where they appear as opaque dots... achieved by splitting transfected cells into 3 plates at different densities for selection). A 2% agarose...are used). This solution is capped, swirled and tested for the correct temperature by placing on the wrist...

...can design, test, and innovate faster than ever. Plus, we've already taken them for a test drive! We validated...increased sensitivity and tailored deactivation rates Addgene's own empty lentiviral backbones New recombinant...increased sensitivity and tailored deactivation rates By Mike LacyGlutamate is one of the most important...Research Campus (Aggarwal et al., 2025).In this latest work, the team designed and screened a large library...potential-evoked axonal glutamate signals. Shading denotes SEM. D) Summary of ΔF/F0, Time-to-peak, Rising ...International license. While the GENIE team tested and deposited versions with both PDGFR and NGR ...increased sensitivity and tailored deactivation rates. bioRxiv, 2025.03.20.643984. https://doi.org/10.1101...

...reinforces behavior (activation of the circuit promotes subsequent, repeated activation), this is an approximation...perceives through taking a drug. The ideal behaviors to test reinforcement are ICSS and place preference.   Historically...neuronal cell-type and temporal precision. In ICSS, a test chamber is used in which a nose-poke at a particular...reinforcement but is considerably simpler than ICSS. The test chamber is divided into two halves that are distinguished... certain technical considerations still apply. Testing stimulation First, In lieu of electrophysiology...targeted neuronal population prior to behavioral testing. One method to determine this is to examine expression...be low or highly variable without the behavioral test. Another readout may be necessary to prove inhibition...

...there, although other restriction sites (including other XbaI sites not preceded by GA or followed by ...occurring restriction modification systems that prokaryotes use to protect themselves from foreign DNA. The...digesting DNA. Why? Well, even though Dam methylation sites are not specifically associated with any restriction...systems, their sequences may overlap with restriction sites, inhibiting enzymes such as ClaI or XbaI, or, conversely...as DpnI require methylation at their recognition sites in order to efficiently cleave DNA. DpnI is often...mutation into your plasmid of interest by PCR generates mutated plasmids with no methylation (there are...commonly used in the lab do not have recognition sites that could overlap with a methylation site. The ...

..., mega, giga $ Yes —beads, columns, plates, buffers 96-well plates, 8-well kit, automation-friendly Not... midi, maxi $ Yes — beads, columns, plates, buffers 96-well plates, bead kits, automation-friendly Mentioned... maxi, mega, giga $$ Yes — columns, plates, buffers 96-well plates, automation-friendly Some Endotoxin-free... maxi, giga $ Yes — beads, columns, plates, buffers 96-well plates Not mentioned Yeast, BAC, transfection-grade... large amounts of high quality DNA. Figure 1 illustrates the three grades of DNA you may need based on...lab. Plastic consumables (including pipette tips, plates, and yes those purification columns we’ve been ...speedy protocols — anywhere from eight to sixteen minutes. (These are mostly miniprep kits! Larger kits generally...

...13]:  Germ cells [14] Hepatocytes [15] Pancreatic β-cells [16] Intestinal tissue [17] Lung epithelial...22] Cardiomyocytes [23, 24] Smooth muscle cells [25] Skeletal myogenic cells [26] Chondrocytes [27...27]         Adipocytes [28] Keratinocytes [29] Photoreceptors [30] Otic hair cells [31] Neurons [32...reverts back to a pluripotent state, which then proliferates and is redifferentiated to a different cell ... from donors. Apart from fibroblasts, human keratinocytes from hair pluck, peripheral blood cells, and...transdifferentiation. Multiple cell types such as fibroblasts, hepatocytes, and pancreatic exocrine cells have been successfully...of induced pluripotent stem cells from human keratinocytes. Nat Biotechnol, 2008. 26(11): p. 1276-84. PubMed...

...results.  Replicates Replicates are another critical control in biological experiments. Replicates can be...of biological replicates such as multiple mice in each group and C, technical replicates or repeated measurements...specificity is to test the primary antibody against wild-type and knockout samples. In this test, wild-type ... control, you will be able to confirm that the testing protocols elicited the expected response and have...statistical power of an experiment. Technical replicates are repeated measurements of the same sample ...difficult to obtain meaningful results.  Biological replicates are distinct samples that are treated identically...mice, for example, it would be better to treat and test multiple mice with the drug rather than rely on ...

...serotypes and promoters to test in your AAV system and b) steps for testing and optimizing your serotypes...Transactivator Correlates with Long-Term Doxycycline-Regulated Transgene Expression in Nonhuman Primates after ...you know that, you’re ready to start selecting, testing, and optimizing three key variables of an AAV vector...titer, and promoter. Note that several steps in testing are effected by multiple AAV variables.    ...transduce your cells. In fact, we usually recommend testing more than one.  Most AAV serotypes have broad tropism...translate to in vivo efficacy. You’ll therefore need to test potential AAV vectors in your specific experimental...harm, your experimental goals when designing and testing your AAV.  Figure 2: Comparison of AAV ...

...prefers ligation of Watson-Crick base pair substrates, it demonstrates significant activity on some mismatch-containing...experimentally-derived DNA Ligase fidelity data. Our work demonstrates that it is now possible to achieve 20+ fragment...amplicon form (shown above) are flanked by BsaI sites in an orientation that results in 5’ four base overhangs...pre-determined manner. If the original insert religates into its original vector, it will subsequently...target construct. Development of Golden Gate Assembly test systems Our research focused on three different ...phenotype upon growth on LB/Cam/X-gal/IPTG agar plates, indicating successful reconstruction of the coding...A final validation of the 5-, 12- or 24-fragment test systems was performed by setting up assembly reactions...