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Enter a sequence to perform a BLAST-based search of Addgene plasmid sequence databases.

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We narrowed to 709 results for: BASE;

Showing: 161 - 180 of 709 results

  1. Plasmids 101: How to Verify Your Plasmid Using a Restriction Digest Analysis

    Type
    Blog Post
    ... expected sequence. Here at Addgene, we use NGS-based quality control to confirm the sequence of all the...used to confirm the rough structure of the plasmid based on the predicted sizes and organization of different...estimate how far down the gel your bands have traveled based on the dye! Always run a ladder. Ladders allow you...you get in your sample lanes. Choose your ladder based on the expected band sizes. Always run control uncut...

  2. 6 Tips for Analyzing and Troubleshooting Sanger Sequencing Results

    Type
    Blog Post
    ...spaced peaks …like these…. 3. Expect to get 500-700 bases of clean reliable DNA sequence Anything less and...uncertain terrain. 4. Never trust the first 20-30 bases of a DNA sequencing read The peaks here are usually...unfortunate side effect of messing up the reaction around base 70-75 of the read (see image below), so I would ...

  3. CRISPR 101: Multiplex Expression of gRNAs

    Type
    Blog Post
    ...modify, whether it be editing CRISPRi, CRISPRa, or base editing. Multiplexing gRNAs: the basics One common...Gibson Assembly or SLIC cloning methods. A BsaI-based E. coli multiplexing plasmid is available from the... efficiently cleaves gRNAs sandwiched between 28 base Csy4 recognition sites. If Csy4 is not expressed...inserted into a Cas9-containing destination vector based on pCAMBIA. Cas9 is plant-optimized, and plasmids...you to assemble type II-A CRISPR arrays for dCas9-based transcriptional repression. The CRISPathBrick plasmid... method that combines CRISPR and recombineering-based MAGE (Multiplex Automated Genome Engineering) technology...only 2-3 hours incubation. Kondo Lab multiplexed base editing in E. coli The Kondo lab expressed a cytidine...

  4. CRISPR 101: Ribonucleoprotein (RNP) Delivery

    Type
    Blog Post
    ... with similar efficiency as compared to plasmid-based expression of Cas9/gRNA and can be used for most...experimental systems that may not be amenable to plasmid based methods. One of the most common techniques for delivery...gRNA RNPs to plants, as an alternative to plasmid based techniques, has been an area of intense study. Two...alleviate many issues that may arise when using plasmid based systems, most notably the ability to perform CRISPR... delivery of proteins enables efficient protein-based genome editing in vitro and in vivo." Nature biotechnology...

  5. Antibodies 101: Introduction to Gating in Flow Cytometry

    Type
    Blog Post
    ...different parameters that your gating strategy will be based upon. We’ll try to keep it short though, promise...SSC: scattering To digitally extract your cells based on their size, the cytometer provides you with two...lymphocyte population (10.7% of all recorded events) based on their expected size. The strong signals close...not of interest can still be gated out later. Based on personal preference, some people like to make...staining signals. For this, you’ll need to gate based on the proportion between H and A (or W and A) within...When you’re interested in measuring a population based on a fluorescent stain, you might be wondering which...

  6. Finding nucleic acids with SHERLOCK and DETECTR

    Type
    Blog Post
    ...has been started based on DETECTR technology with the mission to “provide a CRISPR-based platform on which...SHERLOCK and DETECTR demonstrate the power of CRISPR-based diagnostics. SHERLOCK- Specific High Sensitivity... DNA or RNA with atomolar sensitivity and single base pair mismatch specificity.  SHERLOCKv2 SHERLOCK ...isothermal amplification by RPA. When Cas12a-cRNA base pairs with the dsDNA of interest, the DNase activity...Wadford DA, Chen JS, Chiu CY (2020) CRISPR–Cas12-based detection of SARS-CoV-2. Nature Biotechnology. https...

  7. Quick Guide to Near-Infrared Fluorescent Proteins

    Type
    Blog Post
    ...optogenetics, such as channelrhodopsins and tools based on light-oxygen-voltage (LOV) domain. They can also...interactions, we recommend using NIR split reporters based on miRFPs (Shcherbakova et al., 2016), since they...Filonov et al., 2013). FRET biosensors were developed based on miRFP760-miRFP720 FRET pair, including Rac1 biosensor...intensiometric calcium indicators NIR-GECOs were developed based on mIFP6. Learn more about the characteristics, ...Brightness in HeLa cells vs. iRFP713, % d Ref BphP-based FPs miRFP670 https://www.addgene.org/79987/ 642...720 98,000 6.1 97 Monomer 510 4.5 117 12 CBCR-based FPs miRFP670nano https://www.addgene.org/127443...

  8. Luminescent Imaging with Nano-lanterns

    Type
    Blog Post
    ...system. Biosensors based on Nano-lantern technology are also very robust, with an eNL-based calcium sensor...RLuc8) with Venus. This luminescent technology is based on the principle of bioluminescence resonance energy...They also developed calcium, cAMP, and ATP sensors based on Nano-lantern, showing the technique’s versatility...

  9. Michael Koeris' Journey from Grad Student to Entrepreneur: The Story of Sample 6

    Type
    Blog Post
    ...time was not right for the development of phage-based therapeutics. After a brief stint at the venture...from developing therapeutics to developing phage-based tools for detecting pathogens in food products. ...biotechstart.org Read Sample 6's Paper on Bacteriophage-based Diagnostics Additional Resources on the Addgene...

  10. Viral Vectors 101: Producing Your rAAV

    Type
    Blog Post
    ... let the virions out. We recommend using a Tris-based lysis buffer and sonication.  The obtained virions...particles that can transduce cells, which can vary based on target cells and can be altered by freeze/thaw...experimental outcome and planning.  Both ddPCR- and qPCR-based titering assays measure physical titers, meaning...post.  We generally do not recommend using ELISA-based titering assays, since those will quantify both ...Inactivation of Adeno-Associated Viral Vectors by Oxidant-Based Disinfectants. Human Gene Therapy, 32(13–14), Article...

  11. DNA Purification Without a Kit

    Type
    Blog Post
    ...gravity-based column plasmid maxiprep kit takes 1-1.5 hours to complete, while this syringe-based method...Compared to a commercial magnetic bead-based kit, this cellulose-based method was faster, cheaper, and had... Addgene follows a similar workflow as a column-based plasmid extraction kit. First, you lyse the bacteria...

  12. Bacterial Toxin-antitoxin Systems as Molecular Biology Tools

    Type
    Blog Post
    ...are many protein-based toxin-antitoxin systems. One of the most well known protein-based toxin-antitoxin...counter this, methyltransferases add methyl groups to bases at specific nucleotide sequences, preventing the...system that is regulated by antisense RNA, which base pairs to cognate mRNA to inhibit its translation...Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition." Molecular cell 11.4...

  13. Light Sheet Fluorescence Microscopy

    Type
    Blog Post
    ...for studying colloidal gold (1).  The method was based on using a thin plane (sheet) of light generated...microscopes, optical sectioning of a specimen is based on discriminating the out-of-focus reflected light... combining Ultramicroscopy with tetrahydrofuran-based tissue clearing (13,14). A few years later, Karl...Deisseroth’s lab developed CLARITY, which is a hydrogel-based method that also allows antibody penetration for...recently developed AAV (adeno-associated virus)-based fluorescent labeling methods that can be used with...

  14. CRISPR Plasmids - dCas9-FokI

    Type
    Collection
    ...Browse CRISPR Plasmids By Function Genome Editing Cut Base Edit Nick Prime Edit Transcriptional Regulation ...

  15. Plasmid Tools for Microbiome Studies

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    Blog Post
    ...microbiome studies.  Find the MAGIC plasmids here Paper-based synthetic biology approach to analyze gut microbiota...microbiome, James Collins’s lab developed a paper-based method that can be used to detect microbes and biomarkers...As mRNA expression cannot be identified with DNA-based qPCR methods, the ability to detect mRNA transcripts...Takahashi, Melissa K., et al. "A low-cost paper-based synthetic biology platform for analyzing gut microbiota...

  16. Back to Bacteria: CRISPR gRNA Multiplexing Using tRNAs

    Type
    Blog Post
    ...slightly with either a 1-7 base poly(U)tail in tRNA-gRNA constructs or a 1-4 base tail from the second tRNA... cassettes (considering the gRNA itself is ~100 bases) limit the number of gRNAs that can be packaged ...Pseudomonas aeruginosa to cleave 4 gRNAs separated by 28 base Csy4 recognition sites from a polycistronic transcript...

  17. Plasmids 101: Cre-lox

    Type
    Blog Post
    ...LoxP (locus of X(cross)-over in P1) sites are 34-base-pair long recognition sequences consisting of two...event. This event can have three general outcomes based on the location and orientation of the loxP sites...above, a genetic modification can be restricted based on experimental constraints. This has been used ...asymmetric spacer "NNNTANNN", where "N" indicates which bases may vary from the canonical sequence. Among these...

  18. Technical Design of a Western Blot

    Type
    Blog Post
    ...options come in two categories: protein-based and chemical-based. Before selecting one, check your antibody...concentration. That makes the choice easy! Protein-based blockers include dry non-fat milk or serums like... of blocker, you can also use gelatin.  Protein-based blockers are inexpensive and easily made in the ... tip! If you get a speckled image, your protein-based blocker is either degraded or not completely mixed...mixed together.   Commercially available chemical-based blockers, while much more expensive, are consistent...to another. Since antibody binding varies wildly based on proteins, and their differing amounts of available...Smaller dynamic range; no multiplexing Protein-based blocker Degrades quickly Wet transfer Increased...

  19. CRISPR 101: Engineering the Plant Genome Using CRISPR/Cas9

    Type
    Blog Post
    ...years, deaminase-mediated base editing (cytosine base editor or adenine base editor) and reverse transcriptase-mediated...in Zhu et al., 2019). Both cytosine base editors and adenine base editors have been developed for plants...Belhaj et al., 2013). Nuclease dead Cas9 (dCas9) based activators (such as dCas9-VP64) or repressors (dCas9...

  20. CRISPR Plasmids - Epigenetics

    Type
    Collection
    ...Browse CRISPR Plasmids By Function Genome Editing Cut Base Edit Nick Prime Edit Transcriptional Regulation ...
Showing: 161 - 180 of 709 results