Skip to main content
Addgene

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

In Category

We narrowed to 275 results for: ATC

Showing: 21 - 40 of 275 results

  1. QC Sequencing Technologies at Addgene

    Type
    Blog Post
    Published
    July 15, 2025, 1:15 p.m.
    ...there is a 100% nucleotide match to base identity and plasmid length. Any mismatch or indel flags the sequence...pipeline are now run through an auto-align process to match sequence results to full-length predicted sequences...differences. This script compares the sequence for a 100% match to base identity and length, but disregards the ...discrepancies. Any sequences that are a perfect match from this script can then continue in the auto-align...bioinformatic analysis. At Addgene, we use a mix-and-match approach for sequencing methods and choose the best...

  2. CRISPR 101: Off-Target Effects

    Type
    Blog Post
    Published
    Feb. 8, 2024, 2:15 p.m.
    ...“Off-target effects” a vague catch-all term for unintended consequences in an experiment. For CRISPR ...to select a Cas enzyme with low tolerance for mismatches within the gRNA sequence. Graphic courtesy... or mutated to be more specific for exact gRNA matches (Rabinowitz and Offen). Of note, most of these ...these optimized Cas enzymes prevent cutting at mismatched guide sites, but not necessarily binding to these... activity at those sites, especially when DNA mismatches are involved. Two other approaches have been ...non-targeting’ gRNA, a gRNA which doesn’t perfectly match any site in the genome. While this may effectively...

  3. Identifying Sequence Elements with SnapGene's Feature Database

    Type
    Blog Post
    Published
    Dec. 21, 2017, 2:06 p.m.
    ...devising rules for identifying a feature even when the match is imperfect. SnapGene's feature database The source...detection algorithm that tolerates occasional mismatches or indels. Empirical tests indicated that a reasonable...to allow searches for a perfect protein sequence match even when the DNA sequence has changed. Identifying...database. Another limitation is that by tolerating mismatches, our algorithm could annotate a feature inaccurately... strain to newly sequenced strains through our mismatch tolerant detection algorithm and thereby speed...

  4. SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas

    Type
    Blog Post
    Published
    May 5, 2020, 1:15 p.m.
    ...to the presence of mismatches within the DNA and the positions of these mismatches. To detect SARS-CoV...catalytically active in the presence of two or more mismatches in the cRNA:target duplex and will not give a...dCas9 complexes containing sgRNA that have no mismatches bind to the immobilised target sequences. Upon...making it an affinity-based method. Due to the mismatch sensitivity of FnCas9, this is also a good way...

  5. Tips for a 1st Time CRISPR User (by a 1st Time CRISPR User)

    Type
    Blog Post
    Published
    March 7, 2017, 3:30 p.m.
    ...cleaves double stranded DNA (dsDNA) at basepair mismatches. To use this tool to detect a BRAF gene edit,... control cells, which should contain basepair mismatches at the site of the edit. Using Surveyor nuclease...nuclease followed by gel electrophoresis, these mismatches are indicated by the presence of DNA cleavage ...isn’t in the middle of the PCR product. If the mismatch is in the middle of the PCR product, you would...cells. Surveyor nuclease was used to digest (+) mismatches in DNA duplexes (513 bp), as indicated by the...

  6. Lambda Red: A Homologous Recombination-based Technique for Genetic Engineering

    Type
    Blog Post
    Published
    Dec. 15, 2016, 3:57 p.m.
    ...methyl -directed mismatch repair (MMR) system. MMR’s job is to correct DNA mismatches that occur during...activation.  The first way is to introduce a C/C mismatch at or within 6 base pairs of the edit site. This...when activation of MMR is avoided Introduce C/C mismatches or silent changes in wobble codons to avoid MMR...Enhanced levels of λ Red-mediated recombinants in mismatch repair mutants. Proceedings of the National Academy...

  7. SpyLigase Irreversibly Locks Peptides Together for Efficient Cell Capture

    Type
    Blog Post
    Published
    Aug. 13, 2014, 3:49 p.m.
    ..., just 13 amino acids, but SpyCatcher is a protein. You can fuse SpyCatcher onto things, but even better...particular. They recently introduced the SpyTag/SpyCatcher system, based on a protein isolated from Streptococcus...It came from our work in developing the SpyTag/SpyCatcher system, to be able to grab on to proteins irreversibly...

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

    Type
    Blog Post
    Published
    Aug. 28, 2014, 3:34 p.m.
    ...construct, and verify that the plasmid you received matches the expected sequence. Here at Addgene, we use ... 3) produces bands at 6kb and 1.2kb (red box), matching the backbone and insert, respectively. The results...results on the gel correspond to the predicted sizes. Watch this video for a quick overview of how to analyze...the optimal working conditions for each enzyme. Watch out for methylation issues. Enzymes like XbaI and...

  9. Plasmids 101: Methylation and Restriction Enzymes

    Type
    Blog Post
    Published
    June 30, 2016, 2:30 p.m.
    ...role in regulating genome replication, repairing mismatched basepairs or small indels that occur during DNA... methylase adds a methyl group to the adenine of GATC stretches of DNA Dcm methylase adds a methyl group...and will therefore have methylated adenines in any GATC sequences found in the plasmid. When the PCR products...mutation (as these would also be deficient in mis-match repair functions of Dam), so these strains should...

  10. Career Coaching for Scientists: Why and Where Do I Find One?

    Type
    Blog Post
    Published
    Jan. 29, 2015, 1:25 p.m.
    ...out there, so finding a good one that is a style match for your needs can take some research.  It helps...coaches and I can't tell you which one will be a match for your needs, but here are a number I have come...group is that sometimes this offers the option of matching with the best person in the group for your needs... PhD is in History, I think she would be a good match as a coach for many scientists.  Sometimes it can...

  11. A Guide to Designing a Scientific Poster: Content, Layout, and More

    Type
    Blog Post
    Published
    Oct. 22, 2019, 12:20 p.m.
    ...scientific poster apart? First, a good poster should catch the audience’s eye and draw people in. That can ...may choose to display it as rows. It can be more catchy because it is generally less common and will stand...advantage of being different and potentially more catchy, but it can be trickier to make figures fit nicely...relevant to the work you are presenting. The latter is catchy, but beware. A distracting background or clashing...

  12. Synthetic promoter AAVs for cell-type specific expression in retinal cells

    Type
    Blog Post
    Published
    March 12, 2020, 1:15 p.m.
    ..., the Roska lab built synthetic promoters from scratch and tested to see if they drove cell type specific...channelrhodopsin, fused to a fluorescent GFP marker (CatCH-GFP). The lab deposited AAV plasmids containing ...Synthetic promoters did, however, tend to loosely match the specificity of their source genes, i.e. if a...drive expression of a Cre-dependent fluorescent CatCH-GFP reporter. Expression of GFP will only result...

  13. Design Tips for Prime Editing

    Type
    Blog Post
    Published
    Jan. 23, 2025, 2:15 p.m.
    ...bases. DNA mismatch repair (MMR) is less efficient at identifying these “bubbles” of mismatched bases, enhancing...efficiently targets single-base mismatches (left), but “bubbles” of 3 or more mismatched bases can often evade ...

  14. Plasmids 101: In-house NGS Plasmid Quality Control Now at Addgene

    Type
    Blog Post
    Published
    April 6, 2021, 12:30 p.m.
    ...necessarily expecting a perfect match - we will often find a few mismatches in the origin of replication ...sequencing, we feel confident that these few minor mismatches usually don’t affect the function of the plasmid.... We also confirm that the species of the gene matches the data associated with the plasmid.     Confirming...

  15. Tips for a 1st time AAV user (by a Rookie AAV user)

    Type
    Blog Post
    Published
    Oct. 23, 2018, 11:49 a.m.
    ...interest. Every batch of AAV requires its own MOI optimization to account for batch-to-batch variability....Ultracentrifugation Protocol for more details. Pro tips Watch this AAV purification video! It didn’t exist when...

  16. Tips for Using BLAST to Verify Plasmids

    Type
    Blog Post
    Published
    May 29, 2014, 1:29 p.m.
    ...any discrepancies in Sanger sequences, such as mismatches, deletions, or insertions. We use blastp or blastx... the species that your sequencing result should match, enter the common or scientific name into the Organism...smaller word size and lower scoring penalties for mismatches and gaps in the alignment. If you are curious...Sanger sequencing result and noted any potential mismatches or gaps in the nucleotide sequence, you can run...

  17. 10 Steps to a Perfect Science Talk

    Type
    Blog Post
    Published
    Aug. 23, 2016, 2:30 p.m.
    ...NatureJobs: Interviews: The All-Important Job Talk. 1. Watch other people give great talks We are not talking...are those in the Young Scientist Seminar Series. Watch how these speakers talk without looking at their...entertaining science lab, career, and policy content. Watch Joanne give her "Not" Networking 101 Talk 2. Tailor...of saying “so” and “um” a lot. I hate it when I watch myself speak, but others tell me that I keep the...

  18. Site Directed Mutagenesis by PCR

    Type
    Blog Post
    Published
    Aug. 2, 2016, 2:30 p.m.
    ...either side of the desired mutation (usually 1-3 mismatched bases) is sufficient for your primers to successfully...protocol. Be sure to adjust the extension time to match the size of your template. Amplification of GC-rich...only DNA that is methylated at the adenosine of the GATC recognition site. Transformation: After the PCR ...transform your PCR products into will efficiently patch up the DNA. The resistance marker from the parental...

  19. Plasmids 101: Gibson Assembly and Other Long-Homology Based Cloning Methods

    Type
    Blog Post
    Published
    March 1, 2016, 3:30 p.m.
    ...fragments. As a fun way to start, I highly recommend watching this entertaining video created by our friends...want next to it, so this doesn’t allow for mix and match of many different fragments. One way around this...homology regions, which allows for the mixing and matching of parts. Gibson assembly meets CRISPR Gibson... Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene ...

  20. Save Time and Money by Making Your Own Competent Cells

    Type
    Blog Post
    Published
    Jan. 28, 2014, 3:10 p.m.
    ...least a year when stored at -80oC.   For each new batch of competent cells, don’t forget to do a negative...the number of colonies obtained using your fresh batch of competent cells with those obtained using commercially...commercially available cells or previous batches of homemade competent cells to ensure good efficiency....
Showing: 21 - 40 of 275 results