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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 538 results for: sequence

Showing: 121 - 140 of 538 results

  1. Plasmids 101: Codon usage bias

    Type
    Blog Post
    ...cognate tRNA abundance Repetitive sequences Restriction sites Sequences prone to create secondary structures...Addgene now have full sequence data, we recommend directly analyzing gene sequences for codon optimization...think it’s easy to come up with a workable DNA sequence to encode your peptide of interest and produce... the possible codons at random and expect your sequence to express well in any organism. So what are the...1990). Controlling gene expression through gene sequence - Proteins that are encoded by codons with low...

  2. Isolating Genomic Regions of Interest with the CRISPR System

    Type
    Blog Post
    ...). Like Cas9, dCas9 can bind to a specific DNA sequence via a targeting gRNA. But dCas9 does not cleave...One method required insertion of a recognition sequence into the genomic DNA that could then be recognized...purification of a specific genomic region and RNA sequencing (Fujita et al., 2015). Using similar affinity...gRNA-dCas9 complex. When combined with next-generation sequencing, this method allows for the recovery of a vast...telomeres using a combination of enChIP and RNA sequencing." PLoS One 10.4 (2015): e0123387. PubMed PMID...Toshitsugu, Miyuki Yuno, and Hodaka Fujii. "Efficient sequence‐specific isolation of DNA fragments and chromatin...Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression." Cell 152.5...

  3. CRISPR 101: Cytosine Transversion Editors

    Type
    Blog Post
    ... efficient and precise tools for altering DNA sequences. These first base editors were both deaminases... things base editors really need from Cas9 are sequence specificity and the R-loop structure. In order...requires (1) a guide RNA, (2) a complementary DNA sequence, and (3) a protospacer-adjacent motif (PAM) on... types, although efficacy varied among target sequences. The researchers hypothesized that the CGBE edit...different deaminase and UNG enzymes had different sequence preferences, which they defined thoroughly. Plus...outcomes of their various CGBEs at different target sequences and in different cell types, available at www....target loci (between 4.0% to 29.2% of studied sequences) (Huang et al., 2024). BE4max, a CBE, generated...

  4. "Hall of Fame" AAV Enhancers from the Allen Institute for Brain Science

    Type
    Blog Post
    ...target cell populations Enhancers are non-coding sequences of DNA that regulate gene expression by interacting... recognize and bind motifs within the enhancer sequence, then interact with mediator complexes and the...1). Although all cell types share the same DNA sequence, not all enhancers are functional in every cell...to different DNA motifs, results in a given DNA sequence serving as a functional enhancer in one cell type...tools for brain visualization Putative enhancer sequences for specific cell types can be identified based... potential enhancer candidates. To use these sequences for making functional genetic tools, enhancers...enhancer ID (h, m, or q, respectively). These sequences were then cloned into an AAV backbone containing...

  5. CASTing Off for New Shores in Human Genome Editing

    Type
    Blog Post
    ...targeting power of CRISPR combined with the large sequence capacity of transposons open whole new worlds ...cofactors. The transposon proteins integrate a payload sequence into genomic DNA downstream from the Cas target... double-stranded breaks and can deliver large sequences and even entire genes. Figure 1: Mechanism... transposon proteins (Tns) to integrate large sequences into genomic DNA downstream of gRNA-specified ...site-specific recombinase to achieve insertion of long sequences. In their experiments, PASSIGE had higher efficiency...

  6. Antibodies 101: Chimeric Antibodies

    Type
    Blog Post
    ...hybridoma antibody sequences that have been cloned into plasmids. Because their sequences are known and encoded...non-antigen binding mouse sequence as possible with human antibody sequences.  Additional considerations...chimeric antibodies will inevitably retain some sequence from their parental species which can be bound...

  7. History of CRISPR Cas - A tale of survival and evolution

    Type
    Blog Post
    ...viruses. Evolving to survive Although the CRISPR sequences were initially discovered in E. coli in 1987 (... (1), the concept that these clustered repeat sequences operated as a safeguard against bacteriophages... 30bp in length and paste them into the CRISPR sequence. Separate Cas proteins then express and process...using slightly different Cas proteins and PAM sequences. A total of eight evolutionarily conserved CRISPR... generating a single point mutation in the PAM sequence, preventing the Cas nucleases from re-identifying...

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

    Type
    Blog Post
    ...codons that alter the nucleotide sequence but not the amino acid sequence of the translated protein.  These...however, one of its biggest limitations is that sequence modifications can only be made at restriction ...and deletion of selectable and non-selectable sequences, point mutations or other small base pair changes...recombination of the substrate with the target DNA sequence. This means cloning occurs in vivo, as compared...made by PCR using primers that amplify the DNA sequence of interest and flank it with 50 base pairs of...nucleotides long (20 nucleotides that anneal to the DNA sequence of interest and 50 nucleotides of homology to ...desired alteration(s) located in the center of the sequence. Since lambda red has a higher recombination frequency...

  9. Prime Editing: Adding Precision and Flexibility to CRISPR Editing

    Type
    Blog Post
    ...mismatch between the original sequence on one strand and the edited sequence on the other strand. To guide...transcriptase with a sequence optimized for human codons; additional nuclear localization sequences; and two mutations.... After nicking by Cas9, the homologous pegRNA sequence hybridizes to the target site, and the reverse...Advantages of prime editing Less constrained by PAM sequence location The prime editor extends the reach of...the PE2 enzyme. PEmax: Optimizing prime editor sequence to improve expression and activity In addition...  ✓ SV40 and c-Myc nuclear localization sequences Improve translocation to the nucleus ~ ~...prime editing with a recombinase to install large sequences (up to 10 kb) into the genome (Pandey et al., ...

  10. CRISPR 101: Which Cas9 Do I Choose for My CRISPR Experiment?

    Type
    Blog Post
    ...the gene of interest. This gives you loads of sequences to select from - in many cases several exons’ ...sgRNA), provided it meets two conditions:  1) The sequence is unique compared to the rest of the genome.  ...upstream of a Protospacer Adjacent Motif (PAM), the sequence NGG.  If these conditions apply to your experimental...feasible for your experiment, ensure your sgRNA sequence has little homology to other regions of the genome...polymerizes DNA onto the target strand based on the sequence of the pegRNA. Image from David Liu.   Activation... sgRNA vectors and design your sgRNA targeting sequence using one of the many freely available sgRNA design... cells, it is time to confirm that your target sequence has been modified!  The exact protocol may vary...

  11. CRISPR Plasmids - gRNAs

    Type
    Collection
    ...given gRNA sequence exactly match your genomic target? Variation between a given gRNA sequence and your .... aureus etc.) was this gRNA sequence designed for? A given gRNA sequence may only be compatible with ...upstream of a 5' NGG 3' PAM sequence. Which CRISPR application is this gRNA sequence compatible with? CRISPR...determine if your cell type contains the target sequence before using any of these gRNA plasmids and review...target may reduce the gRNA activity. The variety in sequence decreases the gRNA activity and increases off-...CRISPR knockout experiments use targeting sequences within exons, whereas CRISPR activation or repression...published and unpublished plasmids containing gRNA sequences designed to be used with any CRISPR nuclease and...

  12. Fluorescent Protein Travel Awards - Protein Variants, a Serotonin Sensor, and an Artificial Leaf Replica System

    Type
    Blog Post
    ...simultaneously  With increasing sequencing power, scientists are able to quickly sequence an individual’s genome... develop a method that measures the effects of sequence variants on abundance simultaneously called VAMP-seq..., for Variant Abundance by Massively Parallel sequencing. In VAMP-seq, the abundance of a protein variant...Genomic DNA from each bin are then extracted and sequenced. Chiasson is currently using VAMP-seq to study...

  13. Of Myc and Men

    Type
    Blog Post
    ...different synthetic peptides corresponding to linear sequences within the middle of the human c-Myc protein or...chicken homologs. By comparing the homologous sequences in these species, they found that the N-terminal... as a recombinant antibody. Researchers first sequenced the variable domains of Myc1-9E10 in the late ...affinity for the epitope, a phenomenon known as sequence context sensitivity (Schüchner, et al. 2020). ...Myc-tag antibodies appeared to be less sensitive to sequence context.    So, do Schüchner, et al.’s results...variable epitope recognition dependent on neighboring sequence context. Sci Signal 13. https://doi.org/10.1126...

  14. Cpf1 Update: Comparison to Cas9 and NgAgo

    Type
    Blog Post
    ...orthologs, Cpf1 efficiency varies widely with gRNA sequence. Both groups used multiple methods to examine ...single and double mismatches throughout the 23-base sequence. Double mismatches ablated Cpf1 activity, except... they were present in the 3’ end of the target sequence (bases 19-23). Cpf1 is also sensitive to single...23. Accordingly, the 3’ end of the gRNA target sequence does not have an essential function in Cpf1-mediated...4-6 base deletions at the 3’ end of the target sequence. Cpf1’s strength may lie in its low off-target...post-HDR, repair templates should remove the PAM sequence. Many research and clinical applications require...

  15. CRISPR References and Information

    Type
    Collection
    ...meningitidis Cas9, or Cas12a from your input sequence or list of sequences. Developed by the George Church Lab ...new window) Identifies gRNA target sequences from an input sequence and checks for off-target binding....window) Identifies candidate gRNA target sequences in an input sequence, which can be an accession number, ..., genomic location, pasted nucleotide sequence, or a sequence text file you upload. Currently supports...program that identifies gRNA target sequences from an input sequence, checks for off-target binding and...window) Identification of gRNA target sequences from an input sequence and checks for off-target binding....

  16. Working 9-5: an Addgene Co-op

    Type
    Blog Post
    ...discrepancies between what we sequenced in house and the submitted sequences were a concern to the plasmid... currently working on the QC/QA team as a DNA Sequencing Intern. The application process When I first...approachable.     Fig. 1: Examples of DNA sequencing QC work    In addition to my responsibilities...

  17. Hot Plasmids - May 2022

    Type
    Blog Post
    ...knock-in long sequences with reduced risks of unwanted mutations in mammalian cells. Long sequences traditionally...M-CREATE) dCas9-SSAP with reduced error rate for long sequence knock-ins Visual barcodes for live cell clonal...  dCas9-SSAP with reduced error rate for long sequence knock-ins by: Lucie Wilson Le Cong’s lab has developed...SSAP will make the editing of kilobase-scaled sequences more efficient and less risky.   Fig. 3...

  18. Enabling Precision Functional Genomics with the Target Accelerator Plasmid Collection

    Type
    Blog Post
    ...majority of information on each cancer clinical sequencing report includes rare variants that haven’t been...corresponding to cancer variants found in genome sequencing studies (as well as reference cDNA clones mapping...scientific community through Addgene. These include 634 sequence confirmed mutant cDNA clones corresponding to ... worked with many collaborators to aggregate a sequence-confirmed series of clones corresponding to known...when rare variants are discovered in clinical sequencing studies. At the Broad, my colleague Cory Johannessen...

  19. Screening for Successful Genome Editing with Digital PCR

    Type
    Blog Post
    ...such as this "CRISPR 101" post. Next-generation sequencing technologies are the gold standard but they remain...assays can be designed to detect either a donor sequence integrated through homology-directed repair (HDR...designed to perfectly complement the wild type sequence and is not capable of binding a mutated target... screening tool, it still requires target DNA sequencing to confirm the exact nature of your mutations...great description of the plethora of available sequencing options can be found here. Good luck with your...

  20. New Tool for Lineage Tracing: The ClonTracer Library

    Type
    Blog Post
    ...clonal dynamics over time using next generation sequencing (NGS). The library was developed when Carrie ...population of cells with specifc, easily read sequences that can be used to measure their clonal abundance...barcoded clone can then be monitored over time by sequencing the barcodes in the population (all barcodes ...primers). The abundance of a particular barcode sequence then corresponds to the abundance of a specific...clone; lineage tracing is performed via barcode sequencing. Using the ClonTracer library, Bhang et al. found...
Showing: 121 - 140 of 538 results