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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 430 results for: sequence

Showing: 101 - 120 of 430 results

  1. Comparing Cas9 to NgAgo: Can the Argonautes Best CRISPR?

    Type
    Blog Post
    Published
    June 9, 2016, 2:30 p.m.
    ...other CRISPR enzymes, NgAgo does not require a PAM sequence, so users should have much more flexibility in...et al. tested if NgAgo preferred certain guide sequences - using 5 guides/gene for 10 genes, they did not...represent a key advantage over Cas9, for which gRNA sequence can greatly affect editing efficiency. Smaller...invading genome from “recovering” its original sequence. If you’re looking to disrupt gene function via...repair after base excision would alter the target sequence and preclude future HDR, which could lower HDR...

  2. Hot Plasmids: Summer 2024

    Type
    Blog Post
    Published
    Aug. 27, 2024, 1:15 p.m.
    ...edited sequence anneal with each other, while the 5’ flaps containing the original DNA sequence anneal...yields an edited sequence with the attB/P landing site. A recombinase integrates a sequence from a donor ...technique for precisely integrating large DNA sequences into a genome (Anzalone et al., 2022). While prime...recombinase handles the installation of the donor sequence. The latest work evolves and engineers Bxb1 recombinase...strategy. First, twin prime editing installs two sequences containing attB/P recombinase landing sites on...genome at this site, resulting in the integrated sequence between two attR/L sites. Image reused from Pandey...replacement, integration and inversion of large DNA sequences with twin prime editing. Nature Biotechnology,...

  3. PiggyBac-ing Through the Genome Editing Field

    Type
    Blog Post
    Published
    May 31, 2016, 3:30 p.m.
    ...quickly transfer a DNA sequence from the transposon vector to one of many TTAA sequences distributed throughout...the genome is 1 in every 256 base-pairs of DNA sequence, making it very useful for genetic engineering...transposon in a completely seamless manner, leaving no sequences or mutations behind. Furthermore, piggyBac™ offers...cells, without leaving behind any accessory DNA sequences [2], [3]. Simply put, the piggyBac™ transposon...removed leaving behind no accessory transposon sequences.  The use of PBx is particularly important to ...donor removal, which alters the endogenous DNA sequence and has been suggested to cause cytotoxicity [...removal of the cassette later restores the target sequence. This allows researchers to avoid making unnecessary...

  4. Hot Plasmids - August 2020

    Type
    Blog Post
    Published
    Aug. 18, 2020, 1:15 p.m.
    ...evolution techniques mimic natural selection of sequences that evolve a measurable property of a protein...of tobacco etch virus protease (TEV), a highly sequence-specific protease used to cleave affinity tags...encoding FPs tagged with the plasma membrane targetin sequence derived either from p63(1-29) and Lck. Image from...plasma membrane, they tested different target sequences for improved selectivity and found that the best... of MBP, followed by the desired nanobody (NB) sequence, an AviTAG, and 6xHis tag. The MBP signal peptide...nearly any gene via specific guide RNA (gRNA) sequences. But these approaches rely on continual expression...antiviral method to degrade RNA from SARS-CoV-2 sequences and live influenza A virus. It was demonstrated...

  5. Isolating Genomic Regions of Interest with the CRISPR System

    Type
    Blog Post
    Published
    May 30, 2019, 12:44 p.m.
    ...). 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...

  6. Plasmids 101: Shuttle Vectors

    Type
    Blog Post
    Published
    May 20, 2025, 1:15 p.m.
    ...an autonomously replicating sequence (ARS), a partial centromere sequence (CEN), both, or neither, depending... an autonomously replicating sequence (ARS) a partial centromere sequence (CEN) both or neither ...depending...molecular biologist has seen before, showing how DNA sequences are translated into amino acids. And I was astonished... Yeast shuttle vectors have these replication sequences for their yeast targets as well as a bacterial...incorporated into the host cell’s genome, so no special sequence is needed to retain the vector as cells divide...

  7. Plasmids 101: Codon usage bias

    Type
    Blog Post
    Published
    Sept. 27, 2018, 1:09 p.m.
    ...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...

  8. Minigenomes - a Safe Way to Study Dangerous Viruses Like the Ebola Virus

    Type
    Blog Post
    Published
    March 17, 2016, 2:30 p.m.
    ... signal sequence (gene start) and a transcription termination/polyadenylation signal sequence (gene end...viral sequences (e.g. promoters) can be studied by changing the minigenome cis-acting sequences and monitoring...approximately 19 kb in length. It contains short promoter sequences at its 3’ and 5’ ends that are crucial cis-acting... by the EBOV-specific gene start and gene end sequences. Thus, the minigenome contains all cis-acting ... under control of a T7 RNA polymerase promoter sequence. Thus, T7 RNA polymerase also needs to be present...

  9. CRISPR 101: Cytosine Transversion Editors

    Type
    Blog Post
    Published
    March 25, 2025, 1:15 p.m.
    ... 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...

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

    Type
    Blog Post
    Published
    Sept. 9, 2025, 1:15 p.m.
    ...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...

  11. CASTing Off for New Shores in Human Genome Editing

    Type
    Blog Post
    Published
    June 10, 2025, 1:15 p.m.
    ...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...

  12. Antibodies 101: Chimeric Antibodies

    Type
    Blog Post
    Published
    April 25, 2023, 1:15 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    Nov. 25, 2013, 10:12 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    Dec. 15, 2016, 3:57 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    Jan. 13, 2025, 9:49 p.m.
    ...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., ...

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

    Type
    Blog Post
    Published
    Oct. 13, 2022, 1:45 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    June 4, 2019, 1:02 p.m.
    ...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...

  18. Of Myc and Men

    Type
    Blog Post
    Published
    Jan. 19, 2023, 2:15 p.m.
    ...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...

  19. Cpf1 Update: Comparison to Cas9 and NgAgo

    Type
    Blog Post
    Published
    July 14, 2016, 2:30 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    June 2, 2022, 2:15 p.m.
    ...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...
Showing: 101 - 120 of 430 results