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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: 101 - 120 of 538 results

  1. Plasmids 101: Golden Gate Cloning

    Type
    Blog Post
    ... are theoretically 256 distinct flanking sequences, sequences that differ by only one base may result ... that they cleave outside of their recognition sequence, creating four base flanking overhangs. Since ...these overhangs are not part of the recognition sequence, they can be customized to direct assembly of ...specify assembly order, so fragments with 5’ or 3’ sequence homology cannot be assembled using this method...appropriate oligonucleotides specifying a gRNA target sequence into a Cas9-containing plasmid such as pX330. ...Golden Gate cloning Golden Gate cloning is not 100% sequence-independent: to avoid undesired digestion, the...

  2. High Complexity Golden Gate Assembly with NEB’s DAD

    Type
    Blog Post
    ...depend more on the individual sequence(s) than on how well that sequence fits into the five rules. By ...three or four base-pair sequences, and exclude or include specific overhang sequences, allowing it to be used...specific to your DNA sequence, SplitSet is the tool for you. Once you input a sequence, SplitSet finds optimal...you’d like the tool to use to identify fusion sequences for either a circular or linear assembly. If you...even more specificity, you can exclude specific sequences or set a narrow search window for a site—or sites—that...

  3. CRISPR Antimicrobials

    Type
    Blog Post
    ...custom CRISPR antimicrobials can target specific sequences in a single virulent bacterial species, or even...2014, Citorik et al. and Bikard et al. developed sequence-specific, antimicrobial, plasmid-based, CRISPR... cases, they used 1-2 CRISPR crRNAs targeting sequences found only in certain bacteria (Figure 1). Citorik...targeting either genomic (blue) or plasmid-based sequences (red). Treating a mixed population, represented...targets bacteria with the given genomic or plasmid sequence from a mixed population without affecting the ...the other bacteria. Targeting a genomic sequence results in cell death. Plasmid targeting may result in ...Citorik, Robert J., Mimee, Mark, and Timothy K. Lu. “Sequence-specific antimicrobials using efficiently-delivered...

  4. Advancing Biology with Zebrafish: Genetic Tools for Developmental Studies and More

    Type
    Blog Post
    ...biological process. High quality genome sequence A high-quality sequence assembly of the zebrafish genome was... will help clarify their roles in humans. The sequenced genome also permits “whole-genome/transcriptome...as the field of genetics progresses and genome sequences become available, new hypotheses about specific...organs during embryo development. Single cell sequencing-based lineage tracing Recently, gene expression... embryo has been mapped using single cell RNA sequencing approaches (Harland, 2018). Several different...such as CRISPR/Cas9, Tol2, and the high-quality sequenced zebrafish genome. One study profiled 38,731 cells...produced, rather than novel, abnormal cell types. Sequencing-based lineage tracing can help elucidate the ...

  5. Cpf1: A New Tool for CRISPR Genome Editing

    Type
    Blog Post
    ...plasmid depletion assay to discover FnCpf1’s PAM sequence requirements. Cpf1’s preferred PAM is 5’-TTN, ...in both genomic location and GC-content. After sequencing and searching for cellular RNAs important for...post-HDR, repair templates should remove the PAM sequence. Comparing Cpf1 and Cas9 on-target and off-target...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...

  6. 22 Hot Plasmid Technologies from 2014

    Type
    Blog Post
    ...Timer protein fused to the mitochondrial targeting sequence of cytochrome c oxidase subunit VIII, so that ...exchange and re-use of existing elements. DNA sequences for a desired component are cloned into Golden...channelrhodopsins – Chronos & Chrimson Through de novo sequencing of 127 algal transcriptomes, as well as further...for CRISPR gRNA validation Selecting a gRNA sequence that effectively targets your gene/region of interest...their gRNAs. The first step is to clone the target sequence in between two fragments of EGFP in pCAG-EGxxFP...The EGFP fragments contain 482bp of overlapping sequence that direct Homologous Recombination (HR) or Single... Cas9. If the gRNA effectively cuts the target sequence, the plasmid undergoes HR or SSA to reconstitute...

  7. Plasmid-based Recombinant Monoclonal Antibodies: What They Are and Why You Should Be Excited About Them

    Type
    Blog Post
    ...expressed from a plasmid or from an integrated sequence in a stable cell line. The genes encode the heavy...recombinant antibodies, you first need to know the sequence. Scientists are getting better and better at identifying...mass spectrometry to determine the amino acid sequences of the antibodies and then synthesize the genes...be converted into recombinant form through DNA sequencing of the line and subsequent cloning of the antibody...Hybridomas are much tougher to ship, often lack sequence data, and may genetically drift over time. Antibodies...research tools, it is shocking that the plasmids and sequences for antibodies are not shared. For instance, through...Complete De Novo Assembly of Monoclonal Antibody Sequences. Sci Rep 6: . https://doi.org/10.1038/srep31730...

  8. Plasmids 101: Terminators and PolyA signals

    Type
    Blog Post
    ...polyadenylation? The role of the terminator, a sequence-based element, is to define the end of a transcriptional... A predicted conserved secondary structure and sequence conserved Rho-independent termination annotation...eukaryotic mechanism which requires a consensus sequence for the addition of a poly(A) tail, the addition...Polymerase III, for example, relies on a specific sequence and RNA secondary structure to induce transcript...terminators (SV40, hGH, BGH, and rbGlob) include the sequence motif AAUAAA which promotes both polyadenylation...transcription due to the presence of additional helper sequences (2-3). As alluded to above, termination and polyadenylation...PMC360476. Gil A, Proudfoot NJ. Position-dependent sequence elements downstream of AAUAAA are required for...

  9. Mapping the 4D nucleome with CRISPR/Cas9

    Type
    Blog Post
    ...previously been adapted to fluorescently label a sequence matching its gRNA, facilitating the live study...orthologs is key: due to differences in the PAM sequences required by each ortholog, a gRNA designed for...dCas9 variants using gRNAs specific for telomeric sequences and showed that different fluorescently labeled... are efficiently directed to the proper target sequence. They were also able to label two different pairs...pairs of chromosomes using gRNAs specific to sequences on chromosomes 9 and 13. They next turned their...

  10. Antibodies 101: Antibody Engineering and Directed Evolution

    Type
    Blog Post
    ...instead of forcing sequence diversity using error-prone polymerases, you force sequence diversity using ...primers to get full sequences. In the end, you’ll have a full-length antibody sequence, but with random ...Antibody engineering is the modification of antibody sequences and structures to affect their function. Usually...random errors can give you new and unexpected sequences. Degenerate primers Using degenerate primers is...variety of degenerate codons (different codon sequences that code for the same amino acid) for various... is usually employed to mutate whole antibody sequences, degenerate primers can be designed to selectively...option. In gene shuffling, you chop up your target sequences into fragments, typically using a DNase. Then ...

  11. PITChing MMEJ as an Alternative Route for Gene Editing

    Type
    Blog Post
    ...double-stranded break. HDR copies the sequence from a repair template with flanking sequence homology for error-free...microhomology and the retention of a single microhomology sequence. For more mechanistic details on HDR and NHEJ,...double-stranded break yield precise deletion of the sequence between the microhomologies.MMEJ has certain advantages...to HDR, but it is completed using much shorter sequence homologies. Abbreviated protocol for PITCh...puromycin resistant cells Step 5: PCR amplify and sequence the locus to verify correct GFP-puro insertion...the GFP-Puro cassette into the FBL locus. Upon sequencing of puromycin resistant clones, they found that...

  12. Fluorescent Tagging of Endogenous Genes with SapTrap

    Type
    Blog Post
    ...a genomic site specified by a guide RNA (gRNA) sequence. Users can design gRNAs to induce the break at...directed repair pathway, a new user-defined DNA sequence (like GFP) can be inserted at the DSB. CRISPR ...oligos or synthetic DNA for the desired gRNA target sequence, as well as the 5’ and 3’ homology arm repair ...sites- the first site accepts the sgRNA target sequence for U6 promoter expression and the second site...event, and a variety of connector modules (linker sequences between the tag and homology arms). Digestion ...will insert the desired genetic tag and marker sequence into the targeted loci. The selectable marker ... the culture medium. Any number of regulatory sequences, including protein enhancers and repressors, can...

  13. Choosing a CRISPR Nuclease: Site Accessibility, Specificity, and Sensitivity

    Type
    Blog Post
    ...which genomic sequences can be targeted by the Cas9. This is determined by the PAM sequence recognized by...Cas9, spCas9 from Streptococcus pyogenes, this sequence is 3’-NGG. But Cas9s found in other species can...can recognize a variety of different PAM sequences. Researchers have also used experimental evolution ...previously unavailable. Figure 1: The PAM sequence that the Cas nuclease recognizes determines site... displayed the ability to target multiple PAM sequences (NG, GAA, and GT), greatly increasing the number...

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

    Type
    Blog Post
    ...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...

  15. Hot Plasmids: Summer 2024

    Type
    Blog Post
    ...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,...

  16. PiggyBac-ing Through the Genome Editing Field

    Type
    Blog Post
    ...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...

  18. Plasmids 101: Shuttle Vectors

    Type
    Blog Post
    ...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...

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

    Type
    Blog Post
    ... 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...

  20. Hot Plasmids - August 2020

    Type
    Blog Post
    ...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...
Showing: 101 - 120 of 538 results