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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: 81 - 100 of 430 results

  1. Plasmid Tools for Microbiome Studies

    Type
    Blog Post
    Published
    June 27, 2019, 12:25 p.m.
    ...questions, biologists often use next-generation sequencing. Sequencing the 16S rRNA reveals the identity of the...the organisms present while sequencing of all transcripts gives clues into what the microbes are doing...doing. But aside from sequencing, scientists can also study the microbiome by using engineered genetic tools...While the ability to monitor the microbiome with sequencing is vast, the ability to genetically alter microbiome...biomarkers In clinical and diagnostic labs, deep sequencing and qPCR methods are too costly and time intensive... be designed to bind and detect nearly any RNA sequence. Downstream of the hairpin is a ribosome binding...

  2. Site Directed Mutagenesis by PCR

    Type
    Blog Post
    Published
    Aug. 2, 2016, 2:30 p.m.
    ...mutagenesis can be used to mutate the PAM sequence (an NGG sequence critical for Cas9 cleavage), thereby rendering...modification. Finally, the positive clones are sequenced to confirm the desired modification and the absense...Design As a rule of thumb, 11 bp of complementary sequence on either side of the desired mutation (usually... should be free of palindromic and repetitive sequences, but if present, a minor extension can usually...PCR primers can cause duplication of the primer sequence in the resulting plasmid. An additional restriction...duplications), final validation is performed by sequencing functional regions of the plasmid including the... kb (or are GC-rich and therefore difficult to sequence), it may be easier to subsequently clone a smaller...

  3. Tips for CRISPR Gene Editing in Mice

    Type
    Blog Post
    Published
    June 28, 2016, 10:59 a.m.
    ...Should you cut it at the beginning of the coding sequence to delete the entire gene? Perhaps you are more...simple and easy. Several companies supply gRNA sequences, such as GenScript, ThermoFisher Scientific and...expression cassette reconstitution. When the target sequence was digested by sgRNA guided Cas9 endonuclease...bp genomic fragment containing the sgRNA target sequence can be placed in multi-cloning site (MCS) between...co-transfected with pX330 plasmids containing sgRNA sequences into HEK293T cells. The fluorescence intensity...develop primers to the approximately 500 base pair sequence surrounding your gRNA. Once amplified, you can...you know if there are any major deletions, and sequencing of the PCR products will give specific details...

  4. RNA Interference in Plant Biology: New Tools for an Old Favorite

    Type
    Blog Post
    Published
    Oct. 27, 2020, 1:15 p.m.
    ...a consensus sequence is used (~90% identity between targets) or multiple target sequences are concatenated...and/or fusing your gene target sequence to a fluorescent reporter sequence (discussed below). Examples of... directly fused any gene targeting sequence to a targeting sequence for the adenine phosphoribosyltransferase...downregulation, or “silencing,” of any gene that contains sequence complementary to the dsRNA (Wilson and Doudna,...chromatin modifications of complementary gene sequences (Figure 1). As a result, gene silencing can be...fused to the DNA backbone that contains a target sequence against the fluorescent reporter in an inverted...single hairpin dsRNA is produced that contains sequence against your gene(s) of interest and the reporter...

  5. Plasmids 101: TOPO Cloning

    Type
    Blog Post
    Published
    Oct. 27, 2016, 2:30 p.m.
    ...recognizes the DNA sequence 5´-(C/T)CCTT-3' and digests double stranded DNA at this sequence. The energy from...blue colonies that do not need to be picked and sequenced for potential positive clones. Once you introduce...restriction sites on the ends) and amplify your sequence of interest with Taq polymerase using your favorite...of your insert by PCR, restriction digest, or sequencing. Pro tips Do not add 5’ phosphates to your PCR...virus DNA topoisomerase I in Escherichia coli is sequence specific."  Proc Natl Acad Sci U S A.  1991 Nov...

  6. Visualizing Translation at the Single Molecule Level

    Type
    Blog Post
    Published
    Aug. 1, 2017, 1:15 p.m.
    ...also contains a CAAX sequence to bind the mRNA to the plasma membrane; this sequence prevents diffusion ...requires inserting multiple hairpin sequences into the coding sequence and 3’ UTR. Before beginning experiments...they are bound. These regions are subsequently sequenced and aligned to the genome to determine genome-...dynamics at the single molecule level. The coding sequence of Yan et al.’s reporter contains 24 copies of...

  7. CRISPR 101: Cas9 vs. The Other Cas(s)

    Type
    Blog Post
    Published
    Dec. 8, 2022, 2:15 p.m.
    ...form a clean DNA break, Cas3 locates its target sequence and initiates single stranded DNA degradation....increase cutting efficiency and diversify PAM sequences of Cas12a to further optimize it for therapeutic...sensitive to even a single mismatch in the target sequence Similar to Cas12, it is also significantly smaller...non-complementary ssDNA when engaged by its target sequence. Why would you want to give it a go? The high ...indiscriminately cleaves ssRNA when engaged at its RNA target sequence. The RNA-targeting ability of Cas13 makes it perfect... facts – PAM requirement: protospacer flanking sequence – A, U, or C. Best for: targeting single stranded... facts – PAM requirement: protospacer flanking sequence – none. Best for: targeting single stranded RNA...

  8. Plasmids 101: Golden Gate Cloning

    Type
    Blog Post
    Published
    Aug. 27, 2015, 2:30 p.m.
    ... 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...

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

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

  10. CRISPR Antimicrobials

    Type
    Blog Post
    Published
    May 3, 2016, 2:30 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    Aug. 13, 2019, 12:58 p.m.
    ...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 ...

  12. Cpf1: A New Tool for CRISPR Genome Editing

    Type
    Blog Post
    Published
    Oct. 14, 2015, 2:30 p.m.
    ...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...

  13. 22 Hot Plasmid Technologies from 2014

    Type
    Blog Post
    Published
    Jan. 6, 2015, 5:21 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    May 4, 2021, 1:15 p.m.
    ...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...

  15. Plasmids 101: Terminators and PolyA signals

    Type
    Blog Post
    Published
    March 31, 2016, 2:30 p.m.
    ...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...

  16. Mapping the 4D nucleome with CRISPR/Cas9

    Type
    Blog Post
    Published
    Aug. 11, 2015, 2:30 p.m.
    ...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...

  17. Antibodies 101: Antibody Engineering and Directed Evolution

    Type
    Blog Post
    Published
    Aug. 5, 2025, 1:15 p.m.
    ...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 ...

  18. PITChing MMEJ as an Alternative Route for Gene Editing

    Type
    Blog Post
    Published
    Feb. 23, 2016, 3:30 p.m.
    ...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...

  19. Fluorescent Tagging of Endogenous Genes with SapTrap

    Type
    Blog Post
    Published
    Oct. 12, 2017, 2:26 p.m.
    ...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...

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

    Type
    Blog Post
    Published
    Nov. 5, 2019, 1:28 p.m.
    ...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...
Showing: 81 - 100 of 430 results