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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: 181 - 200 of 538 results

  1. Viral Vectors 101: Preparing Pooled Libraries

    Type
    Blog Post
    ...The amplified library is verified through NGS sequencing to confirm library representation. Transfection...then be used for genetic screening, followed by sequencing and further data analysis. Based on Figure 31.5.2...need to verify your library by next-generation sequencing (NGS). The representation of your amplified library...each library’s page, you can find protocols for sequencing, representative NGS results (read counts or another...whether selecting colonies and performing Sanger sequencing will suffice…and the answer is no. Due to the...

  2. PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs

    Type
    Blog Post
    ...target-complementary spacer, a scaffold sequence, and an extension sequence containing a primer binding site ... and add the upstream and downstream flanking sequences to their input string (Figure 2). This string ...Chromatin-based prime editing efficiency prediction While sequence-based prediction models from self-targeting screens... of prime editing insertion efficiencies using sequence features and DNA repair determinants. Nature Biotechnology...

  3. Bacterial Toxin-antitoxin Systems as Molecular Biology Tools

    Type
    Blog Post
    ... MazF is a ribonuclease that cleaves specific sequences in RNA resulting in a blockage of protein synthesis...endonucleases cleave DNA at or near specific nucleotide sequences. To counter this, methyltransferases add methyl...methyl groups to bases at specific nucleotide sequences, preventing the cognate restriction enzyme from cleaving...coupled. Translation from the Shine-Dalgarno (SD) sequence of mok results in translation of Mok and Hok, ... death. However, the sok antisense-RNA binds a sequence downstream of the mok SD resulting in a double...

  4. Plasmids 101: Multicistronic Vectors

    Type
    Blog Post
    ...eukaryotic cells.1,2 Since then, a variety of IRES sequences have been discovered - many from viruses, but ...leading to separation between the end of the 2A sequence and the next peptide downstream.4 The "cleavage...experimental conditions.   Peptide  Amino acid sequence* T2A: (GSG) E G R G S L L T C G D V E E N P ...of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Pelletier et al (...Multicistronic Lentiviral Vectorswith Peptide 2A Sequences. Ibrahimi et al. (Hum Gene Ther. 2009 Aug;20(8...

  5. Editor's Choice, August 2016

    Type
    Blog Post
    ...walkthrough of how you can use PCR to make small sequence changes to plasmid DNA. This an oldie but a goodie... generate C->T or G->A transitions in a target sequence in live cells. This technique uses catalytically...a deaminase to make the transitions at target sequences specified by gRNAs. Caveats, potential specificity...

  6. CasPEDIA: A Functional Classification of Cas Enzymes

    Type
    Blog Post
    ...without an adjacent PAM or protospacer-flanking sequence (PFS) in some cases. The resource displays these...these requirements in regard to their sequence (NGG, etc.) as well as their orientation relative to the...Adler et al.   You can also search by protein sequence with BLAST, using the homepage search bar. Once... other parameters, such as E-value for protein sequence searches. Additionally, the Phylogeny tool allows...

  7. All in a Twist: dsRNA

    Type
    Blog Post
    ... as a guide to complementary RNA sequence. Once a compatible sequence is found (typically RNA that the...purposes similar to that of vaccines. If you know the sequence of a virus, you could introduce some of its dsRNA...due to their abundance of R-loops and repetitive sequence. All of the R-loops described above play distinct...productive levels of R-loops and putting DNA at risk. Consequences of duplexed RNA Mammalian cells have multiple...sensing systems fail, diseases and steep cellular consequences arise. dsRNA An immune response is activated...Cellular origins of dsRNA, their recognition and consequences. Nat Rev Mol Cell Biol, 23: 286-301 (2022). ...

  9. CRISPR Plasmids - Mammalian Expression

    Type
    Collection
    ...Design your gRNA sequence to direct the dCas9-FP fusion to a specific genomic sequence - potential target...specific location based on a gRNA-defined target sequence. DSBs are preferentially repaired in the cell ...transcription of a specific gene. Design your gRNA sequence to direct the dCas9-activator to promoter or regulatory...promoter/enhancer or the beginning of the coding sequence. If the plasmid you’re using does not also express...dPspCas13b does not require a Protospacer Flanking Sequence (PFS), making it a very flexible editing system... For both enCHIP and CAPTURE, design your gRNA sequence to direct dCas9 to a specific locus, avoiding ...regions. Fluorophores may also be fused to gRNA sequences to produce fluorescence at a target region, as...

  10. Brzezinski Lab CRISPR Collection

    Type
    Collection
    ...-MeCP2 fusion for gene and non-coding enhancer sequence repression dCas9-VPR fusion for gene activation...express dCas9-VPR for activation. Usage Guide sequences can be designed using Benchling or using similar...Golden Gate cloning to insert the desired guide RNA sequence by digestion of the backbone with BbsI followed...phosphorylated oligonucleotides containing the guide target sequence: Up to two guides can be expressed from the same... Dual Guide Protocol (PDF, 990 KB) Plasmid and Sequence Derivative Sources Original pX458 backbone ( Addgene...

  11. Validated gRNA Sequences

    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...accomplish. Validated gRNA Sequence Datatable Target Gene Target Species Target Sequence Plasmid ID Application...and outcomes. Submit Validated gRNA Sequences Validated gRNA sequences can be added to this table from any... the sequences, and email the file to [email protected] with the subject heading "gRNA sequence spreadsheet...Datatable of validated gRNA sequences. Genome...

  12. Human Germline Editing Using CRISPR

    Type
    Blog Post
    ...whole exome sequencing of embryo derived-ES cells.They also conducted whole genome sequencing in selected...rates to untreated controls. Ma et al. performed sequencing of 23 potential off-target editing sites in the...off-target effects, they limited their whole genome sequencing to a small percentage of edited embryos. Since...

  13. Popular Retroviral Vectors and Their Uses in Scientific Research

    Type
    Blog Post
    ...with a 1.9 kb stuffer sequence that can be removed and replaced with an shRNA sequence of your choice. More...libraries and can be combined with high-throughput sequencing to perform multiplexed analysis of cells pre-...backbones) here. Cloning and expressing new shRNA sequences pLKO (Plasmid #10878) This plasmid has been used...

  14. RANbodies: Reporter Nanobody Fusions

    Type
    Blog Post
    ...Yamagata et al used previously published nanobody sequences that targeted the following antigens: GFP, RFP...actin-binding protein gelsolin, but any nanobody sequence could be used to make a RANbody. RANbodies are...secreted from cells due to their IgGκ signal peptide sequence, making them easy to harvest from cell culture...useful RANbody, consider leaving a link to its sequence in the comments below. References Sanes, J.R....

  15. Hot Plasmids and Viral Preps - March 2021

    Type
    Blog Post
    ...easy enough to contemplate DNA in terms of its sequencing, in vivo studies should always take DNA’s chromatin...expression pattern and an auxin inducible degron (AID) sequence attached to your protein of interest. TIR1 interacts...of auxin, this TIR1 complex binds to the degron sequence ultimately leading to the degradation of the AID-tagged...(minimal 44 amino acids auxin inducible degron sequence) tagged proteins. Degradation of your protein ...

  16. Giving gRNAs a Facelift - Synthetic and Beyond

    Type
    Blog Post
    ...phosphate backbone modifications The recognition sequence for CRISPR-Cas9 targeting is led by a ~20 bp gRNA...CRISPR RNA (crRNA). In addition to the 20 bp guide sequence, the crRNA also contains a ~20 bp repeat region...validated gRNA repository to find pre-tested gRNA sequences for your next CRISPR experiment.    Chemical...which is photocaged and unable to engage a target sequence. Upon a brief light exposure (several seconds)...

  17. Reflections and Looking Ahead

    Type
    Blog Post
    ...adding long-read sequencing capabilities to complement our next-generation sequencing, setting new standards... We’re also building a portal to easily share sequences and characterization data for over 150,000 plasmids...

  18. Tag Your Favorite Yeast Genes with Ease

    Type
    Blog Post
    ...containing the modifying sequence flanked by approximately 50 base pairs of sequence homologous to the chromosomal... typically contain both a protein modification sequence and a selectable gene product for isolation of...

  19. Plasmids 101: 5 factors to help you choose the right cloning method

    Type
    Blog Post
    ... reaction for traditional restriction cloning. Sequence and Ligation Independent Cloning (SLIC) could ...Invitrogen and based on lambda phage integration sequences, relies on site-specific recombination reactions...components and define their final order through sequence homology. Similarly, Golden Gate assembly allows...FastCloning: a highly simplified, purification-free, sequence-and ligation-independent PCR cloning method." ...

  20. Transgenic Organisms, Cas9 Gene Drives, and Appropriate Safeguards

    Type
    Blog Post
    ... the exact original sequence, it can restore the original protein-coding sequence using a recoding strategy...synthetic sequence will only spread in transgenic laboratory populations with that sequence2. Both methods...; a subsequent drive can restore the wild-type sequence (save for the residual sgRNAs and possibly cas9...unpredictable ecological effects. Because the consequences of such a mistake would necessarily extend far...
Showing: 181 - 200 of 538 results