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We narrowed to 430 results for: sequence

Showing: 41 - 60 of 430 results

  1. Troubleshooting Your Plasmid Cloning Experiment

    Type
    Blog Post
    Published
    Sept. 24, 2019, 12:55 p.m.
    ...difficulty amplifying your target sequence, or if you want to amplify sequences from a large genome organisms...clones after the screening, sequence the plasmid. Many vectors contain sequences that are complementary to... to standard sequencing primers. If not, design primers to sequence your insert. When you get your sequencing... of the enzymes you chose, and verify that the sequence of the plasmid you are working with is correct...overlap at least 24 bp with the template and if the sequence has high GC or AT content, increase the overlapping... expected size and contains the correct insert Sequence the regions that have been amplified by PCR, putting...to spot whether any discrepancies between your sequencing result and the expected result is due to a PCR...

  2. MXS Chaining

    Type
    Blog Post
    Published
    Feb. 7, 2017, 3:30 p.m.
    ...assemble large DNA sequences, no restriction enzymes needed Not optimal for joining sequences with a high degree...coding sequences), so enzyme choice is critical. May not support in-frame fusions of coding sequences Sladitschek...the systematic combination of different genetic sequences into plasmid DNA. In high throughput cloning techniques... techniques, although the specific sequences of the genetic elements may differ (e.g., a set of various...the combination of multiple fluorescent protein sequences to develop diverse fluorescent reporters is a ...polyadenylation signals, inducible gene-expression sequences, and more. By combining these components, one ...necessarily suitable for combining endogenous sequences. Table 2: High Throughput Cloning Strategies ...

  3. How to Design Your gRNA for CRISPR Genome Editing

    Type
    Blog Post
    Published
    Sept. 24, 2020, 1:15 p.m.
    ...can worry less about sequence optimality because you generally have fewer sequences to choose from). Finally...location and sequence are of approximately equal importance in design – an optimized sequence will do little...modification. Whole-genome sequencing of cells modified by CRISPR indicates that the consequences of off-target activity...your next experiment in Addgene's Validated gRNA Sequence Datatable. A more extended discussion of these...or modulation of gene expression. Location and sequence are important considerations for designing your...you target, but it is important that your gRNA sequence is designed to be highly active and reduce off...means there are so few gRNAs to choose from that sequence preferences must largely be ignored. Created...

  4. CrispyCrunch: High-throughput Design and Analysis of CRISPR+HDR Experiments

    Type
    Blog Post
    Published
    Feb. 7, 2019, 2:16 p.m.
    ...CrispyCrunch is how it mutates guide sequences to prevent re-cutting of the sequence inserted by HDR. Although this...algorithm then compares the guide sequence to every possible 23bp sequence (protospacer + PAM) in the target... often because the HDR inserted sequence splits up the guide sequence.) If neither of the above are options...codons in the guide sequence, one by one, from the PAM outwards so that the DNA sequence is altered but the...needed to design guide RNAs, donor templates and sequencing primers for quality control. At such a scale,...requires the additional step of mutating guide sequences in a way that prevents re-cutting but does not...not be enough to prevent re-binding. Lastly, the sequence inserted by HDR may inadvertently re-create a ...

  5. Optimizing Donor DNA for Enhanced CRISPR Genome Editing

    Type
    Blog Post
    Published
    March 24, 2016, 2:30 p.m.
    ...end-joining (NHEJ) pathway disrupt target gene sequences (thus inactivating genes), while breaks repaired... directed repair (HDR) pathways can modify the sequence of a gene (thus altering its function). HDR is...rational approach to improve the efficiency of sequence replacement by HDR. Understanding Cas9 biophysics...from in vitro studies) to boost the efficiency of sequence replacement in vivo. We discovered that single...from Richardson et al., 2016.   dCas9 enables sequence replacement without cutting Our in vitro results... thus wondered if such a structure could drive sequence replacement in cells. Targeting three dCas9 molecules...molecules to a precisely spaced region allowed sequence replacement rates of approximately 1%. This is...

  6. Progress Towards a PAM-Free CRISPR

    Type
    Blog Post
    Published
    March 7, 2024, 2:39 p.m.
    ...sneaky little bit of sequence that you hope is present next to the "perfect" guide sequence for your genome... a Protospacer Adjacent Motif (PAM) sequence. If the gRNA sequence is suitable, but there is no PAM next...typically selected by the ‘quality’ of the gRNA sequence, including propensity for off-targets, secondary...To add insult to injury, the most utilized PAM sequence, that of SpCas9, is NGG. Assuming all nucleotides...Cas enzyme or evolve one that uses a PAM with no sequence constraints, or at least has looser or different...such as Cpf1/Cas12a, which recognizes the PAM sequences of TTTV. While all of these enzymes certainly ...equal; just because an enzyme recognizes a PAM sequence in your site doesn’t mean it’s suitable for your...

  7. Anatomy of a Plasmid Page at Addgene

    Type
    Blog Post
    Published
    Feb. 4, 2016, 3:30 p.m.
    ... from Addgene’s sequencing reactions (‘Addgene Sequences’).  These sequences are provided in FASTA format... your research! Sequence information: Depositors may provide full or partial sequence information for ...be made available as ‘Depositor Sequences’. Additional partial sequence information is also available from...auto-generate a plasmid map based off of the plasmid sequence and feature information given by our depositors...example) and can be analyzed using Addgene’s Analyze Sequence tool. Excellent, how can I check if the plasmid... own lab.  If depositors have provided primer sequences for use, these are listed.  We also provide a ...a link to our list of common primers used for sequencing. Growth in Bacteria: This section describes how...

  8. Plasmids 101: Methylation and Restriction Enzymes

    Type
    Blog Post
    Published
    June 30, 2016, 2:30 p.m.
    ...specific DNA sequences and companion endonucleases that recognizes and cleave the same DNA sequence if not ...methyltransferases, methylate DNA at particular sequences to prevent them from being degraded by restriction...with any restriction modification systems, their sequences may overlap with restriction sites, inhibiting...therefore have methylated adenines in any GATC sequences found in the plasmid. When the PCR products are...plasmids which can later be verified by Sanger sequencing. How can I tell if my enzyme will cut? Whether...enzyme is affected by methylation, knowing the sequence of the DNA surrounding your restriction site(s...methylation), the figure below illustrates how sequence visualization software (we used Snapgene here)...

  9. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    Published
    June 4, 2024, 1:15 p.m.
    ...the DNA and test for sequence complementarity with its guide RNA. If the sequence is recognized, Cas9 ...bases, or why it’s so important to choose a target sequence with a nearby protospacer-adjacent motif (PAM)...recognize PAMs, so it associates with random DNA sequences (Sternberg et al., 2014). The nuclease lobes are...editing requires three major steps: RNA loading, DNA sequence recognition, and DNA cleavage. RNA loading Once... (left) and transparent (right). The RNA guide sequence is extended as a single unpaired strand in the...anti-repeat duplex of the guide RNA, confirming its sequence. This region of the protein varies between Cas9... RNA loading: the structure to interrogate the sequence isn’t in place yet.     Figure 4: S. pyogenes...

  10. How to Deposit Your Plasmids with Addgene

    Type
    Blog Post
    Published
    Feb. 27, 2024, 2:15 p.m.
    ...   Step 1: Sequences, Maps, and Files Please provide any full or partial plasmid sequences and any vector...The more sequence data available, the better. We highly encourage you to upload full sequence data whenever...files, etc). We can accept sequence files in any format. Figure 6: Add sequence, maps, and files. Step 2...addgene.org along with your GenBank files, plasmid sequences, and/or maps. Add plasmids to your article After...plasmid with one or more genes, protein coding sequences, or other elements inserted into it. You will ...shRNA A plasmid with one or more gRNA or shRNA sequences cloned into it. gRNAs are used for directing CRISPR...expression of mRNAs with complementarity to the shRNA sequence. Empty backbone A plasmid designed for cloning...

  11. 3 Tips to Improve HDR Efficiency for CRISPR Editing in Human Cells

    Type
    Blog Post
    Published
    Sept. 5, 2017, 1:58 p.m.
    ...introduction of specific sequence changes. To generate a specific sequence change the cell must undergo...CRISPR/Cas9 extensively for the purpose of making sequence-specific changes in human induced pluripotent ...oligodeoxynucleotide (ssODN), which contains the intended sequence changes to be incorporated into the edited genome...our excitement turned into frustration when we sequenced our cells and found how inefficiently our edits... – but avoid NAG) or guide RNA target (“seed”) sequence. The idea was that these “blocking mutations” ...mutations prevent CRISPR from re-cutting the target sequence once the desired edit has been introduced. We ...So if the locus does not allow blocking the PAM sequence (e.g. if it would lead to a missense or nonsense...

  12. Plasmids 101: Sequence and Ligation Independent Cloning (SLIC)

    Type
    Blog Post
    Published
    Sept. 26, 2024, 1:15 p.m.
    ...issue is sequence similarity. If fragments in a multicomponent assembly have 5′ or 3′ sequence homology...If cloning methods had personalities, SLIC (sequence- and ligation-independent cloning) would be a true...reliable cloning method, but it is limited by its sequence constraints. The long overhangs must not contain... often limited to specially designed plasmids. Sequence- and ligation-independent cloning: A SLIC makeover...depositor Stephen Elledge. His new method, named sequence- and ligation-independent cloning (SLIC), eliminated...and linearized vectors must have homologous DNA sequences (20–60 bp) on either end and single-stranded 5...multicomponent assembly, as fragments with overlapping sequence homology can be assembled in a unique order with...

  13. Plasmids 101: Cre-lox

    Type
    Blog Post
    Published
    Jan. 13, 2015, 3:47 p.m.
    ... long asymmetric core spacer sequence. The asymmetry in the core sequence gives the loxP site directionality...the canonical loxP sequence is ATAACTTCGTATA-GCATACAT-TATACGAAGTTAT. The loxP sequence does not occur naturally...in P1) sites are 34-base-pair long recognition sequences consisting of two 13-bp long palindromic repeats...inserting loxP sites at deliberate locations in a DNA sequence allows for very specific manipulations as discussed...or on separate pieces of DNA. Both 13bp repeat sequences on a single loxP site are recognized and bound...: If the sites face in the same direction, the sequence between the loxP sites is excised as a circular...indicates which bases may vary from the canonical sequence. Among these are loxN (GtATACcT), lox2272 (GgATACtT...

  14. CRISPR/Cas9 FAQs Answered!

    Type
    Blog Post
    Published
    March 13, 2014, 4:08 p.m.
    ...target sequence) in my HR template an issue? A8: Yes. If you have intact protospacer+PAM sequence within... to mutate the PAM 'NGG' sequence in the HR template. Since the PAM sequence is required for successful...from the Zhang group. Q2: Should I add the PAM sequence to the oligo when cloning my target spacers into...backbone? A2: There is no need to add the NGG PAM sequence. Because the 'NGG' of the PAM is used to select...Q3: When designing oligos for cloning my target sequence into a backbone that uses the human U6 promoter...to add a G nucleotide to the start of my target sequence? A3: The human U6 promoter prefers a 'G' at the...adds it when they order the oligo. If your spacer sequence starts with a 'G', you naturally have one and ...

  15. Plasmids 101: Using Transposons in the Lab

    Type
    Blog Post
    Published
    July 6, 2021, 1:28 p.m.
    ...: The transposon is the DNA sequence that moves around. This DNA sequence encodes the proteins the transposon...the protein that’s required for the transposon sequence to move from one DNA site to another. This protein...Different transposons insert at different DNA sequences or target sites. Integration of most transposable...results in the duplication of this target site sequence at the site of insertion.  Types of transposons...behind the CAG DNA footprint from its terminal sequences at the excision site after cleavage by the transposase...transposons, it does not leave behind a DNA footprint sequence after excision. piggyBac can mobilize DNA over...Beauty and piggyBac, Tol2 has a weak consensus sequence for its preferred target integration site: TNA...

  16. Four Ways to Package Transgenes That Exceed the Size Limit of Adeno-associated Virus

    Type
    Blog Post
    Published
    Sept. 1, 2020, 1:15 p.m.
    ... site donor and acceptor sequences were tested and with the optimal sequences, the group achieved ~80%... non-endogenous sequences, such as a 77bp long highly recombinogenic homology sequence derived from the...trans-plicing, splice site donor and acceptor sequences are used to reconstitute the two pieces of the...step, but optimization of the exon-splitting site sequence can enhance the rate of trans-splicing (Lai et..., the 5’ half of the transgene, a splice donor sequence and the region of homology. The AAV encoding part...contains the region of homology, a splice acceptor sequence, the 3’ half of the transgene. The full length...mechanism. The splice site donor and acceptor sequences and the homologous region of the two vectors can...

  17. Visualizing Genomic Loci with CRISPR-Sirius

    Type
    Blog Post
    Published
    April 18, 2019, 12:53 p.m.
    ...localized to specific loci based on the guide RNA sequence. A year later, they developed CRISPRainbow (Ma...set of gRNA scaffolds that contain two hairpin sequences (either MS2, PP7, or boxB) that each recruits ... CRISPRainbow labeling. Two MS2, PP7, or boxB sequences inserted into the sgRNA generates blue, green,... labeling. A combination of MS2, PP7, or boxB sequences in the same sgRNA will generate additional colors...living cells. Broccoli aptamers are nucleic acid sequences that bind to the small molecule, DFHBI-1T to induce...of the success of the MS2 and PP7 RNA hairpin sequences in CRISPRainbow, they knew they could be good ...created another sgRNA containing the PP7 hairpin sequence (sgRNA-Sirius-8XPP7) to recruit GFP to the loci...

  18. Harnessing TnpB for Genome Editing: A Compact and Versatile Tool for Your Research

    Type
    Blog Post
    Published
    July 29, 2025, 1:15 p.m.
    ... Guide Sequence Identify a TAM site (5′-TTGAT-3′) in your target gene. Choose a 20-nt sequence immediately...guide insertion by Sanger sequencing using either 92F or M13R as the sequencing primer. Step 7: Transformation...) near the target DNA, TnpBs also need a short sequence motif called a TAM (transposon-associated motif...located just downstream (3′ end) of the target sequence, while for Cas12a and TnpB, the motif is found...Deinococcus radiodurans (Dra2TnpB) recognizes the TAM sequence 5′-TTGAT-3′, while TnpB from Deinococcus geothermalis...right-end element, and a 20-nucleotide (nt) guide sequence that is complementary to the DNA target. The 20... 20-nt guide region binds to the DNA sequence immediately downstream of the TAM. This RNA-DNA hybrid formation...

  19. CRISPR 101: Making a Knock-In Cell Line

    Type
    Blog Post
    Published
    Dec. 22, 2022, 2:15 p.m.
    ...homologous sequence to the right and/or left of the knock-in site. The length of that sequence and the makeup...Knock-in mutations typically require an exact DNA sequence to be incorporated at a precise genomic location...introduce the edit. Finally, you must stipulate what sequence to introduce, which is done through the design...to the targeted locus on either side of the new sequence. This homology will guide the cell to use the ...which will result in the incorporation of your sequence, a.k.a a knock-in! So how does the donor get used... can efficiently knock-in a few hundred bps of sequence. However, if you have a larger knock-in (200 bp...al., Nat Chem Biol). Mutate the PAM or sgRNA sequences Cas9 likely goes through multiple rounds of cleavage...

  20. Golden Gate Assembly Upgrades: More Fragments, Faster Assembly, and Higher Fidelity

    Type
    Blog Post
    Published
    Oct. 11, 2018, 12:30 p.m.
    ...achieved by the sequencing of plasmids isolated from blue or white colonies. Sequencing of blue colonies...showed the expected complete sequence for the lacI/lacZ genes (1), while sequencing of white colonies showed...overhang sequences under standard reaction conditions. This data set allows quantitation of sequence-dependent...restriction enzymes and careful choice of junction sequences guided by experimentally-derived DNA Ligase fidelity...indicating successful reconstruction of the coding sequence for beta-galactosidase in the lacI/lacZ cassette... Gate assembly through application of ligation sequence-dependent fidelity and bias profiling." bioRxiv... Potapov, Vladimir, et al. "A single-molecule sequencing assay for the comprehensive profiling of T4 DNA...
Showing: 41 - 60 of 430 results