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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: 81 - 100 of 538 results

  1. To Codon Optimize or Not: That is the Question

    Type
    Blog Post
    ...anticodon,  a three nucleotide sequence complementary to the mRNA sequence. The 3’ end of  the tRNA binds...the amino acid that corresponds to the anticodon sequence. That means there are 61 possible tRNAs. Cells...and thus protein expression without altering the sequence of the protein. As DNA synthesis has become quite...scientists to re-synthesize DNA with the most optimized sequence. Unfortunately, it is not always easy to identify... certain systems, synonymous changes to a gene sequence can cause unexpected detrimental results to the...could remove information encoded in the primary sequence of a particular gene which could affect translation...available online to both determine and synthesize DNA sequences for optimal expression in your system of choice...

  2. Multiplexed Capture of Promoter-enhancer 3D Chromatin Structures Using CRISPR

    Type
    Blog Post
    ...They found that DNA sequences targeted by the gRNAs were the top enriched sequences in the experiment and...supporting roles. Enhancers are cis regulatory DNA sequences that, when bound by transcription factors, can...looping with the photo “developed” by analyzing DNA sequencing data. While “pictures” generated with current...chimeric DNA fragments by PCR or next-generation sequencing. Figure 1: Overview of the key steps of... DNA fragments can be detected by PCR or deep sequencing. A drawback of the original CAPTURE method...gRNA expression. Additionally, CAPTURE 3C-based sequencing requires a large number of cells (~5x107). Together...BioTAP-tag is a 69 aa long biotinylation targeting sequence that is recognized by biotin ligases normally ...

  3. Kiran Musunuru on the Newest TALEN Genome-Editing System

    Type
    Blog Post
    ...desired sequences. TALENs are much more reliable. If you design them for a particular sequence, there ...can be programmed to bind to essentially any DNA sequence desired. This technology allows you to create ...do you use this kit to target a particular DNA sequence? Musunuru: The kit includes 832 plasmids containing...DNA-binding domain to recognize any desired 15 base pair sequence in the genome in rapid fashion. The two remaining...there is a much better chance they will bind that sequence. That’s the revolutionary aspect: TALENs take a...: The power here is that you could potentially sequence a large number of individuals and find several...

  4. CRISPR-Cas14: a family of small DNA-targeting enzymes enabling high-fidelity SNP genotyping

    Type
    Blog Post
    ...cleave a targeted sequence of ssDNA. Unlike Cas9, Cas14 does not require a PAM sequence. In addition to ... types of nucleic acids and required a certain sequence specificity in the middle of the gRNA to be activated...mutations. By providing a gRNA specific of a viral sequences, for instance, the enzymes are activated and can...Fluorescent signal indicates the presence of this viral sequence in the assay. By adding Cas14 to the mix, you ...

  5. Making CRISPR Plasmids Using Fragmid

    Type
    Blog Post
    ... and then plasmid sequencing if you can. To quote Doench, “Whole plasmid sequencing is just part of doing...enzyme that cleaves outside of its recognition sequence. This means that each component can be designed...? The Doench lab tested the Fragmid system by sequencing 60 individual assemblies created over five months...82 of the correctly banded clones for plasmid sequencing and found 98% of the plasmids were perfectly ...confirm that at least one plasmid was the correct sequence for every individual assembly. What destination...051 (for stable fly cell lines; attL and attR sequences for genome integration by phiC31) Drosophilia...pRDB_053 (for transgenic flies; gypsy insulator sequences; white + selectable marker; attB site for genome...

  6. Genome-wide Screening Using CRISPR

    Type
    Blog Post
    ...next-generation sequencing (E). Considerations and tips for successful screens Next-generation sequencing - CRISPR...guide RNA (gRNA). The ~20 nucleotide targeting sequence within the gRNA is defined by the user, and it...immediately 5’ to a protospacer adjacent motif (PAM) sequence. Co-delivery of wild-type Cas9 and a gRNA generates...screening due to the broad range of potential target sequences and ease of generating gRNA-containing plasmids...generate lentivirus. Be sure to use next-generation sequencing to check the quality of your amplification. If...by a unique barcode on each plasmid. As such, sequencing CRISPR libraries after amplification and after... a screen requires the use of next-generation sequencing. Representation - Most libraries contain 3-6 ...

  7. Recombinase-based State Machines Enable Order-dependent Logic in vivo

    Type
    Blog Post
    ...machines (RSMs), which take on a particular DNA-sequence configuration (state) based on the identity and...RSMs work? The state of an RSM is defined by the sequence within a prescribed region of DNA termed the “...straightforward way to read the state of an RSM is to sequence the register. In our paper (1), we allowed individual... register region and sent the PCR product for sequencing.  A less straightforward, but more population-wide...of state interrogation mentioned above (Sanger sequencing, qPCR, and fluorescent reporter-based) each come...with their advantages and disadvantages. Sanger sequencing is simple and the most accurate method as it ...the state of a register. However, each Sanger sequencing reaction can only be performed on one register...

  8. Hot Plasmids June 2018 - Reverse transcriptase, nanobody, and protein-DNA interaction tools

    Type
    Blog Post
    ...transcription of RNA such as long-read cDNA sequencing and RNA sequencing of complex heterogeneous RNA samples...functional element (tyrosine sulfation consensus sequence, fluorophore, or APEX2), allowing for quantitative...Caspex’ construct is guided by a pre-defined sgRNA sequence to a specific genomic locus and labels the proteins...radius of approximately 20 nm of a specific DNA sequence in only 1 min. Using these lentiviral plasmids...Shield1 inducible CMV promoter and targeted to a sequence of interest with an sgRNA expressed from a separate...

  9. Behind-the-scenes of the Isolation of the Thermostable IgnaviCas9 From a Yellowstone Hot Spring

    Type
    Blog Post
    ...that remained unexplored. Using new single-cell sequencing approaches, the lab was able to eliminate the...cultures to study these microbes. From 16S rRNA sequencing, hot springs were known to be diversity hotspots... characterized a few samples by 16S rRNA gene sequencing which showed the presence of many “dark matter...samples, and years later, several whole genome sequencing projects were launched in the Quake Lab. Identifying...mini-metagenomics method using microfluidic parallelization to sequence this highly complex hot spring sample. The sample...separated into smaller samples of 5-10 cells each for sequencing, allowing for lower complexity with higher throughput...

  10. FastCloning: A Newer, Simpler Cloning Technique

    Type
    Blog Post
    ...and amplification of a recombinant DNA without sequence alteration. Molecular cloning techniques are some... DNA polymerase, the construction of specific sequences for base pair overhangs, insert and vector purification...products, nor does it require the use of specific sequences. Read on to learn how easy this process is and.... The primers used to amplify the insert have sequences specific to the insert with an additional 15-17...with the appropriately sized product, purify and sequence the plasmid to confirm no mutations were introduced...FastCloning: a highly simplified, purification-free, sequence-and ligation-independent PCR cloning method." ...

  11. CRISPR 101: Multiplex Expression of gRNAs

    Type
    Blog Post
    ...Deleting a large region of the genome by removing the sequence between two target sites. Modifying multiple genes... oligonucleotides for your chosen gRNA target sequences and clone them in just as you would for a single...enzymes, which cleave outside of their recognition sequence, creating flanking overhangs. These overhangs ...the oligonucleotides specifying each gRNA target sequence into distinct expression vectors using the enzyme...the promoter-gRNA construct, but with different sequences adjacent to the sites. When digested with the ...Type IIS enzyme, the unique flanking overhang sequences can link together to allow for ordered assembly...schematic below.   Figure 2: gRNA target sequences (colored rectangles) are cloned into various plasmids...

  12. Plasmids 101: Gibson Assembly and Other Long-Homology Based Cloning Methods

    Type
    Blog Post
    ...primers that contain the appropriate homologous sequences. NEB recommends an overlap of 15-40 bp, with a... insert both the gene of interest and the tag sequences into the vector in one step without scars as depicted...might be anticipated to occur within a terminator sequence), since this would directly compete with the required...assembling multiple fragments in one step with no scar sequences remaining in the final product. The long overlapping...fragments as compared to the smaller overlapping sequences left with a restriction digest. A study in 2013...around this is to use a combination of standard sequences with overlap regions, such as in the case of MODAL...overlap-directed methods (Casini 2014). In this case linker sequences are added before the homology regions, which allows...

  13. SARS-CoV-2/COVID-19 Detection Methods Based on CRISPR/Cas

    Type
    Blog Post
    ... the Cas12a-sgRNA complex binds to the target sequences, Cas12a activity gets activated. This unleashes... of interest. Cas13 uses a complementary crRNA sequence to bind to the sample and upon binding, gets activated...trans cleavage reaction that cleaves a nearby RNA sequence that contains a fluorophore that is quenched when... Unlike Cas12a, Cas13a does not require strict sequence preferences at the target site, while Cas12a requires...SHERLOCK diagnostic test, this test varies in the sequence of steps and the Cas protein used. Here, all the...to one strand of the reverse-transcribed target sequence that are present close to the primer recognition...binds to the complementary region in the target sequence and this activity results in the trans cleavage...

  14. Plasmid Tools for Microbiome Studies

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    Blog Post
    ...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...

  15. Site Directed Mutagenesis by PCR

    Type
    Blog Post
    ...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...

  16. Tips for CRISPR Gene Editing in Mice

    Type
    Blog Post
    ...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...

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

    Type
    Blog Post
    ...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...

  18. Visualizing Translation at the Single Molecule Level

    Type
    Blog Post
    ...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...

  19. Plasmids 101: TOPO Cloning

    Type
    Blog Post
    ...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...

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

    Type
    Blog Post
    ...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...
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