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We narrowed to 383 results for: plasmid dna

Showing: 141 - 160 of 383 results

  1. Finding nucleic acids with SHERLOCK and DETECTR

    Type
    Blog Post
    Published
    April 16, 2020, 1 p.m.
    ... the Doudna lab has used Cas12a’s non-specific ssDNA degradation to develop the method termed DNA Endonuclease...specific DNA sequence, such as the Human papilloma virus (HPV) genome, via a crRNA. An ssDNA-fluorescently...signal when the ssDNA is degraded, is added to the reaction. To enhance sensitivity, the DNA is first amplified...quantified to determine the presence and quantity of DNA, RNA or a mutation of interest. Together SHERLOCK... increase the sensitivity of the assay, targeted DNA or RNA from a sample is first amplified using RPA...coupled with T7 transcription to convert amplified DNA to RNA for subsequent detection by Cas13. This amplification...with the ssRNA reporter enables SHERLOCK to detect DNA or RNA with atomolar sensitivity and single base ...

  2. CRISPR 101: Cytosine and Adenine Base Editors

    Type
    Blog Post
    Published
    Feb. 13, 2025, 2:15 p.m.
    ...rescue! Base editors chemically modify DNA bases without breaking the DNA backbone, sidestepping the problem...uracil without cutting DNA. Uracil is then subsequently converted to thymine through DNA replication or repair...unmodified DNA strand so that it appears “newly synthesized” to the cell. Thus, the cell repairs the DNA using...strand of DNA and converts a C to U without producing a double strand break. UGI = uracil DNA glycosylase...Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature, 551(7681), 464–471. https...editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 533(7603), 420–424...homology-directed repair (HDR), the pathway for resolving DNA double-strand breaks (DSBs) preferred by researchers...

  3. Antibodies 101: Beyond Surface Labeling

    Type
    Blog Post
    Published
    June 27, 2024, 1:15 p.m.
    ...incorporated into the DNA during DNA synthesis and then diluted with subsequent rounds of DNA synthesis (cell... for panel design. Find streptavidin plasmids and biotin plasmids at Addgene!     Figure 1: Indirect...found within the cytosol/nucleus, or visualizing DNA instead of proteins. Some stains can diffuse through...targets include transcription factors, histones, and DNA repair enzymes. Note that when using the nuclear ...Dye stains are non-antibody-based stains that bind DNA or free amines of proteins. Depending on the application...previously induced gene knockout. Besides amine- and DNA-binding dyes, nucleoside analogs like bromodeoxyuridine...stains are membrane-permeant or -impermeant and bind DNA or free amines, depending on the application. Paul...

  4. 27 Hot Plasmids from 2016

    Type
    Blog Post
    Published
    Dec. 22, 2016, 3:03 p.m.
    ...PubMed PMID: 26950006 Plasmid ID Plasmid Name Plasmid Type 74309 pcDNA3.0-TRPV4-p2A-ferritin-p2A-mCherry...highlight a subset of the new plasmids in the repository through our hot plasmids articles. These brief articles...features and applications of a partiular plasmid or set of plasmids. We hope that these articles make it ... you to find and use the plasmids you need. You can find all the hot plasmids from 2016 below. With over...over 45,000 plasmids, we can't write posts for every great plasmid that comes into the repository, but...write about your plasmids in a future blog post. No time to read? Listen to our hot plasmids segment on the...alone involves much literature searching, DNA synthesis, and plasmid assembly. Luckily, researchers from Douglas...

  5. Viral Vectors 101: Inverted Terminal Repeats

    Type
    Blog Post
    Published
    Oct. 19, 2023, 1:15 p.m.
    ... ITRs are the elements that make an AAV plasmid an AAV plasmid.  Within the AAV genome, ITRs serve as...they are in the same DNA molecule as the gene that they package. In a transfer plasmid, the transgene is ...the single stranded DNA genome of AAV in the native virus. In an AAV vector plasmid, they flank the gene...growth culture and result in a high percentage of plasmid DNA with mutated ITR sequences. Using recombinant-deficient...gene of interest in a cell or animal model. AAV plasmids contain several important elements, but among ...located immediately outside of the ITRs in the plasmid backbone and do not properly assemble, but these...

  6. What's New in CRISPR - November 2021

    Type
    Blog Post
    Published
    Nov. 18, 2021, 2:15 p.m.
    ...CRISPR guide Find CRISPR plasmids by function Find recently deposited plasmids Topics: CRISPR, Other CRISPR... where we highlight a few of the newest CRISPR plasmids available at Addgene. If you want to read more...will cover: Miniature CRISPR-Cas systems SEND plasmids Prime editing improvements Miniature CRISPR-Cas...scaffold gRNA and making strategic mutations in the DNA binding cavity of Cas12f. The CasMINI system is less...Read the paper in Molecular Cell Find the CasMINI plasmids Efficient CRISPR editing with a hypercompact ...paper in Nature Biotechnology Find the Cas12f-GE plasmids Programmed genome editing by a miniature CRISPR-Cas12f...cells using various delivery methods, including plasmid, ribonucleoprotein, and AAV.  Read the paper in...

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

    Type
    Blog Post
    Published
    Nov. 12, 2020, 2:15 p.m.
    ... usage bias in Plasmids 101: Codon usage bias Read more about plasmids in our Plasmids 101 blog series...without altering the sequence of the protein. As DNA synthesis has become quite cost-effective it seems...seems easy for scientists to re-synthesize DNA with the most optimized sequence. Unfortunately, it is not...algorithms/resources (Athey et al., 2017) and many DNA synthesis companies, such as IDT, Genewiz and GenScript...available online to both determine and synthesize DNA sequences for optimal expression in your system of... (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic...Reference Read about genetic code expansion Browse our plasmid collection page  ...

  8. Tips for Screening with Yeast Two Hybrid Systems

    Type
    Blog Post
    Published
    Oct. 22, 2015, 2:30 p.m.
    ...transforming both fusion plasmids, or mating two single haploid yeast fusion plasmid transformants into a ... in the cell, including protein-protein, protein-DNA and protein-RNA interactions. The 1980s saw a flurry...format of some transcriptional activators: that the DNA binding domain (DBD) and transcriptional activation...reporter system (e.g. the Gateway-compatible bait Y2H plasmid pEZY202  from Yu-Zhu Zhang’s lab) is an example...interaction detection methods (6). In order to bind DNA and activate a reporter gene in eukaryotic cells,...Keegan, L., Gill, G., and Ptashne, M. Separation of DNA binding from the transcription-activating function...eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell. 1985...

  9. CRISPR 101: Mammalian Expression Systems and Delivery Methods

    Type
    Blog Post
    Published
    Sept. 24, 2015, 2:30 p.m.
    ...you will also need to deliver a donor plasmid or single-stranded DNA oligonucleotide, so you will need to...editing? Do you want to deliver the components as DNA, or would mRNA or protein delivery be more suitable...transduction or injection as either protein, RNA, or DNA. Finally, once you have identified the best expression...generate stable cell lines. Packaging and Envelope plasmids provide the necessary components to make lentiviral...for in vivo viral delivery. Cas9 mRNA and gRNA Plasmids containing gRNA and Cas9 are used in in vitro ...efficiency of CRISPR delivery. There are a few plasmids at Addgene that have been published as CRISPR ...genome target sequence into EGFP reporter. Target DNA reporter system: Can evaluate component delivery ...

  10. Twenty Years of Sharing Science!

    Type
    Blog Post
    Published
    Jan. 8, 2024, 3:25 p.m.
    ...repository for DNA-based materials, including our popular kits and libraries. This DNA-based materials...trying.  When we started in 2004, we were the plasmid repository. In 2016, we added viral vectors, and...addgene.org! Fun fact! Did you know you can search for plasmids from a publication by pasting the paper's title...Our first request was on September 8, 2004 (for pcDNA-p160MBP, if you're curious.) Since then, we've distributed...

  11. pCXLE toolkit: Efficient episomal plasmid-based method to reprogram peripheral blood cells to iPSCs

    Type
    Blog Post
    Published
    Dec. 14, 2017, 2:08 p.m.
    ...Episomal vectors- extrachromosomally maintained DNA plasmids that express reprogramming factors To date,...viral origin of DNA replication, OriP and the EBNA-1 sequence that encodes for the DNA binding protein...and to model diseases in vitro. Find stem cell plasmids at Addgene Many sources of adult somatic cells... amplification of the episomes concurrently with DNA amplification in the host cell. This enables relatively...group is an optimized mixture of three episomal plasmids (Table 1) encoding the reprogramming factors. ...enhance the reprogramming efficiency, an extra plasmid, pCXWB-EBNA-1 is used in the reprogramming cocktail...increases protein expression from the other episomal plasmids. When used on PBMCs, the pCXLE episomal vector...

  12. CRISPR 101: Anti-CRISPR Proteins Switch Off CRISPR-Cas Systems

    Type
    Blog Post
    Published
    July 23, 2020, 1:20 p.m.
    ...inhibiting crRNA loading, inhibiting DNA binding, or inhibiting DNA cleavage.   Five ways to anti-CRISPR...Bondy-Denomy J, Corn JE, Doudna JA (2017) Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv 3:e1701620...proteins can also be used to prevent dCas9 tethering to DNA. Since these early anti-CRISPR studies, scientists...block CRISPR activity one of three ways: Inhibit DNA binding Example:  AcrIIA4 blocks Cas9’s interaction...crRNA-Cas complex (Zhu et al., 2019). Inhibiting DNA cleavage Example: AcrIIC1 binds to the HNH endonuclease...endonuclease domain of Cas9 and prevents target DNA cleavage (Harrington et al., 2017). Figure 1: Anti-CRISPR...CRISPR   Resources on Addgene.org Find CRISPR Plasmids for Your Research Interested in light-inducible...

  13. RNA Extraction Without A Kit

    Type
    Blog Post
    Published
    March 24, 2020, 1:15 p.m.
    ...Read blog posts related to plasmid protocols Find protocols for purifying DNA without a kit Resources ...precipitate RNA, but not DNA and proteins. Lastly, using a DNase (there are several DNase enzyme products on...As with DNA isolation, scientists commonly rely on RNA isolation kits to make their life easier. Recently...Recently, we published a blog on DNA purification without a kit that outlined several reasons why doing ... one should take care whenever doing any type of DNA or RNA purification to avoid contamination, take ...RNA extraction. RNA is inherently not as stable as DNA- it is single stranded and its ribose groups are ...There are many alternative methods for isolating DNA without a kit. However, that isn’t the case for RNA...

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

    Type
    Blog Post
    Published
    Dec. 8, 2022, 2:15 p.m.
    ...its method of DNA cleavage. Instead of cleaving DNA at a defined site to form a clean DNA break, Cas3 locates...sequence and initiates single stranded DNA degradation. Cas3 DNA digestion can proceed up to multiple kilobases...fidelity ssDNA targeting. RNA targeting Cas enzymes Move over Cas9, CRISPR isn’t just for DNA anymore!...highlighting their similarities and differences to Cas9. DNA targeting Cas enzymes Cas9 – The genome engineering...genome where it will proceed to generate a blunt DNA double strand break. Cas9 has been studied for genome...expanding number of others. Best for: a wide range of DNA edits.   Cas3 – The shredder What sets Cas3 apart...but it is effective at wiping out large regions of DNA and has anti-viral application potential as a result...

  15. What's New in CRISPR - May 2019

    Type
    Blog Post
    Published
    May 28, 2019, 12:49 p.m.
    ...CRISPR plasmids available at Addgene. We will still periodically focus on specific CRISPR plasmid tools...CRISPR guide Find CRISPR plasmids by function Find recently deposited plasmids ...genome-wide CRISPR inhibition Covalent tethering of DNA template to Cas9 SECURE base editors Nme2Cas9 CRISPR...CRISPR inhibition library Covalent tethering of DNA repair template to Cas9 Homology-directed repair ...Communications Biology Find the Cas9-PCV and PCV-Cas9 plasmids Selective curbing of unwanted RNA editing (SECURE...paper in mSphere Find the dCas9 and dCas9-Mxi1 plasmids If you have a new CRISPR tool you’ve recently...

  16. CRISPR-mediated Plant Base Editors

    Type
    Blog Post
    Published
    Jan. 3, 2019, 1:35 p.m.
    ...editing of a target base in genomic DNA without double-stranded DNA cleavage." Nature 533.7603 (2016): ...Programmable base editing of A• T to G• C in genomic DNA without DNA cleavage." Nature 551.7681 (2017): 464. PubMed...all CRISPR plasmids and resources at Addgene Find CRISPR base editors Find CRISPR plasmids for plants ...frequencies and relies on the efficient delivery of donor DNA to facilitate repair. Since the development of CRISPR-mediated...Cas9 nickase (nCas9). nCas9 creates a nick in the DNA by cutting only a single strand, dramatically reducing... detrimental indel formation. After binding with DNA, the CBE deaminates a target cytosine (C) into a ...this change. However, there are no naturally known 'DNA adenosine deaminases' which would theoretically give...

  17. Hot Plasmids: Spring 2025

    Type
    Blog Post
    Published
    June 3, 2025, 1:15 p.m.
    ...of the new plasmids, antibodies, and viral preps in the repository through our Hot Plasmids articles. ...in a scientist's toolkit is the empty plasmid backbone: the DNA vector that contains everything needed...Explore our empty and EGFP retroviral plasmid set, our bacterial plasmid set for expressing tagged proteins...and AAV plasmid sets launching later this year!  Find Addgene's own Lentiviral backbone plasmids here! ...backbones New recombinant antibodies for Glypicans DNA editing with STITCHR Dynamic protein labeling with... synaptic imaging applications. Find iGluSnFR4 plasmids here! Aggarwal, A., Negrean, A., Chen, Y., Iyer... swap sequences effortlessly.  We built these plasmids for flexibility and speed, so you can design, ...

  18. Visualizing Protein Turnover In Situ

    Type
    Blog Post
    Published
    Jan. 16, 2018, 3:20 p.m.
    ...other can the DNA strands take part in rolling circle DNA amplification. The amplified DNA segment is labeled...Fluorescent protein plasmids Use FRET to study protein-protein interactions Deposit plasmids with Addgene! ...Tagged protein can easily be overexpressed from a plasmid but overexpression may interfere with the system.... Both antibodies have a short antibody specific DNA strand added to them. Only if the proteins of interest...

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

    Type
    Blog Post
    Published
    July 2, 2020, 12:40 p.m.
    ...chromatin, the complex of DNA and proteins that forms chromosomes. These long range DNA interactions are often...digest cuts DNA into smaller pieces, and proximity ligation creates chimeric circles of DNA that are distant...CAPTURE method. After protein and DNA complexes are cross-linked, DNA is digested into smaller pieces. ...ligated together to create loops of DNA. This is key to linking pieces of DNA that are far away from each other...important supporting roles. Enhancers are cis regulatory DNA sequences that, when bound by transcription factors... looping with the photo “developed” by analyzing DNA sequencing data. While “pictures” generated with ...picture” is then developed by detecting these chimeric DNA fragments by PCR or next-generation sequencing. ...

  20. Reaching out to China: Canton Nucleic Acids Forum (CNAF) 2015

    Type
    Blog Post
    Published
    Dec. 1, 2015, 3:30 p.m.
    ...to defend against both DNA and RNA viruses - 2 cas systems regulate at the DNA level and 1 at the RNA ... Addgene’s experience helping scientists share plasmids, especially those of the CRISPR variety (see slides...is in one of the top 10 countries in number of plasmid requests from Addgene. Addgene - Canton Nucleic...Opening talks – Genomics discoveries and moving beyond DNA Eric Green, Director of the National Human Genome... inheritance that might be less error prone than DNA replication. He too mentioned how “surprising” small...ribosome is in a complicated conformation “not like DNA which has a boring structure.” That certainly summed... dna...
Showing: 141 - 160 of 383 results