...evidenced by all the CRISPR publications, press, and plasmids out there, it’s obvious that CRISPR is a ground-breaking...that Cas9 cutting efficiency increases when target DNA strand separation is stabilized (2,3). Stable strand...interactions between the groove and the negatively charged DNA and therefore destabilize basal strand separation...cutting. Figure 1: Strand separation and target DNA binding to the Cas9 nuclease. Stable strand separation...sequence independent interactions between Cas9 and DNA, then they could diminish off-target cutting (4)....between Cas9 and the phophate backbone of the target DNA strand via mutations N497A, R661A, Q695A, and Q926A...compared to eSpCas9(1.1) and SpCas9-HF1. The HypaCas9 plasmids are available from Addgene here! Future possibilities...

...target any sequence of DNA. Second, NgAgo target specificity is dictated by a DNA guide sequence rather...(2016). 3. "NgAgo: Genome-editing by a DNA-guided enzyme." DNA-scissors (blog). Blog website. 4. Hsu, ...be produced from a plasmid in cells. Additionally, in vitro assembly of NgAgo/ssDNA requires incubation...genome editing! Check Out Other Argonaute Plasmids from the Doudna Lab Many thanks to our Guest Blogger ...sequencing on select regions of all distributed plasmids as part of quality control, but does not perform...sharing the stage with much-lauded CRISPR-Cas9 is DNA-guided endonuclease NgAgo! We'll discuss how NgAgo...methods have their own pros and cons (2). The NgAgo DNA guide is inexpensive and can be 5’-phosphorylated...

... Resistance Gene Plasmids 101: Yeast Vectors Plasmids 101: Mammalian Vectors Plasmids 101: The Promoter...other plasmids? If we all use the same molecular code, can I transfect any old bacterial plasmid into ...of replication (ori), where DNA replication begins, so a bacterial plasmid needs a compatible ori that...is transfection. In stable transfection, DNA from the plasmid is incorporated into the host cell’s genome...blog Plasmids 101: Transformation, Transduction, Bacterial Conjugation, and Transfection Plasmids 101:...molecular biologist has seen before, showing how DNA sequences are translated into amino acids. And I ...plant-infectious bacteria that can incorporate foreign DNA into plant genomes. Eukaryotes are a bit more complicated...

... Blog Plasmid Cloning by PCR Perform Site Directed Mutagenesis by PCR Catch up on Your Plasmid Background...isolation, insertion and amplification of a recombinant DNA without sequence alteration. Molecular cloning techniques... due to excessive PCR cycles or low fidelity Taq DNA polymerase, the construction of specific sequences...be enough time to completely digest the template DNA. Note—templates must have been isolated from methylation...appropriately sized product, purify and sequence the plasmid to confirm no mutations were introduced during ...PCR or any subsequent steps. Using high fidelity DNA polymerases, I have never had any mutations introduced...Amplification efficiency is highest when using high fidelity DNA polymerases like phusion. An 18-cycle PCR leads to...

...This serves to stabilize DNA-protein interactions for subsequent sheering of DNA by sonification. Though...protocols Browse CRISPR plasmids for isolating a genomic locus Browse FRET plasmids for studying protein ...limitations and makes it easier for you to map protein-DNA interaction with limited biological materials. Problems...Though it helps capture weaker or more transient DNA-protein interactions, the reliance on fixation does increase...CUT&RUN, an enzyme-based protocol for identifying DNA binding patterns that overcomes some of the limitations...collected in a single day. CUT&RUN works by using the DNA cutting activity of a Protein A fused micrococcal...micrococcal nuclease (MNase) to specifically isolate DNA that is bound by a protein of interest. First, nuclei ...

...consider your plasmid's compatibility with one or more other plasmids. Generally speaking, plasmids with the...purify your plasmid DNA: The insert Bacteria tend to maintain fewer copies of plasmids if they contain...elements. The ori is the place where DNA replication begins, enabling a plasmid to reproduce itself as it must...replicons of plasmids are generally different from the those used to replicate the host's chromosomal DNA, but...cell. Figure 1: A plasmid map showing the standard features of a plasmid. So, how do you choose...have only one plasmid type in your cells at a time? Do you want to make a lot of your plasmid? Is the gene...avoid plasmid incompatibility In other words, the best choice of ori depends on how many plasmid copies...

...CRISPR plasmids available at Addgene. We will still periodically focus on specific CRISPR plasmid tools...CRISPR plasmids to tag human transcription factors with GFP. As part of the Encyclopedia of DNA Elements...CRISPR guide Find CRISPR plasmids by function Find recently deposited plasmids ...identified Jennifer Doudna’s lab recently identified Cas14, a family of small DNA-targeting Cas proteins... unlocking) to detect single molecules of RNA or DNA. Now they have developed this further to provide ...Read the paper in Science Find the new SHERLOCK plasmids More precision with dual-nuclease Cas9-Cas9 ...Nature Communications Find the Cas9-Cas9 chimera plasmids A modular toolkit for genome editing in plants...

...stability of modified Ti plasmids during plant infection, as well as plasmid yield during preparation ...selectable marker. Left and right T-DNA borders specify the region of DNA that will be transferred to the ...GreenGate Plasmids Interview: Nicola Patron on Plant Synthetic Biology, MoClo, and More Plasmids 101: Origin...Agrobacterium carries a “tumor-inducing” or Ti plasmid, which allows it to transfer genetic material into...in two species: Agrobacterium and E. coli. Like plasmids used in other systems, binary vectors are cloned...It’s a lot of information to fit into a single plasmid, so most first-generation binary vectors are quite...pKM24KH.To reduce vector size, they shortened the T-DNA borders to 25 bases each. By switching the E. coli...

...comprise a DNA binding domain and an endonuclease domain. What’s distinctive is that the DNA-binding domain... to target a particular DNA sequence? Musunuru: The kit includes 832 plasmids containing prefabricated...effector nuclease (TALEN) kit consisting of 834 plasmids. The researchers showed they could use their TALEN...and can be programmed to bind to essentially any DNA sequence desired. This technology allows you to create...prefabricated pieces that allow you to build a DNA-binding domain to recognize any desired 15 base pair sequence ...the genome in rapid fashion. The two remaining plasmids in the kit have the rest of the protein in place...fluorescent proteins used to sort the cells after the plasmids have been introduced by transfection or electroporation...

...repair DNA. The DNA ends are chewed back to reveal homology, allowing the strands to anneal. DNA synthesis...PITCh plasmid to release the cassette, and an insertion-locus-specific gRNA cleaves genomic DNA. These...Guide Pages Find CRISPR Plasmids for Your Experiments Deposit Your New Plasmid Tools with Us  ...Integration into Target Chromosomes). Using their PITCh plasmids, GFP knock-in cell lines can be created in about...Introduction There are three primary methods for repairing DNA after a double-stranded break. HDR copies the sequence... knock-ins, some labs have used NHEJ for whole plasmid integration; however, since NHEJ is error-prone...additional nucleotides flanking the insertion. If the DNA ends anneal incorrectly, MMEJ may also introduce,...

...disrupting it with an piece of DNA designed in the lab. Specially constructed plasmids can be used to replace ...gene. Here, we'll describe the techniques and the plasmids used to inactivate specific genes in mammalian...mind when choosing a knockout strategy! Knockout plasmids Homologous recombination is a mechanism to accurately...exchanged between two similar or identical molecules of DNA. Gene targeting takes advantage of this natural process...randomly integrated all or large portions of the plasmid. Deliver your construct to your target cells. After...Cre-mediated recombination.   Knockout/Knock-in plasmids Gene targeting methods also make it possible to... and insert GFP into the genome, we’d create a plasmid similar to the one shown below, where the sequence...

...samples at Addgene - DNA sent from depositors, bacterial glycerol stocks, prepped DNA ready for our quality...bacteria with the plasmid can grow. As the bacteria divide, they replicate and retain the plasmid. This allows... Inside Addgene Posts! Learn all about Plasmids in our Plasmids 101 series! ...Every plasmid sample enters Addgene the same way. A package is delivered by a mail courier and then the...dishes, but close to 80% of samples are received as DNA in a microcentrifuge tube. Once a sample enters Addgene...about Developing Lab Management Software    The plasmid's journey begins First, each package is opened and... to hundreds of samples, with an average of 10 plasmids per deposit. Each week an average of 16 deposits...

...Wenning Qin. Single-stranded DNA repair templates Short single-stranded DNA templates have been shown to...editing. How to use Addgene plasmids for Easi-CRISPR You can use Addgene plasmids to create a repair template...of Addgene plasmid options for templates - see the example at right using blue flame plasmid pmScarlet_...desired insert (e.g., mScarlet).   Plasmid ID Plasmid Name Tags 69090 pMJ915 MBP (N ...out our CRISPR Guide Find Plasmids for Cas9 Purification Find CRISPR Plasmids for Mammalian Expression ...pmScarlet_C1! After creating the T7-DNA template, you'd use ivTRT to create the ssDNA construct as described in ...pre-CRISPR was very arduous. First, you’d construct a plasmid with your desired changes, long homology arms and...

...This post is part of our ongoing Plasmids 101 series. Plasmids 101 will provide you with an overview ...of the Plasmids 101 posts here. Now that we have covered antibiotic selection here at Plasmids 101, we...α-complementation plasmid. This way you can quickly and easily identify colonies that not only have your plasmid (antibiotic...rescued by genes supplied on the transformed plasmid. Such plasmids may contain genes that allow for the use... able to select for colonies that contain your plasmid is a great start when cloning, but how about being...being able to choose those that contain plasmid with an insert? Blue-white selection is a widely used ...far, so good, but how does this help us screen plasmids? Blue-white screening in the lab Scientists discovered...

...effects when compared to DNA transfection of gRNA and Cas9 expression plasmids. These results are in line...infiltrate cells. Options for CRISPR delivery include plasmid transfection, RNP electroporation, and viral transduction...Nanoblades because they think of these particles as tiny DNA cutting ninjas that deliver CRISPR to multiple types... Gag in place of SpCas9. gRNA A gRNA targeting a DNA sequence of interest is expressed in 293T cells and...types they tested. Interested in using Nanoblades? Plasmids are available from Addgene. Genome editing primary...generally having lower off-target edits compared to DNA transfection.  Homology directed repair (HDR) with...-based HDR allows for the precise insertion of a DNA sequence ranging from a single nucleotide change ...

...without sickle cell anemia, two DNA fragments are observed because the DNA has the site where MstII cuts... cell anemia the enzyme does not cut the DNA so only one DNA fragment is observed. Today Southern blotting...detects and quantifies a gene or DNA sequence of interest by recording DNA abundance throughout the amplification...mapping informs on DNA sequence through the use of restriction enzymes that cut DNA at specific sites ...specific fragments of a DNA sequence of interest to create a physical map of the DNA. Starting in the 1970s...innovation is nanopore-based DNA sequencing which reads the nucleotides of a DNA strand as it slips through...technologies nanopore-based DNA sequencing machines are relatively small meaning that DNA sequencing could move...

..., DIY DNA ladders. You can find additional hot plasmids in our newsletter or on our hot plasmids webpage...Improved CRISPR Base Editors Hot Plasmid 4: pPSU Plasmids for generating DNA molecular weight markers.  Listen...webpage.   Hot plasmids covered in this segment Hot Plasmid 1: Photocleaveable PhoCl protein for controlling...In the third episode of our Hot Plasmids podcast series, you'll learn about optogenetics tools for controlling.... Listen to Our Segement on PhoCl Segment  Hot Plasmid 2: Ouabain selection for increased CRISPR editing...Listen to the Segement on Ouabain Selection  Hot Plasmid 3: CRISPR base editors with enhanced range and ...Listen to the Segement on the pPSU Plasmids Special thanks to our sound engineer/producer, Eddy Page!...

...created DNA ladders (aka DNA molecular weight markers) that can be used to measure the size of DNA fragments...highlight a subset of the new plasmids in the repository through our hot plasmids articles. These brief articles...articles provide a synopsis of a plasmid or group of plasmids' functions and applications. We hope that... you to find and use the plasmids you need. You can find all the hot plasmids from 2017 below. With over...over 50,000 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...editing for precise genome modification. Plasmid ID Plasmid Name Cas9 Variant Speacial Features 85169...

...subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These articles...recent plasmid deposits and we hope they'll make it easier for you to find and use the plasmids you need... CRISPR plasmids are always being added to the repository. To find all of the CRISPR plasmids available...known or suspected to be involved in DNA damage response and DNA repair.  A new CRISPR pooled library ...only required three components: a master mix, the DNA of interest, and cell extract.    Graphical...They allow single-nucleotide modifications to edit DNA without requiring a double-stranded break. The Xiao...Xiao Wang Lab has recently deposited a set of plasmids that helps identify base edited cell populations...

...once in the plasmid backbone and another enzyme that cuts within the insert. If the plasmid contains the...or absence of DNA using lysed bacterial colonies, without the need to prep your plasmid. In this case,... PCR product if the plasmid contains the insert and no PCR product if the plasmid does not contain the...precise order of nucleotides within a DNA molecule, in this case a plasmid. Sequencing is one of the surest...resources on the Addgene blog Get all the plasmid basics in our Plasmids 101 series Find more molecular biology...If you’re cloning a plasmid, you’ll need a way to find the needle in the haystack: the one perfect clone...clone that contains the plasmid you’re looking for out of the many cells that don’t. One way to begin ...