...toolbox. Natural plasmids, also called environmental plasmids, are all around us! A plasmid is a small piece...colicin-producing plasmids have been referred to as “Col plasmids” or “Col factors.” Virulence plasmids: microbial...Old Solution but a New Problem Plasmids 101: What is a Plasmid? Plasmids 101: Transformation, Transduction...F. (2023). Plasmid classifications. Plasmid, 126, 102684. https://doi.org/10.1016/j.plasmid.2023.102684...when we think of plasmids, both Archaea and Eukaryota can also harbor these circular DNA passengers. Most...., 2001) Beneficial traits of natural plasmids Natural plasmids often convey a variety of functions that...functions of natural plasmids. Created with BioRender.com. Resistance (R) plasmids: microbial defense...

... frequent DNA repair mechanism in general. On average, it accounts for less than 10% of DNA repair, with...though exogenous DNA can be used as well. Below are some considerations for designing donor DNA for successful...homology-directed repair pathway, designing the best donor DNA, and avoiding common mishaps in this class of genome...knock-out. The goal of a knock-out is to disrupt DNA translation by generating a frameshift mutation. ...knock-ins. Knock-in mutations typically require an exact DNA sequence to be incorporated at a precise genomic ...which is done through the design and use of a donor DNA molecule. Your donor molecule will need to have homology...This homology will guide the cell to use the donor DNA as a template for repair, which will result in the...

...Chromatin is a complex of DNA and histone proteins that compacts cellular DNA into chromosomes and reduces...reduces the risk of dangerous DNA damage. If the way DNA is wrapped around histones changes, then gene expression...methyl- groups to the DNA, which mostly occurs at CpG islands (regions of the DNA with a high frequency...gene expression that do not involve any changes to DNA sequence (Epigenetics literally means ‘on top of ...This is how most cells in the body contain the same DNA but have very different structure and function, and...change as well. The more frequently and tightly bound DNA is to histones, the more compacted it becomes. This...associated with reduced life-span, but no changes in the DNA sequence could be found. Angelman syndrome and Prader–Willi...

...the transfer plasmid, a plasmid encoding rep and serotype-specific cap genes, and a plasmid encoding adenoviral...transfer plasmid Addgene uses a rigorous barcode matching system that follows the sample from the DNA tube.... coli. In addition, plasmids are typically prepared using endotoxin-free plasmid purification kits.   ...confirmation of transfer plasmids used in Addgene’s viral production. Barcoding allows our DNA and virus to be ...of the viral genome and the absence of unexpected DNA contaminants. The data is also used to determine ...contamination is minimized by using an endotoxin-free plasmid purification protocol. To minimize the immunogenic...lentiviral vector, incubated for 72 hours, and genomic DNA is extracted. Primers and probes targeting integrated...

...Mobile-CRISPRi ICE element forms a conjugative plasmid-like DNA circle and is transferred to recipient bacteria...Browse our CRISPR interference plasmids Find bacterial CRISPR plasmids Read our CRISPR guide ... into the genome and is propagated during normal DNA replication and cell division. Mobile-CRISPRi does...transposon system. This system has two parts: a plasmid expressing the Tn7 transposition genes (tnsA, tnsB... tnsB, tnsC, tnsD, and tnsE), and a plasmid that contains the Mobile CRISPRi cassette flanked by left ...copy of the RP4 transfer machinery mobilize these plasmids for transfer to recipient cells during a tri-parental...due to site selection by TnsD, a sequence-specific DNA binding protein. Selection removes donor bacteria...

...primers flanking my edits in genomic DNA and doing PCR on genomic DNA. The surveyor assay itself was relatively...BRDN0000561167) (Plasmid #80034) and BRAF gRNAs (BRDN0001145345 and BRDN0001146266) (Plasmid #76479 and #76480...that Surveyor nuclease cleaves double stranded DNA (dsDNA) at basepair mismatches. To use this tool to ... denature and renature the dsDNA. Upon renaturation, you will generate DNA duplexes with one strand from...viruses, but you can find a list of validated gRNA plasmids on our website. There are a few reasons to target...gRNA-transduced Cas9-A549 cells are used as a control. DNA was analyzed by PAGE. The basis of the Surveyor...these mismatches are indicated by the presence of DNA cleavage products. The appearance of the 428 bp band...

...reflection of the large size of the plasmid or silencing of the plasmid by DNA methylation. Another downside...into cells as a donor plasmid containing the transposon, along with a helper plasmid that expresses the ...reprogramming factors. Non-replicating Plasmids: Generating iPSCs with plasmid-based expression requires serial... generating iPSCs by plasmid transfection where 2 of 11 clones tested had plasmid integration. Another...the dose of plasmid the cells receive over the whole reprogramming period and the plasmid will get diluted...larger plasmids have lower rates of transfection. Minicircles: Minicircles are like mini-plasmids. They...periods of time than traditional plasmids due to lower activation of DNA-silencing mechanisms. While minicircles...

... consists of a Ti plasmid, into which the GOI is inserted, and a Ti "helper" plasmid, which contains Vir...necessary for T-DNA processing and insertion into the plant genome. B) The Ti plasmid and helper are transformed... to plant cells. The region of the Ti plasmid between the T-DNA borders (yellow) are recognized by the...for creating plant expression plasmids, including plant CRISPR plasmids from the Yiping Qi lab and the...plant-specific modifications to commonly used CRISPR plasmids are necessary to use the CRISPR system in plant...et al., 2013). Addgene carries Cas9-containing plasmids for knockout, activation and repression of target...expression of both Cas9 and the gRNA off of the same plasmid. Delivering CRISPR components to plant cells Once...

...CRISPR plasmids available at Addgene. We will still periodically focus on specific CRISPR plasmid tools...scaffold and a domain needed for DNA unwinding. They’ve deposited plasmids for active and inactive CasX for...CRISPR guide Find CRISPR plasmids by function Find recently deposited plasmids ...Jennifer Doudna’s lab discovered a new Cas protein, CasX, from metagenomic analysis of microbial DNA from ...In this system, Cas9 generates a double-stranded DNA break at the genomic loci of interest and on either...vector sequence. Homology arms that flank the donor plasmid cargo are complementary to either side of the double-stranded...expression. Read the paper in Nature Find the CasX plasmids Drug inducible transcriptional activation and...

...complementary DNA (cDNA), and then use PCR and molecular cloning to insert the cDNA into the desired plasmid backbone...experiments in planarians with their recent plasmid deposit. These plasmids enable two main types of experiments... cloned into plasmids to investigate for each of these planarian species. These plasmids all have a PR-T4...dsRNA. Students can produce DNA templates via PCR off of the same plasmid and use these to create riboprobes...off of linearized DNA templates which they can easily generate off of a circular plasmid via PCR. Typically...Resources at Addgene.org Find plasmids from the Sánchez lab Find plasmids for other developmental models...of specific gene expression. The 49 deposited plasmids enable students to study gene expression and functions...

...to the genomic DNA of interest  Figure 1. When ABEs are in action they bind DNA so that the TadA...Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551:464–471 . https://doi....TadA domain can edit the short single-stranded DNA stretch that is accessible. Image from Gaudelli et al...in 40 new ABE8 variants. When comparing on-target DNA editing efficiency in a human cell line for these...ABE8.x-m/d constructs demonstrated a 2.1x on-target DNA-editing efficiency in a human cell line while reducing...pyogenes Cas9 requires the target site in the genomic DNA to contain a specific protospacer adjacent motif ...followed by 2 guanines). This limits the use of ABEs as DNA sites that do not contain a suitable PAM cannot be...

...of the DNA. Finally, in 1953, Franklin along with James Watson and Francis Crick resolved the DNA double...letters of the DNA get translated into the twenty amino acids. Once scientists established that DNA encoded ...dinosaurs by extracting the DNA from fossilized amber and supplementing it with the DNA of present-day frogs ...enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain (FokI). Zinc finger nucleases...designed in 2005. The DNA-binding domain can be engineered to target specific DNA sequences while FokI ...TALENs) were engineered. TALENs follow a DNA-binding and DNA-cleaving strategy similar to the ZFNs, but...mutations, delete short stretches of DNA and even insert new DNA at the target genomic loci.  A last ...

...Split-BioID plasmids Find CRISPR plasmids for labeling genomic regions Find CRISPR plasmids for purifying...it feels like DNA and protein get all the attention.There are numerous ways to detect DNA-protein interactions...interest, much like using ChIP for studying protein and DNA interactions. Unfortunately, using proteins as bait... however, knock-in of BoxB sites into endogenous DNA sequences could allow one to study RNAs expressed...question that RaPID could help answer? The RaPID plasmids are available from Addgene! References Ramanathan...PubMed Central PMCID: PMC5886736. Find the RaPID Plasmids Here! McHugh, C.A., Russell, P., & Guttman, M...Additional Resources on the Addgene Blog Study Protein-DNA Interactions with CUT&RUN Study Protein-Protein Interactions...

...synthesize complementary DNA copies of their genome upon infecting a host cell. This viral DNA (also called proviral...proviral DNA) is then inserted into the host's genome and is used to make more virus. The most studied ...their required components are very similar. While plasmids containing virus-specific elements such as the...Adeno-associated virus (AAV) is a small, single-stranded DNA parvovirus. AAV can infect humans and some other ...integrate, and the addition of a helper virus or plasmid allows it to replicate episomally, essentially ...can replicate and divide along with the endogenous DNA. AAV also has low immunogenicity, meaning it does...Adenovirus Adenovirus has a linear, double stranded DNA genome which is non-enveloped. It can infect humans...

... Hot Plasmid list. Other popular plasmids & blog posts @Addgene: The 10 Most Distributed Plasmid Technologies...inducible inactivation. Find the Robinson plasmids or the Royle plasmids and get to work! Robinson et al...designed the pOSIP (one-step integration plasmid) series of plasmids, vectors that convey both the sequence...recognition sites that flank a DNA module in an inverse orientation, so that multiple DNA components can directionally...mGRASP plasmids. Additionally, the lab recently described the use of another set of mGRASP plasmids in their... favorite plasmid technologies? Email us at [email protected]  and let us know what plasmids you would ...sgRNA libraries expand upon the CRISPR family of plasmids by offering a lentivirus-based mechanism for sgRNA...

...this evolving field! Find prime editing plasmids! Find plasmids from David Liu's lab! This post was originally...the CRISPR guide Find CRISPR plasmids by function Browse our entire plasmid collection ...possible without double-strand breaks (DSBs) or donor DNA templates.  Figure 1: An overview of prime...transcriptase. The Cas9 nickase is guided to the DNA target site by the pegRNA — a guide RNA that also...encodes the desired edit and homology to the genomic DNA locus. After nicking by Cas9, the homologous pegRNA...copies the desired edit, directly polymerizing new DNA onto the nicked target strand. The initial result... with overlapping strands of edited and unedited DNA. The heteroduplex is resolved by the cell’s mismatch...

...with the central dogma - replication of DNA, transcription of DNA to make RNA, translation of RNA to make...Drew Endy's lab at Stanford develops engineered DNA systems capable of storing data and computing inside...Addgene through the Biobrick Public Agreement (BPA) Plasmid Collection along with a BIOFAB kit comprised of..."Addgene is one of the leaders in distributing plasmids amongst the academic community. On the BioBricks... BioBricks Foundation to distribute the physical DNA samples, for when that's the preferred mode of receiving... with Endy more about the BIOFAB and BIL gates plasmid kits, the Biobricks Public Agreement, and the future...first to be made available via Addgene and the BPA Plasmid Collection - enable? Endy: The BIOFAB collection...

...many cases several exons’ worth of DNA. Any ∼20 nucleotides of DNA can serve as the target for Cas9’s ...Prime editor engaging target DNA. The reverse transcriptase polymerizes DNA onto the target strand based...great choices. Check out our SpCas9 containing plasmids, optimized for a variety of species.   Specificity...Cytidine deamination takes place on the free strand of DNA and converts a C to U without producing a double ... platform to deliver various cargo to a specific DNA locus by directly fusing the cargo to dCas9.  This...frequently fused to Cas9 for this purpose. dCas9-KRAB plasmids for repressing target genes in a variety of species...additional RNA-binding transcriptional activator. Plasmids for activating target genes in a variety of species...

... treated so that the protein and DNA are no longer bound, and the DNA can then be isolated and studied...proteins of interest to any DNA they were bound to (2) fragmented the DNA (3) used antibodies to specifically...your antibody:protein:DNA complexes and finally (5) isolated the DNA from your antibody:protein:DNA complexes...preserve more of the protein:DNA complexes. Once you’ve finished fragmenting the DNA, spin down the samples...interactions, and can give valuable insight into DNA expression and protein interactions, including epigenetic...proteins are not likely to remain attached to the DNA throughout the sample processing and therefore will...modifying proteins, which bind quite strongly to DNA, crosslinking may not be necessary. This is known...

... from Addgene Plasmids 101: How to Verify Your Plasmid Plasmids 101: Control Plasmids 6 Tips for Analyzing... on our plasmid pages - links to articles citing this plasmid. Now you can learn how a plasmid has been...your deposited plasmids Increased visibility of your plasmids in the "Associated Plasmids" lists Benefits...Find other related plasmids in the "Associated Plasmids" lists Properly citing plasmids you've requested...Citing This Plasmid" list. Email us at [email protected] with the Plasmid Name, Addgene Plasmid ID #, and...Troubleshooting DNA Sequencing Results ICYMI: Addgene’s Plasmids 101 eBook Protocols and Plasmid References...'ll find the plasmids listed below the citation. An example of these "Associated Plasmids" is shown in...