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  1. Natural or synthetic? How Addgene’s dataset reveals trends in biological innovation

    Type
    Blog Post
    Published
    Nov. 8, 2018, 3:47 p.m.
    ... sequence identity was a different story - the team found that the percent sequence identity between the...) and comparative properties (percent sequence identity and percent query coverage) that could be determined...synthetic or natural. They saw that a percent sequence identity below 85% correlates with synthetic sequences.... The researchers then used their classifier to identify synthetic and natural sequences in Addgene’s database...have practical applications in monitoring the accidental or intentional release of engineered organisms...
  2. Addgene's Top 10 Blog Posts of 2015

    Type
    Blog Post
    Published
    Dec. 7, 2015, 6 p.m.
    ...per month in November 2015. We will continue to provide you with more fascinating, informative, and actionable...technology in their own labs. We’re overjoyed to provide you with these fantastic educational resources ... you’d like to see on the blog or to contribute ideas for your own guest posts by e-mailing us at blog...inversions, deletions, and translocations. It also provides researchers with many different ways to control...the right one. In this post, Addgenie Melina Fan guides us through the basics of the validation process...experiment? In this post, Addgenie Chari Cortez guides us through some common controls and why you might...
  3. 5 Great Apps for Lab Life

    Type
    Blog Post
    Published
    Sept. 22, 2016, 2:30 p.m.
    ...interwebs for lab resources, and instead conveniently provide them on your smart phone. 1. Lab Archives by LabArchives...Gibco Cell culture manual and basic instructional videos. The search function in the manual just highlights...with NEB enzymes, the app is quite helpful and provides a list of directions including which buffers to...primer, you only need to skim the alphabet on the side of the screen to find the sequence for your enzyme...explain the properties of or draw an amino acid or peptide for some reason. It contains all twenty amino acids...allow you to write your colleagues’ names in a polypeptide chain, except if their names have a B, J, X, ...
  4. Creating accessible biology activities in schools with BioBits

    Type
    Blog Post
    Published
    Aug. 2, 2018, 12:56 p.m.
    ...enough to have the funding and the resources to provide them to their students. My desire to create a set... cell-free (FD-CF) components. Making proteins outside of a cell - cell free extracts Typically, if you...used in high school classrooms, but it could be widely adapted and used in a variety of settings. If you...are an instructor at the college level, perhaps consider using some elements of BioBits to transition your...researcher interested in adapting your research ideas into hands-on educational activities using the BioBits... Resources on Addgene.org Browse our protocol videos to learn simple lab techniques Check out our molecular...
  5. Plasmids 101: Gram Negative and Positive Bacteria

    Type
    Blog Post
    Published
    Aug. 2, 2022, 1:15 p.m.
    ...stain for 1 minute. Rinse the slide briefly with tap water. Flood the slide with Gram's iodine solution....staphylococci and streptococci. Gram negative bacteria, or diderms, have a thinner peptidoglycan membrane and an outer...safranin counterstain for 30 - 60 seconds. Rinse the slide in tap water until the runoff is clear, blot gently...types. In water, the dye dissociates into CV+ and Chloride (Cl-) ions. When the negatively charged iodine...into a specific bacterium, it can be important to consider the type of bacteria it is being used in, and ...
  6. R Bodies: Membrane-Rupturing Microscopic Tools

    Type
    Blog Post
    Published
    April 14, 2016, 2:30 p.m.
    ... proteins. Video by ACS. For a more cartoony explanation of R-bodies, check out this video. Most types...by propagating through an enormous lattice of identical subunits. A brief history of R bodies R bodies...proteins and remain functional, 2) break membranes outside of their natural context or 3) be modified to extend...fluorescent protein fusions allowed us to image R bodies inside cells, and these constructs may be useful to future...soluble when extended (see figure to the right), we identified R-body mutants that extend at both lower and ...
  7. Management for Scientists: Delegating is Key

    Type
    Blog Post
    Published
    Feb. 20, 2015, 8:30 p.m.
    ... More people in leadership roles leads to more ideas, initiative and creative thinking. The team members... must usually take on all tasks that involve confidential information. No matter who you delegate to, ...can help ensure successful results.  Can you provide the information and resources needed for the assignment...Setting someone up for failure by delegating is a bad idea. How do I make sure it goes well? As with most ...even if it is just 15 minutes a week. Clearly identify constraints and boundaries. Where are the lines...issues do you want to know about right away? Provide adequate support. The manager must be available...
  8. Finding and Joining Your Dream Lab

    Type
    Blog Post
    Published
    April 8, 2014, 2:50 p.m.
    ... perhaps surprising, yet important, factors to consider when seeking your dream lab. The principal investigator's...benefits. Therefore, lab selection should focus on identifying a lab that fits both work style and development...development needs. These two factors will provide a solid foundation on which to thrive during time spent as ... factor. The following questions can serve as a guide for the quest of a perfect "fit". How competitive...want a non-academic career path?  If you are considering this, make sure to choose an advisor that supports... into place frequently and you sometimes feel confident in your abilities. You have intense periods of...
  9. Top Requested Lentivirus and AAV of 2016

    Type
    Blog Post
    Published
    Jan. 6, 2017, 3:56 p.m.
    ...With this initial success, we will continue to provide and expand this diverse and useful collection of...inventory is based on CRISPR tools, though we do provide a few non-CRISPR related viral preps. Cas9 is the...with a second vector that delivers gRNA, such as lentiGuide-Puro. The alternative single-vector systems typically...gRNA lentiviruses easily made in your own lab. We provide protocols and useful tips for generating your own...exclusively activated by the small molecule clozapine N-oxide (CNO) (Krashes et al., 2011). Viruses expressing..., Shalem O, Zhang F. Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods. 2014...
  10. Hot Plasmids December 2018 - C. elegans RNAi, TurboID, Detecting Viral Outbreaks, and Protein Binding Specificity Tools

    Type
    Blog Post
    Published
    Dec. 6, 2018, 1:34 p.m.
    ...through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and ...to prevent the incorporation of non-specific nucleotides into the dsRNA leading to increased RNAi efficiency...This tetramer cleaves chlorophenol red-b-D-galactopyranoside on the assay paper turning it purple, allowing...30370338.  SH3 domain collection reveals novel peptide ligand motifs Article contributed by Michael Lemieux...specificity landscape of the SH3 proteins using peptide-phage display and deep sequencing, revealing that...protein stability, small molecule binding screens, peptide arrays, and phage display selections. In addition...
  11. GCE4All: Making Genetic Code Expansion Accessible

    Type
    Blog Post
    Published
    June 15, 2023, 1:15 p.m.
    ...impact both translation and fidelity of translation, leading to system-wide effects. And on top of that...modification, or add in fluorescent or chemically reactive side chains, all of which can help determine structure...reagents accessible to your lab. The solution GCE provides almost endless possibilities for researchers, ...researchers can easily implement in their own labs. They provide resources, knowledge, and most importantly, validated...that is by using Addgene’s Blue Flame award to identify highly requested GCE plasmids. But they’d also...
  12. From Lab Bench to Leadership: Transitioning into Management as a PhD

    Type
    Blog Post
    Published
    Jan. 21, 2025, 2:15 p.m.
    ...arises when managers fail to set expectations or provide timely feedback, leading to unproductive dynamics... mentors who have made similar transitions can provide you with insights, lessons from their experiences...work. On the other hand, it’s perfectly valid to decide that managing isn’t for you at this point in your...focusing on molecular biology and metabolism. He now guides fellow PhDs in their careers with actionable steps...Coursera, LinkedIn Learning, or edX. Podcasts: HBR IdeaCast Coaching for Leaders More resources on the ...Makes a Good Leader Anyways?  Transferable Skills Guide: Managing a Team  ...
  13. 3 Challenges in Plant Synthetic Biology

    Type
    Blog Post
    Published
    July 22, 2014, 5:46 p.m.
    ...biotechnology that are ripe with opportunity. We’ve decided to jump into one of those unexplored areas with...food, not medicine, and not mandatory – people can decide for themselves if they want this beautiful flower...begun to pivot towards plant biotechnology and provide a much needed boost to basic molecular plant research...are well understood. Additional work has also identified and characterized mechanisms and components of...you to our guest bloggers! Nikolai Braun grew up outside of Washington D.C. and has always enjoyed exploring...laboratory and received her M.S. from CSU in 2014. Outside of the lab, Keira enjoys spending time with her...
  14. Plasmids 101: Modular Cloning Applications and Kits

    Type
    Blog Post
    Published
    May 14, 2024, 1:15 p.m.
    ...construct. Once you’ve identified your experimental requirements, it’s a good idea to select an available...biofuels, and natural products without the undesirable side products generated during chemical synthesis of ...find the perfect combination. The EcoFlex Kit has a wide array of DNA parts that can be assembled into individual... are endless: genetic circuits with multiplexed guides, mini screening libraries, direct edit optimization...cells. Need more MoClo? Check out Addgene's MoClo Guide! Customizing MoClo for your needs As you probably...Resources on Addgene.org Modular Cloning (MoClo) Guide Addgene’s eBook Collection More resources on the...
  15. Special Delivery: Fluorophore Targeting for FRET Studies

    Type
    Blog Post
    Published
    July 19, 2016, 2:30 p.m.
    ... donor and acceptor fluorophores, it’s best to consider these cases separately when talking about the ...the tools that are available. Let’s consider the donor first where labeling specificity is most important...hardwire the molecule directly into the protein’s peptide sequence. Thus, all synthesized target protein ...addition, labeling contrast can be improved using disulfide-containing compounds such as British anti-Lewisite...described above can be paired together to measure a wide range of molecular distances (see Table). However...covalent labeling of recombinant protein molecules inside live cells." Science281.5374 (1998): 269-272. PubMed...Protein Fusions Check out Our Fluorescent Protein Guide ...
  16. dTAG - You're it!

    Type
    Blog Post
    Published
    June 21, 2018, 2:06 p.m.
    ...degradation. Remarkably, small molecule degraders provide distinct advantages over pharmacological inhibitors...Nabet et al., Nature Chemical Biology additionally provides detailed information on cloning procedures used...molecules by conjugating a CRBN-binding ligand (thalidomide) to an FKBP12F36V binding ligand (ortho-AP1867...commercially available in the near future, and we will provide an update with vendor and catalog numbers. As we...or Jay Bradner ([email protected]). Considerations when getting the dTAG system up and running...while quantitative proteomics experiments will provide the best confirmation of selective FKBP12F36V fusion...
  17. Antibodies 101: Secondary Antibodies

    Type
    Blog Post
    Published
    Dec. 21, 2021, 2:15 p.m.
    ...signaling molecules to identify each protein of interest, this gel-based method identifies proteins solely by... blog posts, then you likely already have a good idea of the basics of immunoimaging. A scientist conjugates...place over multiple days. Increased run time is considered one of the major drawbacks of the indirect method...interest - the secondary antibody needs careful consideration before selection. If all the primary antibodies...themselves able to approach immunoimaging assays more confidently, collect a broader array of data, and occasionally...
  18. What's New in CRISPR - November 2021

    Type
    Blog Post
    Published
    Nov. 18, 2021, 2:15 p.m.
    ...recently identified Cas12f systems from uncultivated archaea are much smaller and would be ideal for such...different labs have recently published work that provides a solution to this problem. A miniature CRISPR-Cas...editing with a hypercompact Cas12f1 and engineered guide RNAs Yong-Sam Kim’s lab also created a miniature...Biotechnology paper showcases an improved design of the guide RNA that caps the 3’ end with a structured RNA motif...sheet Resources on Addgene.org Read our CRISPR guide Find CRISPR plasmids by function Find recently deposited...
  19. All in a Twist: dsRNA

    Type
    Blog Post
    Published
    Feb. 2, 2023, 2:15 p.m.
    ...into agriculture as species-specific pesticides and insecticides, an advancement over previous chemical...which detect dsRNA in the cytoplasm and use it as a guide to complementary RNA sequence. Once a compatible...processes and functions, but they also have a darker side. When ssRNA engages one strand of a dsDNA molecule...if endogenously synthesized dsRNA finds its way outside of the mitochondria, the same inflammatory response...or anticipating this response are important considerations when using these reagents. RNA:DNA hybrids...
  20. CRISPR Meets Synthetic Biology: A Conversation with MIT’s Christopher Voigt

    Type
    Blog Post
    Published
    April 22, 2015, 2:06 p.m.
    ...assembling the toolbox needed for anyone to begin considering genetic engineering projects in a very big way...limitless number of DNA binding proteins with Cas9 guided by different promoters. The challenge in building...therapeutics, if you want to program a cell to identify and target a malignant cell, then you’d need the.... You couldn’t do it without repeating the same guide RNA twice. The second problem was the shape of the...also difficult to build larger circuits with many guide RNAs connected because the signal degrades at each...now? Voigt: We are working on this now, we have ideas, but so far nothing that has worked. I don’t have...
  21. Engaging with science and society at pgEd

    Type
    Blog Post
    Published
    Sept. 20, 2018, 12:17 p.m.
    ... religious affiliation, and ethnic or personal identity. We do this through a variety of activities, including...experiment, the case of Henrietta Lacks, the Havasupai incident, and the sterilization of women in marginalized...with different organizations and individuals, to identify ways of collaborating, and to organize events ...Having a broad interest and awareness of issues outside of your field of research will allow you to better...better engage these diverse audiences and to identify issues or topics that are matters of concern for ... future work in these areas, and in helping you decide whether you enjoy this kind of work. It is also...
  22. Educational Planarian Tools for Teaching Developmental Biology Techniques

    Type
    Blog Post
    Published
    May 24, 2018, 1:20 p.m.
    ... creatures commonly found in freshwater ponds, provide a good potential solution to this problem. Planarians...companion resource called “cutting class” which provides more detailed materials and protocol resources...synthetically made RNA (riboprobes) with modified nucleotides (for example, Digoxigenin-labelled Uracil) that...dsRNA feedings. Some of the phenotypes are not evident until after amputation. For example, the dramatic...odf2 gene knockdown results in an observable “sidewinder” phenotype that disrupts wildtype locomotion....dsRNAs into PR-T4P. The Sánchez lab protocol also provides step-by-step instructions for the “the bravest...
  23. Hot Plasmids May 2018 - Optogenetics, Decaffeination, Biosensors, and Fluorescent Protein Tools

    Type
    Blog Post
    Published
    May 15, 2018, 12:43 p.m.
    ...through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and ..., CRY2clust, was created by adding a 9-residue peptide to the C-terminus of human codon-optimized  cryptochrome...conditions. With its additional 9 amino acid peptide, the CRY2clust domain enables fast and reversible...original version containing CRY2 without the extra peptide. CRY2clust should prove a useful tool to further...supplied in the media, these bacteria are unable to divide. However, if fueled with caffeine and equipped ...Dronpa flanked a PKA substrate fused to the phosphopeptide binding domain FHA. The FHA1 domain binds to...
  24. Plasmids 101: Modular Cloning

    Type
    Blog Post
    Published
    March 12, 2024, 1:15 p.m.
    ...given peptide can easily be tested by generating Level 1 TUs with unique promoters, and the ideal phosphatase...behave in a cell. For unpredictable cases, MoClo provides two answers: first, sets of parts with characterized...for more complex CRISPR experiments (e.g., many guides/parts delivered) in certain model organisms. In...combinations of different candidate genes at once to identify the best cocktail of genes when the relationship...Resources on Addgene.org Addgene’s Modular Cloning Guide EcoFlex MoClo Kit CIDAR MoClo Kit MoClo Plant Parts...
  25. CRISPR 101: Targeting Non-Coding RNAs with CRISPR/Cas9

    Type
    Blog Post
    Published
    Nov. 14, 2024, 2:15 p.m.
    ...that are around 20 base pairs long. Using a single guide RNA (sgRNA) to create a double-strand break works...non-coding RNAs (lncRNA). lncRNAs are over 200 nucleotides in length and lack an open reading frame, so ... a number of different options. By carefully considering your ncRNA of interest, you should be able to...references Resources on addgene.org Addgene's CRISPR Guide Addgene's CRISPR 101 eBook CRISPR resources More...Doudna JA, Charpentier E. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity...051410-092902 Liu Y, Cao Z, Wang Y, et al. Genome-wide screening for functional long noncoding RNAs in ...
  26. Corralling and Cornering the Goldilocks Antibody

    Type
    Blog Post
    Published
    Aug. 9, 2022, 1:15 p.m.
    ...scientists’ pockets. They allow researchers to identify and isolate very specific biological targets. ...can then be used by thousands of scientists to confidently choose reliable and consistent antibodies for...antibodies, creating a potentially unlimited supply of identical antibodies (See Fig 1.). rAbs are a relatively...collaborates with these companies to create and provide general availability of their recombinant antibodies...creating a database for goldilocks antibodies and, alongside that, a publicly available 2D/3D mouse atlas from...atlas will enable scientists to have an intuitive guide for checking their staining and neuroanatomy without...
  27. Plasmids 101: FLEx Vectors

    Type
    Blog Post
    Published
    April 28, 2016, 2:30 p.m.
    ...using either loxP or lox511 sites, leaving two identical sites on one end of the DNA fragment (Figure 1...recombination event then excises the DNA between the identical loxP or lox511 sites (Figure 1, bottom). Since...only one loxP and lox511 site will remain on either side of the DNA fragment, any additional recombination...genetics, FLEx is currently being used to study a wide variety of in vivo conditional gene rescue experiments... silent until a cell or tissue-specific Cre is provided. Since the FLEx switch ensures Cre-dependent reporter...inverse Orientation), FLEx systems are generally considered "Cre-On" meaning that your gene of interest starts...
  28. Illuminating Epigenetics with A FRET Based Biosensor

    Type
    Blog Post
    Published
    Nov. 19, 2015, 3:30 p.m.
    ... of the DNA with a high frequency of C and G nucleotides). The conversion of cytosine to 5-methylcytosine... to study epigenetics Epigenetic research uses a wide range of molecular biologic techniques to further...enzyme digestion, DNA adenine methyltransferase identification, and bisulfite sequencing. However none of ...consists of one substrate (the histone-derived peptide) which can localise the construct specifically ..., which binds selectively to lysine-methylated peptides. This construct is in the middle of a FRET pair...When methylation occurs at the histone-derived peptide, the methyllysine binding domain causes a structural...
  29. Plasmids 101: Knockout/Knock-In Plasmids

    Type
    Blog Post
    Published
    Dec. 1, 2016, 3:30 p.m.
    ...breaks, in which nucleotide sequences are exchanged between two similar or identical molecules of DNA....homology to the locus of interest. To give you an idea of the process, we’ll walk through an experiment... gene have been cloned into the vector on either side of an antibiotic resistance gene. To avoid selecting...HSV thymidine kinase (HSV-tk) is included just outside one of the homology arms. When we select cells ...creating knockout animals or cell lines, please consider sharing them by depositing with Addgene! Figures...
  30. Multiplexed Capture of Promoter-enhancer 3D Chromatin Structures Using CRISPR

    Type
    Blog Post
    Published
    July 2, 2020, 12:40 p.m.
    ...While “pictures” generated with current 3C methods provide useful information about chromatin interactions...streptavidin IP. Biotinylated dCas9 goes along for the ride throughout all of these steps, until its connection...off-target sites. Long-range chromatin interactions identified with the multiplexed CAPTURE 2.0 largely replicated...replicated interactions previously identified with the original CAPTURE method. Both CAPTURE methods outperformed...both the number of unique chromatin interactions identified and the level of on-target enrichment. 2. Determining...on Your CRISPR Background with Addgene’s CRISPR Guide Page ...
  31. Chromoproteins: Colorful Proteins For Molecular Biology Experiments

    Type
    Blog Post
    Published
    Feb. 4, 2020, 2:15 p.m.
    ...fluorescent proteins and luminescence have been widely used in biological research for a long time, chromoproteins... give colors in ambient light. In contrast, the widely used green fluorescent protein (GFP) gives a bright...early 2000s, a handful of chromoproteins were identified in sea anemone (Chan et al., 2006). Why do these... sequencing are more definitive, but visual identification is a good place to start before taking on more...could get around this problem. There is no single “ideal” chromoprotein plasmid that combines the most desirable...is an orange light-absorbing chromoprotein that Hideji Murakoshi’s lab developed as an acceptor for fluorescence...
  32. AAVs in Retinal Gene Therapy

    Type
    Blog Post
    Published
    July 31, 2018, 12:55 p.m.
    ...was in its infancy, but the eye was identified early on as an ideal target. It is an easily accessible ... time advances in human genetics led to the identification of several disease-causing genes, including...However, AdV was abandoned early on due to its considerable immunogenicity and its transient expression....have broad tropism in the eye. AAV-2, the first identified serotype and the one used in Luxturna™, can efficiently...therapies is impressive: clinical trials for choroideremia, X-linked retinitis pigmentosa, achromatopsia...
  33. AAVs CREATed for Gene Delivery to the CNS and PNS

    Type
    Blog Post
    Published
    Sept. 28, 2017, 2:01 p.m.
    ...an IV injection is an ideal way to deliver AAV to the PNS. It’s a happy accident that AAV.PHP.S targets...barrier - only those that cross the barrier can be identified by PCR later. The PNS presents a different problem...Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. Nature biotechnology...Additional Resources on the Addgene Blog Important considerations when using AAVs Learn more about using AAV ...Vectors to use with your research. Visit Our AAV Guide Page for info on AAV components, common uses of ...
  34. Don’t FRET: Bimolecular Fluorescence Complementation Makes Visualizing Protein-Protein Interactions Easy

    Type
    Blog Post
    Published
    Aug. 27, 2020, 1:15 p.m.
    ...validated for BiFC (Kodama and Hu, 2012). Having a rough idea of how your PIPs might interact will allow you to...each PIP and empirically test which combination provides the best fluorescent signal. As for linker sequences...experiments. In either case, overexpression should be avoided because it can generate high background fluorescence...critical to the success of BiFC experiments. The ideal control is a mutated variant of one or both of your...that you empirically test a number of mutants to identify those that inhibit BiFC in your cellular system...endogenous PIPs is expressed at increasing levels alongside your BiFC constructs. If your PIPs actually interact...
  35. Antibodies 101: Producing Recombinant Antibodies

    Type
    Blog Post
    Published
    Aug. 13, 2024, 1:15 p.m.
    ... Protocol Addgene's Video Antibody Purification Protocol Addgene's Antibody Guide References Trimmer JS...the periplasmic space to be oxidized and form disulfide bonds (Frenzel et. al., 2013). If you’re using...stained, the heavy and light chains become visible alongside your ladder and a protein standard. The density...calculated using imaging software. Any bands on the gel beside the heavy and light chains can also be measured...multiple contaminating bands or a few strong ones, consider increasing the number of washes performed during...
  36. Deep Dive: Fixing and Permeabilizing for Immunofluorescence

    Type
    Blog Post
    Published
    Aug. 30, 2022, 1:15 p.m.
    ...method into six general steps and outlined the considerations to be made during each step. Now that you know...take a slightly deeper dive into those steps and provide you with more details to help you plan and optimize.... If your target is already on the extracellular side of the membrane, then this step may not be necessary...binding to any target protein that is still on the inside of the cell. However, assuming you do need to permeabilize... of fixatives or permeabilizers, but how do you decide which ones to use? Here are some tips for making... then optimizing from there is a good option.  Consider your target - if you are studying a membrane protein...
  37. Minigenomes - a Safe Way to Study Dangerous Viruses Like the Ebola Virus

    Type
    Blog Post
    Published
    March 17, 2016, 2:30 p.m.
    ...Vector Plasmids Read Our Lentiviral Vector Guide Read Our AAV Guide  ...the cell when the appropriate viral proteins are provided in trans (see Other Important Components of EBOV...separate plasmids and are co-transfected into cells alongside a plasmid encoding the minigenome. These genes...The power of reverse genetics. Springer Berlin Heidelberg, 2004. 1-41. PubMed PMID:15298166. 3. Hoenen,...Posts on Viral Vectors Check out Our Scientist's Guide to Ebola Contribute to the Addgene Blog Resources...
  38. The Importance of a Fun Workplace: Company Culture at Addgene

    Type
    Blog Post
    Published
    Sept. 3, 2015, 2:30 p.m.
    ...mission by hard work, we genuinely enjoy each other’s ideas and company. The Addgene summer picnic This past...though she generously offered. Instead we picniced outside of our new office space on the nicely manicured...together is that when it’s time for fun, everyone is confident that their teammates and project collaborators...events over the years. To keep the organizational side of things from taking too much of your time, scroll...(or more popularly- cookies). 3. Do something outside of your ordinary environment Team building events...something fun happening! Addgene actually has chimes outside of our break room. A ring of the chimes means something...
  39. Bacterial Toxin-antitoxin Systems as Molecular Biology Tools

    Type
    Blog Post
    Published
    Nov. 1, 2018, 12:35 p.m.
    ...substances are part of toxin-antitoxin systems that are widely present in bacteria. They consist of a toxin which...systems have been used as biological tools for a wide range of applications in molecular biology or in...Applications of ccdB in plasmid cloning Perhaps the most widely used application of CcdB is GatewayTM cloning, ...toxin-antitoxin systems and their applications MazE/MazF Aside from CcdB/CcdA, there are many protein-based toxin-antitoxin... endonucleases cleave DNA at or near specific nucleotide sequences. To counter this, methyltransferases...methyltransferases add methyl groups to bases at specific nucleotide sequences, preventing the cognate restriction enzyme...
  40. Plasmids 101: Codon usage bias

    Type
    Blog Post
    Published
    Sept. 27, 2018, 1:09 p.m.
    ... DNA sequence to encode your peptide of interest and produce that peptide in your organism of choice. ...as easy as it sounds. Even for relatively short peptides, there can be many possible ways to encode them... the native organism.” This is possibly a better idea and has been used successfully in the past (Angov...2008), but there are still many more features to consider when designing a full gene. A non-exhaustive list...PubMed Central PMCID: PMC4794256. This review provides a great overview of codon usage bias 8. Tuller...
  41. Overcoming the AAV Size Limitation for CRISPR Delivery

    Type
    Blog Post
    Published
    Sept. 16, 2020, 1 p.m.
    ...600 Cas9 orthologs and found that they could be divided into two groups: longer orthologs approximately...Split inteins are a pair of naturally occuring polypeptides that, when at the ends of two proteins, mediates... CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566:218–223 . https://doi.org...2014) Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell 156:935–949. https://doi.org...doi.org/10.1038/s41467-018-08224-4  Swiech L, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, Sur... Resources on Addgene.org Check out our CRISPR Guide Find CRISPR Plasmids ...
  42. Hot Plasmids - August 2020

    Type
    Blog Post
    Published
    Aug. 18, 2020, 1:15 p.m.
    ...through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and ...might not localize to the right places, which can provide misleading information on where exactly a structure... via BirA and AviTAG. pMAK contains the signal peptide of MBP, followed by the desired nanobody (NB) sequence...sequence, an AviTAG, and 6xHis tag. The MBP signal peptide allows the NB to be exported to the periplasm of... the expression of nearly any gene via specific guide RNA (gRNA) sequences. But these approaches rely ... viral aliquots from our plasmid collection to provide ready-to-use viral preps. Here are some of the ...
  43. Bioinformatics at Addgene

    Type
    Blog Post
    Published
    July 14, 2022, 1:15 p.m.
    ...have accumulated more than 300,000 individual nucleotide sequences. More than half of these sequences ...assembly algorithms meant that we already had a clear idea of the necessary steps to perform:      ...entire package to run. The small, portable system provided by a container is sequestered from other programs...container because of the reproducibility containers provide and for convenient compatibility with our internal...complete pipeline however, required more than just identifying criteria that we needed. Prior to using Nextflow...that the desired data was available so we felt confident we were using the input and output to link the...
  44. Hot Plasmids - November 2023

    Type
    Blog Post
    Published
    Nov. 14, 2023, 3:35 a.m.
    ...with no additional off-target edits, making them ideal for size-limited AAV delivery. PE6c and PE6d are...modalities and has the potential to reduce negative side effects. This platform offers a promising approach... TransitID By Mike Lacy Proximity labeling can identify protein interactions or map a local proteome, ...dual-enrichment and mass spectrometry workflow identifies proteins bearing both labels (which had therefore...locations. C) Enrichment of dual-labeled proteins identifies proteins that had been trafficked from the “source...bioRxiv, under CC-BY-NC 4.0 license. This system provides a unique new way to record and quantify the dynamics...
  45. New Acoustic Reporter Genes: Ultrasound Imaging of Gene Expression

    Type
    Blog Post
    Published
    Jan. 24, 2023, 2:15 p.m.
    ...Fluorescent and bioluminescent reporter genes are widely used to study gene expression in cells. But these... by tissue. Ultrasound, on the other hand, is a widely available and inexpensive imaging modality with...high spatial and temporal resolution, making it ideal for visualizing gene expression in vivo.  But what... be easily expressed heterologously by bacteria inside the body. So we screened gas vesicles gene clusters...origin of replication (p15A) worked best under a wide range of inducer concentrations (0.1-1% L-arabinose...bARGSer-expressing E. coli. The GV-specific ultrasound signal inside the tumors was overlaid with the anatomical B-mode...
  46. Deep Dive: qPCR

    Type
    Blog Post
    Published
    Sept. 29, 2022, 1:15 p.m.
    ...others can provide you with the highest form of flattery - imitation! Use the MIQE guidelines (Bustin, ...primer and be at least 25 bp away from each primer, ideally located close to either the forward or the reverse...across the plate is fine; a 5% positive error on one side and a 5% negative error on the other will introduce...triplicates in multiple configurations can help you identify pipetting or evaporation errors. And if time allows...look at their 551 page e-book on applying MIQE guidelines! With these kinds of resources, you will soon...Shipley GL; Vandesompele J; Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative...
  47. Introducing Addgene's Microbiology Pages

    Type
    Blog Post
    Published
    June 13, 2016, 7:08 p.m.
    ...and find our guides, plasmid kits and other resources for microbial research. Kits, guides, plasmids, ...biology, gene cloning and expression, as well as guide pages for Synthetic Biology and Bacterial Expression... our Genome Engineering Overview and our CRISPR guide to find out how to use genome editing techniques...Expression and Insert Species filters on the right-hand side of the search page to narrow your keyword search...
  48. Summer Fun at Addgene!

    Type
    Blog Post
    Published
    May 12, 2022, 1:15 p.m.
    ...Twitter for the official launch!  Videos Look out for our next protocol video, “Western blots,” coming soon...also be building our video library all summer long, with additions to our other video series.   And if you...as excited as we are! Come join us in our blog, video, and social media endeavors - in between some much-deserved...
  49. Adeno-associated Viruses (AAVs) for Genome Editing

    Type
    Blog Post
    Published
    March 27, 2018, 1:32 p.m.
    ...frequency three orders of magnitude higher than identical targeting vectors delivered through transfection...AAV effect remains unclear, it is likely not a coincidence that the AAV genome is composed of single stranded... selection, individual gene edited clones are identified by PCR. Then, if necessary for subsequent experiments...disadvantages to the AAV-based approach that must be considered when deciding whether to use AAV or CRISPR for...for the generation of knockins, it is not always ideal. Because of these limitations, the AAV approach ...variety of cell types, now you know that AAVs can provide a powerful boost to genome editing experiments....
  50. Treating Muscular Dystrophy with CRISPR Gene Editing

    Type
    Blog Post
    Published
    Jan. 26, 2016, 3:30 p.m.
    ...for DMD treatment. Clinical trials have used oligonucleotide exon skipping (OEN) to remove mutated exons... dystrophin transcript. Unfortunately, the oligonucleotides only modestly improve muscle function, and...Dystrophin and genome editing Since complex oligonucleotide treatment comes with many challenges, researchers...rigorously examined over a long period of time. High fidelity Cas9s such as eSpCas9 and SpCas9-HF should be ...Covello G, Denti MA. Exon-skipping antisense oligonucleotides to correct missplicing in neurogenetic diseases... Resources on Addgene.org Check out Our CRISPR Guide Pages Find CRISPR Plasmids for Your Research Find...
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