Skip to main content
Addgene

Enter a sequence to perform a BLAST-based search of Addgene plasmid sequence databases.

In Category

We narrowed to 749 results for: Tro;

Showing: 151 - 180 of 749 results

  1. Viral Vectors 101: Voltage Indicators

    Type
    Blog Post
    Published
    Jan. 30, 2024, 2:15 p.m.
    ...action potentials, muscle contractions, and the control of voltage gated ion channels all depend on transmitting...been successful even at the single neuron level in vitro. In vivo monitoring has also been achieved with ...effective at the single cell level as they are in vitro. Factors like photobleaching, lack of red-shifted...rhodopsin. FP-fusion to rhodopsin resulted in electrochromic FRET capable GEVIs, with rhodopsin quenching...membrane as well. Another flavor of these tools is Voltron, which uses rhodopsin as the voltage sensing component...genetically encoded component is delivered in vivo or in vitro and a small molecule is added exogenously to measure...Optogenetics Fluorescent Proteins 101: Introduction to FRET ...

  2. Antibodies 101: Flow Compensation

    Type
    Blog Post
    Published
    May 16, 2024, 1:15 p.m.
    ... APC control, with APC and APC-CY7 plotted against each other. Since it is a single-color control, you...example with single color control. Flow plots showing an APC single-color control sample before (A) and after...recommended to start compensating with single-color controls before moving onto your experimental samples. ...samples without needing to use your single-color controls as a starting point. Applying compensation to ...experimental samples as they did with your single control samples: if the population needs to be shifted ...School.   More resources on the Addgene blog Introduction to Gating in Flow Cytometry Antibodies 101: ...

  3. New Viral Vectors - March 2024

    Type
    Blog Post
    Published
    March 5, 2024, 2:15 p.m.
    ...AAV PHP.eB Controls Wilson New viral vector pENN.AAV.EF1a.eGFP.WPRE.rBG AAV PHP.eB Controls Wilson New...pAAV-CaMKIIa-EGFP AAV PHP.eB Controls Roth New serotype pAAV-hDlx-Flex-dTomato-Fishell_7 AAV2 Controls Fishell New serotype...  AAV PHP.eB Controls Gradinaru New serotype pAAV-CaMKIIa-mCherry  AAV PHP.eB Controls Deisseroth New...New serotype pAAV-Ef1a-mCherry  AAV PHP.eB Controls Deisseroth New serotype Looking for more viral...

  4. Great Results Start with Great Standard Curves

    Type
    Blog Post
    Published
    Aug. 15, 2024, 1:15 p.m.
    ...unknown sample. To do this, you serially dilute a control sample of known concentration and measure a specific...example, a BCA assay uses a serial dilution of a control protein, incubated alongside an unknown sample ... absorbance of both is then measured on a spectrophotometer and concentration versus absorbance is plotted... a standard curve by serially diluting a known control sample, called a standard. The ideal standard curve...curve accordingly.    Figure 1: A 1 mg/mL control is diluted in a series ranging from 1:2 to 1:32... for each run. To validate, include a positive control of known concentration in the experiment and use...  Include both a standard curve and a positive control in every run.  When setting up your dilution series...

  5. CRISPR 101: Ribonucleoprotein (RNP) Delivery

    Type
    Blog Post
    Published
    Sept. 6, 2018, 12:02 p.m.
    ...28b-Cas9-His from Alex Schier’s Lab. gRNAs can be in vitro transcribed from ssDNA, which can be generated by... advantage has allowed scientists to perform in vitro and in vivo CRISPR studies in experimental systems... common techniques for delivery of RNPs is electroporation (A in the figure above), which generates pores...through a process known as CRISPR-EZ (CRISPR RNP Electroporation of Zygotes) (Chen et al. 2016). For CRISPR ...CRISPR experiments that involve HDR, electroporation can be combined with cell-type specific reagents in a ...approach using RNPs has recently been described in vitro, with the hope of eventually using this method for...genome editing by CRISPR ribonucleoprotein electroporation of zygotes." Journal of Biological Chemistry...

  6. Uncovering Ancestral Bias in CRISPR Research

    Type
    Blog Post
    Published
    Nov. 29, 2022, 2:15 p.m.
    ...only a few, very strong associations.   Unexpected results Their results showed 96 strongly correlated genetic...may be the result of a technical artifact that introduced an ancestry bias into their experiments instead... prevent Cas9 from cutting, both of which can introduce significant bias into the results. But the reference...mapped to a SNP would be ignored. Working with Lia Petronio and Katherine Huang from Broad’s Pattern team,... of ancestral bias into genome-wide screens, introducing bias into all work based on these and any other...an ancestry group what is actually an artifact introduced by bias within the design of the experiment or...Noorbakhsh, Isabella Boyle, Joshua Dempster, Lia Petronio, Katherine Huang, Alham Saadat, Thomas Green, ...

  7. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    Published
    June 4, 2024, 1:15 p.m.
    ...very weakly, most likely through unstructured electrostatic interactions. It also can’t recognize PAMs, ... present in the sample. Other techniques, like electron microscopy and FRET, can offer more information...well described in the closed conformation, recent electron microscopy studies have also found Cas9:RNA complexes...loops 2 and 3 are not strictly necessary for in vitro cleavage, but they improve cutting efficiency and...pairing in the seed sequence.   Figure 6: Electron microscopy structure of S. pyogenes Cas9 bound...structure (left, PDB ID 4ZT0) with Cas9:RNA:DNA electron microscopy structure (right, PDB ID 7S4X), viewed...conformational state of the HNH domain also allosterically controls RuvC activity through a hinge region between the...

  8. Plasmids 101: Shuttle Vectors

    Type
    Blog Post
    Published
    May 20, 2025, 1:15 p.m.
    ...the vector to survive while the auxotrophic cells die. Some auxotrophic selection markers can be used across...autonomously replicating sequence (ARS), a partial centromere sequence (CEN), both, or neither, depending on...autonomously replicating sequence (ARS) a partial centromere sequence (CEN) both or neither ...depending ...choose to ensure it works in your host species! Auxotrophic selection Another option is to use a different...different method of selection entirely. Auxotrophic selection relies on the host organism being unable to synthesize... example, in both S. cerevisiae and E. coli. Auxotrophic selection is especially common in yeast experiments...spontaneously develop resistance to selection toxins. Auxotrophic selection is useful for producing stable mammalian...

  9. Save Time with Transient Plant Leaf Transformations

    Type
    Blog Post
    Published
    July 25, 2019, 12:03 p.m.
    ...tobacco. Studying gene function in C. roseus is strongly limited by the availability of methods. Infection...check for GUS-like activity of your tissue. Run a control with Agrobacterium lacking the GUS gene since plants...promoter activity, for example. Useful positive controls could include: pSB96 - pL2_pSB90_2x35S::fLUC-I...days in the dark after the transformation. Use introns Plant promoters can be recognized or leaky in Agrobacterium...Agrobacterium, but not the plant. For example, we have seen strong expression of the GUS gene with the commonly used...Agrobacterium. This can be easily avoided by the use of introns, which will be removed from the transcripts in ...plants, check out this interview with the Nicola Patron, who shared the MoClo plant kit via Addgene. For...

  10. New Tools Enable CRISPRa for Neuroscience Applications

    Type
    Blog Post
    Published
    July 2, 2019, 12:51 p.m.
    ...spatiotemporal control over its expression. Constitutive or inducible Cre recombinases can be introduced by AAV...SPH mice CRISPRa has largely been limited to in vitro settings due to the large size of Cas9 activators...in vivo, they should be screened for activity in vitro and then packaged into AAV for in vivo delivery....developed neuron-optimized lentiviral vectors for in vitro and in vivo CRISPRa (Savell et al., 2019). This ...immediate-early gene Bdnf, which encodes brain-derived neurotrophic factor (BDNF). Bdnf is expressed early in response...of other CNS cell types, including microglia, astrocytes, and oligodendrocytes, provided that reporter...preferable for individual gene activation in select in vitro and in vivo applications, the tools described above...

  11. Important Considerations in Optogenetics Behavioral Experiments

    Type
    Blog Post
    Published
    Oct. 1, 2015, 2:30 p.m.
    ...  Historically, ICSS was done by implanting an electrode and non-specifically electrically stimulating ...opposite chamber) [2]. Laser activation is usually controlled automatically using motion capture software such...apply. Testing stimulation First, In lieu of electrophysiology, it would be convenient to know if you are...targeted brain region after stimulation compared to controls without Chr2. c-Fos is a reliable and widely used...easiest way to resolve these issues is with electrophysiology. Concluding thoughts and moving beyond the...PMC4181379. 3. Kheirbek, Mazen A., et al. "Differential control of learning and anxiety along the dorsoventral ...silencer: development and application to optogenetic control of non-human primate cortex." Frontiers in systems...

  12. Let There Be LITE Plasmids

    Type
    Blog Post
    Published
    Nov. 21, 2013, 3:56 p.m.
    ...Under those optogenetic controls, gene expression levels reliably increased in vitro by a factor of 10 to...what the LITEs now enable. In a Nature paper introducing the optogenetic tool, Konermann and Zhang showed...populations. They demonstrated use of the LITEs to control gene expression in mouse neurons and in the brains...both quickly and significantly. Genes under LITE control showed a rise in transcription in as little as ...to establish it as “a novel mode of optogenetic control of endogenous cellular processes." The LITE system... Reference: Silvana Konermann et al. "Optical control of mammalian endogenous transcription and epigenetic...

  13. Plasmids 101: Biotinylation

    Type
    Blog Post
    Published
    Nov. 15, 2018, 1:50 p.m.
    ...extremely strong affinity for one another. Actually the bond between them is one of the strongest noncovalent...that scientists began to exploit biotin and its strong interaction with avidin for molecular biology and...papers and webpages are listed below: EMSA (Electrophoretic Mobility Shift Assays) ELISA (Enzyme-Linked... biotinylate macromolecules of interest both in vitro and in vivo. Biotinylation reagents Biotin’s exposed...attached to a photoreactive arylazide group. Under strong visible light, the arylazide group becomes reactive... Krijgsveld, J., Katsantoni, E., Heck, A., … Strouboulis, J. “Efficient biotinylation and single-step ...Schwartz, S. A. “Biotinylated probes in the electrophoretic mobility shift assay to examine specific dsDNA...

  14. Identifying Sequence Elements with SnapGene's Feature Database

    Type
    Blog Post
    Published
    Dec. 21, 2017, 2:06 p.m.
    ...place the most important controls front and center, and make specialized controls available when needed....sequence and display frequently used genes and control elements. Development of this tool required creating... DNA sequence has changed. Identifying plasmid control elements Coding sequence features are relatively...relatively straightforward to define, but for control elements such as promoters and transcription terminators...obvious. We found that the annotated boundaries for control elements in commercial plasmids were inconsistent...how we use SnapGene during the plasmid quality control process Check out full plasmid sequencing at Addgene...

  15. Technique: Probe Phage Genomes for Host Binding Proteins

    Type
    Blog Post
    Published
    Sept. 29, 2016, 2:30 p.m.
    ...or Salmonella, or any cells that bind strongly to nitrocellulose, over-incubation of plates can lead to...forcing DNA through a small opening using compressed nitrogen gas; this shears DNA at random locations and allows...containers that can easily be attached with a hose to a nitrogen gas tank with a pressure regulator. Other methods...cells, isolated colonies will be lifted onto nitrocellulose membranes and exposed to IPTG in order to induce...release recombinant proteins directly onto the nitrocellulose for subsequent probing for cell-binding activity...First, cut out 20 Petri dish-sized circles of nitrocellulose membrane and press each gently down onto a ... helpful to spot this protein directly onto nitrocellulose and carry out the steps from blocking the membrane...

  16. Generating Mouse Models Using CRISPR/Cas9

    Type
    Blog Post
    Published
    July 12, 2016, 2:30 p.m.
    ...1980s, gene targeting technology was invented to introduce specific changes into the mouse genome. With these... early technologies, a researcher would first introduce a mutation into a mouse embryonic stem cell (ESC...chromatogram showing the telltale signs of a mutation introduced by CRISPR. The sequence started clean and then...handling embryos ex vivo, the components can be electroporated into the oviduct of pregnant females, a technique...gRNA, Cas9, and donor oligonucleotide can be electroporated into the mouse zygote (Qin et al., 2015).  ...targeting. CRISPR tools were recently used to introduce a 25 kb human gene into the mouse genome. However...Goodwin LO, Morgan JL, Juan WC, Roca X, Ong ST, Bergstrom DE (2018) Viable Mice with Extensive Gene Humanization...

  17. Plasmids 101: Restriction Cloning

    Type
    Blog Post
    Published
    Feb. 18, 2016, 3:42 p.m.
    ...on the left, your digested DNA (and undigested controls) are loaded at the top of the gel in wells positioned... uncut sample of each plasmid to help with troubleshooting if your digests don’t look as expected. Once...to insert. It is critical to set up a negative control ligation reaction with no insert DNA added. This...much less total DNA (<1ng) or if you are having trouble getting colonies, you might want to use higher ...to be very large (>10kb) you might want to use electro-competent cells instead of the more common chemically-competent...minimum, two transformations after a ligation: 1. Control Transformation containing the ligation mixture ...see any colonies, you should conduct a positive control to ensure that your transformation worked. You ...

  18. New and Upcoming Viral Vectors - September 2019

    Type
    Blog Post
    Published
    Sept. 12, 2019, 1 p.m.
    ...will continue to add more controls, and have recently released these controls: pAAV-hSyn-DIO-EGFP (50457...sensors Optogenetics Recombinases And more! Control AAV For many AAV experiments, we recommend validating...aliquots in AAV1, AAV2, AAV5, AAV8, AAV9, and AAV Retrograde. You can also request the specific serotypes ...entire collection! We are expanding our entire control AAV inventory to give scientists access to a wide...AAV5 and 112677-AAVrg): The EF1a promoter directs strong, ubiquitous expression. This is a Cre-dependent... Email us or check our website to access them! Controls pAAV-hSyn-hChR2(H134R)-EYFP (26973-AAVrg) pAAV-hSyn-hChR2...

  19. Addgene-Seeding Labs plasmid grant round 3: microbial drug resistance and biofilms, antidiabetic plant components, visualizing brain injury - and a glowing robot fish

    Type
    Blog Post
    Published
    Nov. 27, 2018, 2 p.m.
    ...etiopathomechanisms of ischemic stroke, the most common type of stroke and the third leading cause of ...-Seeding Labs plasmid grant we are excited to introduce the 5 awardees and their research. These researchers... is necessary to improve tuberculosis care and control. In her current research, Sheen aims to identify...taraxacifolia (Willd), an annual herb of Western Tropical Africa typically known as wild lettuce. Aside ...of death and disability worldwide. An ischemic stroke occurs when arteries leading to the brain become ...of interesting combinations: biomedicine and astrobiology. During the last 11 years he has studied various...

  20. Antibodies 101: Isotypes

    Type
    Blog Post
    Published
    Oct. 19, 2021, 1:15 p.m.
    ...you can select an appropriate isotype control. An isotype control has the same constant heavy chain domain...heavy-chain constant region (see Antibodies 101: Introduction to Antibodies for a refresher). There are five...molecules are recruited by the antibody to help destroy and remove a pathogen. Different isotypes also ...doesn’t bind your antigen of interest. Isotype controls are used to make sure the staining you see is ... than nonspecific background staining. Isotype controls are used in antibody-based applications including...techniques that you can use antibodies for in our Intro to Antibodies post Check out our Antibodies 101:...

  21. 15 Years of Addgene: The Top 15 Plasmids

    Type
    Blog Post
    Published
    Jan. 8, 2019, 1:54 p.m.
    ...generation lentiviral packaging plasmid from the Didier Trono lab that expresses the HIV gag, pol, rev, and tet...pMD2.G. Find psPAX2. pMD2.G - Also from the Didier Trono lab is pMD2.G, a VSV-G envelope expressing plasmid...envelope protein for producing lentiviral and MuLV retroviral particles. It can be used with packaging plasmids...as pCMV-dR8.2 dvpr (lentiviral) or pUMVC (MuLV retroviral). Fun fact: published in 2003, this plasmid predates...generation lentiviral packaging plasmid from the Trono lab contains the rev gene. It’s meant to be used...generation lentiviral packaging plasmid from the Trono lab that contains the gag and pol genes. It also...shRNA. This scrambled shRNA is used as a negative control for mammalian RNAi experiments.  Find the scrambled...

  22. Viral Vectors 101: Biosensors

    Type
    Blog Post
    Published
    July 6, 2023, 1 p.m.
    ...The calcium is strong here….I can sense it….sound like a plot to an biology scifi movie? Or maybe it’...neurotransmitter, such as norepinephrine, or an electrolyte such as calcium. This varied component, which...For one, many viral platforms, such as AAV or retrovirus, can either permanently integrate and/or express...serotypes can be used to affect or determine viral tropism—the type of cells the viral particles infect. This... sensor, whether you choose lentivirus, gamma retrovirus, or AAV as your vehicle, we’ve got you covered...Resources References  Bhalla N., Jolly P., et al. Introduction to Biosensors. Essays Biochem. 2016 Jun 30;60... Susanna Stroik...

  23. CRISPR 101: Non-Homologous End Joining

    Type
    Blog Post
    Published
    April 16, 2015, 3:45 p.m.
    ...consequently the principal means by which CRISPR/Cas9-introduced breaks are repaired. The following factors are...ends tends to be the point where mutations are introduced. Repair of Cas9-induced breaks by NHEJ As illustrated...microhomologies”). NHEJ doesn’t obligatorily introduce indels. Given the end structure of the Cas9 DSB...hundreds of base pairs or more can simultaneously introduce a pair of chromosome breaks, and could result ...single strand break; when two such breaks are introduced near each other, in opposite strands. This “double...j.cell.2013.08.021 Waters CA, Strande NT, Pryor JM, Strom CN, Mieczkowski P, Burkhalter MD, Oh S, Qaqish BF...Video] Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens        ...

  24. Antibodies 101: Validation

    Type
    Blog Post
    Published
    March 24, 2022, 1:15 p.m.
    ...that antibody works as expected, you will see a strong antibody signal in the retinal sample, but little...you see a similar antibody signal between your control and your knock-out sample, you should be concerned...antibody binding in the transfected cells but not in control cells. But (there is always a ‘but’), you should...encoding this protein, which we will call Negative Control Gene (NCG) (A). Then you lyse the cells and run... your antibody (B). Your results show a lovely, strong band from the cells transfected with your protein...well as a third unrelated antibody as a negative control (A). The two antibodies to your protein of interest...sample using the antibody and then uses mass spectrometry to identify the captured proteins. If the antibody...

  25. When Fidelity Matters: A frank discussion about ligase fidelity

    Type
    Blog Post
    Published
    March 6, 2018, 1:49 p.m.
    ...phosphorylated DNA termini to 3 ́-OH DNA termini (1-4). In vitro, ligases (notably T4 DNA ligase) are critical reagents...circularization of dsDNA (6). Less commonly utilized in vitro, Taq DNA ligase will ligate only nicks (5-8). Taq...identifiable and quantifiable by capillary electrophoresis (CE) (see below). This method allowed screening...gene PCR-ligase detection reaction-capillary electrophoresis assay." Journal of clinical microbiology 45.6...PMC1933048. 16. Cheng, Changming, et al. "Electrochemiluminescent assay for detection of extremely rare mutations...mixed population of excess wild‐type DNA." Electrophoresis 34.9-10 (2013): 1415-1422. PubMed PMID: 23463388... PMID: 17466627. 25. Luo, Jianying, Donald E. Bergstrom, and Francis Barany. "Improving the fidelity of...

  26. 9 tips for a successful postdoctoral experience

    Type
    Blog Post
    Published
    Oct. 9, 2018, 12:21 p.m.
    ...anticipated outcomes? What are your controls? Will these controls enable you to interpret your results...e.g. an R01 from the NIH, in the United States) Strong letters of reference that attest to your talent...figures are missing? For example, are additional controls necessary? As you build your story, are additional...person makes time for you, as needed, this is a strong indicator that this person cares about your science... together, all of this means that you need to introduce yourself to and talk with more senior scientists...you and your research exposure. Use meetings to introduce yourself to and interact with the members of your...Medical Institute. His interests include the quality control of secretory proteins in the Endoplasmic Reticulum...

  27. Plasmid Tools for Microbiome Studies

    Type
    Blog Post
    Published
    June 27, 2019, 12:25 p.m.
    ...identified seven genera in in vitro experiments, possibly because in vitro conditions did not optimally...situ Conjugation (MAGIC). With MAGIC, scientists introduce an Escherichia coli donor strain into the microbiome...antibiotic selection. The team tested this system in vitro and in vivo. They identified cells from 19 genera...from different bee species. BTK can be used to introduce fluorescent markers to visualize localization ...protein. The expression of this fusion is under control of the arabinose-inducible promoter. Cells are ...showed that this method can be used for both in vitro and in vivo studies. Find distributed cell division...

  28. Stabilized Bacterial Promoters: Constant Gene Expression at any Copy Number

    Type
    Blog Post
    Published
    Sept. 4, 2018, 12:53 p.m.
    ...eliminate fluctuations due to copy number by introducing genes of interest into the chromosome. But this...input signal that both positively and negatively controls the output. In this case, plasmid copy number ...gene increases its expression. However, if you introduce negative regulation by using a promoter that is.... placed a trans-acting RepA protein under the control of IPTG. Because RepA is a plasmid replication ...Segall-Shapiro et al. placed the genes under the control of a constitutive promoter and then moved them ...decreased. But when the genes were placed under the control of a stabilized promoter, deoxychromoviridans titers...the joys of a p-value < 0.05, having such fine control of gene expression is useful for many metabolic...

  29. Human Germline Editing Using CRISPR

    Type
    Blog Post
    Published
    Aug. 10, 2017, 2:19 p.m.
    ...autosomal dominant mutation in MYBPC3 that leads to hypertrophic cardiomyopathy. An adult male with a heterozygous...containing Cas9 and two different gRNAs, and electroporated them with an ssODN repair template in induced...wild-type copies of MYBPC3 (versus 47.4% of untreated controls.) 27.6% of embryos carried indels at the mutation...blastocyst stage at similar rates to untreated controls. Ma et al. performed sequencing of 23 potential... conducted whole genome sequencing in selected control and CRISPR-Cas9 injected embryos. In all cases,...challenging for homozygous mutations. Moreover, introducing new DNA seems impossible with current tools, ...applicable in many situations. In the case of hypertrophic cardiomyopathy and other genetic disorders, ...

  30. Special Delivery: Fluorophore Targeting for FRET Studies

    Type
    Blog Post
    Published
    July 19, 2016, 2:30 p.m.
    ...needed and when is it not? What are the proper controls needed to pressure-test your FRET assay to make...pyrrolysyl-tRNA synthetase Mammalian Cells pCMV-DnpK dinitrophenyl hapten Mammalian Cells pANAP AnapRS Mammalian...commercially available as Lumio Green and Lumio Red from Invitrogen (now ThermoFisher Scientific). These reagents...molecular distances (see Table). However, proper control experiments are needed to establish the dynamic...These experiments include producing a positive control construct where the donor and the acceptor fluorophore... each other on the same protein and a negative control experiment conducted on donor-only labeled protein...biarsenical− tetracysteine motif determined by NMR spectroscopy." Journal of the American Chemical Society 131.13...
Showing: 151 - 180 of 749 results