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  1. How to Deposit Your Plasmids with Addgene

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    Blog Post
    ... next insert. Repeat as needed for more inserts. When you are finished entering your gene/insert data,...cloning a gene/insert into it. Empty backbones often contain epitope tags or fusion proteins that are appended...within your insert (or targeted by a gRNA/shRNA) and select the species that the gene or insert sequence ...include the total size of the insert and the GenBank ID associated with your insert. Pro Tip! If the correct...of the insert (when cloned into the vector backbone). If your plasmid has more than one insert, click .... For instance, if your plasmid is designed to allow you to produce large amounts of your insert in E....it. If your plasmid has multiple inserts, enter details for each insert individually.   Figure 9: Add ...
  2. Plasmids 101: Screening Strategies Used in Plasmid Cloning

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    Blog Post
    ... either side of the expected insert. If the plasmid contains your insert, you will see two bands: one ...another enzyme that cuts within the insert. If the plasmid contains the insert, you will see two bands but if...the plasmid contains the insert and no PCR product if the plasmid does not contain the insert. If you’re...but it won’t tell you whether the vector contains the gRNA insert or not. A blue-white screen, however, ...sized bands depending on whether the plasmid contains your insert of interest or not. For example, choose ...the other representing the insert. If the plasmid doesn’t contain the insert, you will just see the vector...PCR to detect your insert, either by using primers that are specific to your insert or by using primers...
  3. Troubleshooting and Optimizing a Western Blot

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    Blog Post
    ...isolating proteins from a specific compartment. If your proteins are nuclear- or DNA-binding proteins, you ...step: protein degradation, incomplete lysing/insoluble proteins, and protein aggregation. Protein degradation...gel box. If overheating remains an issue, which can happen with large proteins, try lowering the voltage...transferring are smaller proteins going completely through the membrane or larger proteins not transferring completely...sizes for different proteins: try using a 0.2 µm (psi) membrane for small proteins (< 15 kDa) and a 0.45...which works better for small and medium proteins. If your proteins are compatible with electroblots/dry ...migration of smaller proteins through the membrane while increasing the ability of proteins to stick to the...
  4. Technical Design of a Western Blot

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    ...primary antibodies conjugated to fluorescent proteins, instead of the more common chemiluminescent methods...or β-mercaptoethanol.  Denaturing proteins To denature your proteins, you'll want to use SDS and either...-life; can alter proteins due to high pH Bis-tris 6–400 kDa MES for proteins <40 kDa 180 V, ...weight proteins Long running time   It’s important to note that Bis and Tris gels run proteins in different...They work well for proteins of most sizes and are worth considering if your proteins of interest vary wildly...protein you are expecting.  Fluorescent proteins Fluorescent proteins, while more expensive, allow for multiplexing.... Protein preparation Before you can blot your proteins, you’ll need to lyse and denature them. If you...
  5. An Integrin Antibody Toolkit from IPI

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    Blog Post
    ... the Institute for Protein Innovation (IPI), a Boston-based, nonprofit protein research institute, partnered... closed states, integrins are inactive, with low affinity for ligands. When integrins interact with extracellular...the role of specific integrins in cellular processes.   Figure 1: Integrins can shape into three...recognition site for one subfamily of integrins, the RGD-binding integrins. Six of the 11 IPI antibodies contain...Targeting integrins in the lab The Ha and Springer labs recently showed RGD-binding integrins demanded ...RGD-binding integrins, individually and in combination, showing that among the three αV integrins expressed...Integrins are essential cell surface receptors involved in complex signaling pathways and the linkage...
  6. Changing Labor Laws Bring Increased Postdoc Wages

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    ...wages, overtime tracking? What are institutions doing? Institutions are now preparing to comply with the...resource on what institutions are actually doing (using the list of 340 institutions with postdocs in .... Most institutions suggest that postdocs should be paid according to the National Institutes of Health...In 2014, 89% of institutions had a minimum salary policy: of those, 51% of institutions set their postdoctoral...should be on the lookout for what their institutions, or institutions they're thinking about applying to, ...salaries will have to double at some institutions; and that institutions which can more easily provide bridge...scientists and those in technical roles. Therefore, institutions are responsible for ensuring that either all...
  7. Avoiding the Dark Side of Fluorescent Protein Fusions with mOX FPs

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    ...integral membrane proteins and membrane associated proteins (i.e. GPI-anchored proteins), which are more... National Institutes of Health and he is currently an Associate Professor at Albert Einstein College of...tagging to detect proteins expressed from cloned genes: deletion mapping functional domains of Drosophila ...Fluorescent Proteins Browse Our Fluorescent Protein Pages Find the mOX Fluorescent Proteins at Addgene  ...to many microscopy experiments with fluorescent proteins (FPs) localized to compartments other than the... a resident endoplasmic reticulum (ER) protein instead localizes to the cytoplasm? Or more troubling, ...approximately 40% of human (and most eukaryotic) proteins localize to chemically distinct subcellular environments...
  8. Visualizing Protein Turnover In Situ

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    ...incorporated into newly synthesized proteins instead of methionine. The labeled proteins can be detected using click-chemistry...turnover of individual proteins in situ.  For the visualization of specific proteins in situ immunocytochemistry...audiences. Right now, she is a science instructor at The Innovation Institute in Boston. When Eugenia is not ...protein is decreased in Alzheimer’s disease patient’s brains. However, it is not known why or how this happens...degradation. These processes control the abundance of proteins in cells. Homeostatic regulation of protein abundance...type. However, we cannot distinguish new from old proteins within that pool. Therefore, it is not possible...used to facilitate the visualization of specific proteins in cells. Tagged protein can easily be overexpressed...
  9. Uncertainty about Labor Law Brings More Uncertainty to Postdoc Wages

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    ...were at institutions focused only on tracking hours, and 22% of postdocs were at institutions where no... of some public institutions) to cancel plans to raise salaries. What are institutions doing after the...planning unionization at their institutions. One clear message that institutions have sent, with the lack of...their institution is doing from Future of Research over social media, not from their institution), is ...raise were: postdocs at institutions like Stanford and the Whitehead Institute, where salaries had already...street from these institutions) are raising salaries. Postdocs at the Salk Institute in La Jolla California...This post discusses how a nationwide injunction against the FLSA is affecting universities' decisions to...
  10. Antibodies 101: Immunoprecipitation

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    ...interest. Tagged proteins are typically expressed at much higher levels than endogenous proteins. Data obtained...Immunoprecipitation (IP) uses immobilized antibodies, or immunoglobulins, to isolate a specific protein out of a complex...study how a target protein interacts with other proteins or nucleic acids. Read on to learn more about ...optimized strategies for differing amounts of target proteins or antibody bonding strengths.    . Steps...from cells or tissues contain a complex mix of proteins seen as green squares, purple circles and blue...collected by centrifugation or a magnet. 4) Unbound proteins are washed away. 5) The target protein is eluted...eluted.     In the first method, an antibody against a target protein is immobilized, or tethered, on...
  11. Proximity Labeling: A Powerful Tool for Protein Complex Purification and Proteomic Mapping

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    ...interactions as well as be used for both soluble and insoluble proteins, which can be a challenge for classic antibody...can take hours to label proteins and APEX2, although it can rapidly label proteins, requires H2O2 which ...interacting proteins in one simple experiment. PCA is an in vivo technique where two proteins are fused ...interaction of two proteins while also biotin labeling and purifying additional proteins from a complex of... and an RNA component that contains an RNA motif of interest. Any proteins that bind the RNA motif will...interacting cell surface proteins with a biotin tagged LPETG peptide. Biotin tagged proteins can then be purified...There are approximately 2-4 million proteins per cubic micron in bacteria, yeast, and mammalian cells...
  12. Antibodies 101: Introduction to Antibodies

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    ... the presence of proteins from samples containing a mixture of proteins. The proteins are separated based... Antibodies, also known as immunoglobulins, are ~150 kDa, Y-shaped proteins that are both a natural part...region. Two immunoglobulin (Ig) heavy chains and two Ig light chains make up each antibody molecule. The...the Ig heavy chains, and the rest of the Fab regions are completed with the Ig light chains. The variable...Flow cytometry is used to detect proteins on the surface of or inside whole cells. Antibodies - typically...antibodies are produced by B cells. They bind to proteins on the surface of extracellular pathogens such...such as parasites or microbes, or to proteins expressed on the surface of cells that have been infected ...
  13. 22 Hot Plasmid Technologies from 2014

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    ...Margaret Robinson’s lab, and more recently used by Stephen Royle’s lab, acutely depleted proteins from their...induction heterodimerization of proteins that contain rapamycin-binding domains, such as FKBP and FRB. The ...inactivation. Find the Robinson plasmids or the Royle plasmids and get to work! Robinson et al., Dev Cell...light-oxygen-voltage (LOV) sensing domains from algae into chimeric Opto-RTKs. The LOV domains bind flavin cofactors...phosphoserine (SP218) insertion was moderately enhanced while two phosphoserine insertions (SP218/SP222) was... to generate random mutagenesis libraries or to insert heterologous genes, reporters, or other markers...demonstrate that they can successfully create GFP fusion proteins with a variety of genes across the genome. Although...
  14. Antibodies 101: The Basics of Western Blotting

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    ...mix of proteins with a broad size range to be separated on a single gel.  Immobilizing proteins on a membrane...albumin or other proteins. The sticky areas on the membrane will bind to the proteins in the buffer, blocking...labeled. Instead, a conjugated species-specific secondary antibody is used to visualize the proteins. In this...Introduction to western blotting  In a western, proteins are: (1) separated by size, (2) transferred to...absence of a protein, but can also determine if proteins are being up- or downregulated in a system, detect... to standards, detect the cellular location of proteins, and can be a readout for protein interaction ...applied to the gel causes the negatively charged proteins to migrate toward the positive charge at the bottom...
  15. INTEGRATE: Bacterial Genome Engineering Using CRISPR-Transposons

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    ...manner to Type I-F, but instead employ a Cas12k protein instead of three Cas proteins (Fig. 1A, bottom), and...transposase proteins (TnsA, TnsB, TnsC). The donor DNA (aka mini-transposon), which contains the DNA cargo...programmability: depending on the transposases involved, they insert either randomly, or at fixed genomic target sites...generation of tools for efficient and programmable insertions of large DNA cargos into bacterial genomes. This... This new capability was named INTEGRATE (Insertion of Transposable Elements by Guide RNA-Assisted Targeting...spacer sequence specifying the target site. Four proteins (TniQ, Cas8, Cas7, Cas6) that forms the QCascade...INTEGRATE. The requirement for multiple Cas proteins to form the Cascade targeting complex is a hallmark...
  16. Tips for Screening with Yeast Two Hybrid Systems

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    ... prey proteins after screening. It is also possible to screen libraries of bait and prey against each ... expression of target proteins in heterologous systems (e.g. mammalian proteins in S. cerevisiae). ...activation and cell biology. During this period, proteins were successfully expressed as fusions that retain...domain (DBD) and transcriptional activation (TA) domains retain their individual activities when separated...could be combined effectively (3). In Figure 1 for instance, the DBD of the fusion protein shown is still ...also called the interaction trap), genes encoding proteins of interest(POI’s) are fused to TAs and DBDs (... then co-expressed in a yeast strain that also contains a reporter gene cloned downstream of a promoter...
  17. Plasmids 101: CcdB - The Toxic Key to Efficient Cloning

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    ...contain your insert of interest. Simply stated, ccdB makes cloning easier by selecting against vectors that...vector “backbone” in this system contains ccdB. A successful insertion will completely replace ccdB with...vectors in mind, any plasmid that contains the F plasmid (F’ strains) will also be resistant to CcdB, ...popular lab strains, such as NEB Stable, JM109, XL1 Blue or XL10 Gold, that are F’. These strains could possibly...that did not take up your insert. But exactly how does ccdB accomplish this? Let’s start with a brief ...antitoxin protein (CcdA) that protects the cell against the toxic CcdB. Cells that lose ccdA through the..., an investigator were to successfully clone an insert into the vector, the ccdB reading frame would be...
  18. Fluorescent Tagging of Endogenous Genes with SapTrap

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    ...for each insertion. Also, it remains challenging to screen for the genetically modified strains that contain...tagging proteins in a tissue specific manner, as well as 3-site destination vectors for inserting a tag ...tagging endogenous proteins with an auxin-inducible degron (AID) tag to generate proteins which can be rapidly...years ago, the growing spectrum of fluorescent proteins (FPs) has been an invaluable resource for studying...with FPs. Overexpression of fluorescently tagged proteins can lead to improper protein localization, protein...new user-defined DNA sequence (like GFP) can be inserted at the DSB. CRISPR has allowed scientists to tag...contain your newly tagged gene. Most insertions can only be detected by labor-intensive processes like...
  19. Plasmids for Endogenous Gene Tagging in Human Cells

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    ...at allencell.org and the Allen Institute website at alleninstitute.org. A classic challenge in cell biology...at allencell.org and the Allen Institute website at alleninstitute.org. References 1. Roberts, Brock, ...contributed by the gene editing team at the Allen Institute for Cell Science. Learn more by visiting the Allen...tagging and visualization of specific, individual proteins under endogenous regulatory control. But even ...even with the advent of CRISPR/Cas9 technology, inserting large tags into a precise location in the genome...genomic tagging experiments. Browse the Allen Institute for Cell Science Plasmid Collection Fluorescent...C-terminal tag, as shown in the example above, we inserted a linker and GFP tag at the end of the last exon...
  20. Optogenetics + CRISPR, Using Light to Control Genome Editing

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    ...pdDronpa domains to the sites flanking the DNA-binding cleft of Cas9, the fluorescent domains dimerize... Cas9 activity Anti-CRISPR proteins are a highly diverse group of proteins that are able to block CRISPR-Cas...The use of nickases, prime editing, anti-CRISPR proteins, and other techniques all aim to improve targeting...uses genetically encoded tools, such as microbial opsins, to control cellular activities using light. In... calcium and integrin-binding protein 1 (CIB1) proteins. The goal of both groups was to create a system...developed by the Sata lab is composed of two fusion proteins: 1) the genomic anchor - an inactive, dead Cas9...Once triggered by blue light, the CRY2 and CIB1 proteins heterodimerize and move the activator into position...
  21. Neuronal labeling with Spaghetti Monster

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    ...neuronal synapses for instance. Also these tags need to be fused to scaffold proteins in order to be expressed... by red fluorescent proteins such as tdTomato or RFP or blue fluorescent proteins like Cyan. The issue...expressed proteins than standard tags and can be used to distinguish highly similar proteins. For example... neuronal populations in the brain. The Allen Institute and the Janelia Research Campus in the USA have...Neuronal tracers such as epitope tags and fluorescent proteins (FP) have also been important in mapping, monitoring...tags and even multimeric tags are frequently insufficient for detection when the POI is weakly expressed...expressed. As these epitopes tags have no intrinsic visual signal, they cannot be detected directly in live...
  22. Which Fluorescent Protein Should I Use?

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    ... photoconvertible proteins are PA-GFP, Dendra2, and the mEOS proteins. Some proteins are reversibly switchable...you really know how fluorescent proteins glow?   Fluorescent Proteins (FPs) were first discovered over...categories of fluorescent proteins Photoactivatable / Photoconvertible: These proteins can switch their color... less).  For LSS proteins, the Stokes shift is ≥ 100nm. Specifically, these proteins are excited by UV...when labeling proteins that interact. Indeed, FRET is often used to determine if two proteins interact. ...wavelength than the exciting wavelength. Thus, FPs are proteins with this unique capacity. Many of these FPs are...thus tracking the localization of that biomolecule inside living cells. FPs classified by the emission color...
  23. Plasmids 101: Using Transposons in the Lab

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    ...model organism, they insert into the host’s genome. Then, the transposon insertion sites are detected with...transposase proteins (TnsA, TnsB, TnsC), and 4) the donor DNA or mini-transposon that contains the DNA cargo...and result in human disease. While transposon insertions can be detrimental, it also drives genomic evolution...that moves around. This DNA sequence encodes the proteins the transposon needs for transposition. Transposition...transposition.  Target site: Different transposons insert at different DNA sequences or target sites. Integration...duplication of this target site sequence at the site of insertion.  Types of transposons Transposable elements ... reverse transcribe back into DNA before being inserted into new target sites. This is similar to how ...
  24. Choosing the B(right)est Fluorescent Protein: Photostability

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    ...fluorescent proteins that are photostable. On top of photobleaching, fluorescent proteins may display ...performed with soluble fluorescent proteins or localized fusion proteins and do not require dedicated plasmids...performed on purified fluorescent proteins. To avoid diffusion, the proteins are (i) trapped in microdroplets...course of the experiment. The best fluorescent proteins for live cell imaging can be excited many times...fluorescent protein. This can differ between fluorescent proteins in the same spectral class (Cranfill et al, 2016...confocal laser scanning microscopy, fluorescent proteins are excited with very intense light (for a brief...compare the photostability of different fluorescent proteins? Measuring photostability Since it is clear that...
  25. Antibodies 101: Beyond Surface Labeling

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    ...   Dye stains Dye stains are non-antibody-based stains that bind DNA or free amines of proteins. Depending...cytosol/nucleus, or visualizing DNA instead of proteins. Some stains can diffuse through the cell membrane...transmembrane proteins, such as receptors, or post-translational modifications on those proteins, like glycosylation...kits allow for labeling of cytosolic proteins, as well as proteins of the secretory pathway. Those can ...buffer to label intranuclear proteins of interest, you can label cytosolic proteins alongside the intranuclear...like many of the cluster of differentiation (CD) proteins found on immune cells. However, there are more...methods can include labeling markers with multiple proteins/antibodies, targeting markers found within the...
  26. Using Phosphoserine to Study Protein Phosphorylation

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    ...phosphoserine-incorporated proteins The generation of pSer-incorporated proteins requires a molecular toolkit... Sep-OTS, contains the components required for the translation of pSer-incorporated proteins on a single...Niemi, a postdoctoral fellow at the Morgridge Institute for Research in Madison, Wisconsin. It is commonly...cited that approximately one-third of cellular proteins are modified through phosphorylation (1). However...of a protein for characterization. However, phosphoproteins are often low abundance, and thus difficult...incorporation of phosphoserine directly into recombinant proteins (5). Optimization of this system defined three...effectively incorporate phosphoserine into recombinant proteins, such as the kinase MEK1 (5). MEK1 is inactive...
  27. Opto-Nanobodies: Using Light to Manipulate Cell Signaling and Protein Purification

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    ...generate two more OptoNBs, one against mCherry and one against GFP. Insertion of AsLOV2 into loop 1 always...how AsLOV2 insertion into mCherry or GFP nanobodies affected binding of their target proteins. The surface-exposed...opposite effects: insertion into loop 1 caused dark-induced binding while loop 6 insertion caused blue-light... you wash several times to remove non-specific proteins, and then elute YFP.  Option #2: Opto-Nanobodies... purification You skip adding a tag to YFP and instead use OptoNBs. You fill a column with OptoNB coated... the lights, OptoNBs bind YFP and non-specific proteins flow through. To elute YFP, you turn on the blue...ability of its nanobody partner, so it’s important to insert AsLOV2 at a spot in the nanobody that preserves...
  28. Hot Plasmids: Spring 2025

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    ...vector that contains everything needed to replicate inside a host cell but with space to insert your genetic...highly-specific recombinant antibodies against three of the six human glypican proteins (GPC1, GPC3, and GPC4). All...mini counterpart label nearby proteins with biotin. The biotinylated proteins can then be isolated and identified...validated viral packaging and strong expression after inserting EGFP and provide step-by-step protocols for viral...our bacterial plasmid set for expressing tagged proteins, and stay tuned for mammalian expression and AAV...and therapeutic potential. Our partners at the Institute for Protein Innovation (IPI) recently released...with the pithy name "site-specific target-primed insertion through targeted CRISPR homing of retroelements...
  29. In Living Color: The Skinny on In Vivo Imaging Tools

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    ...scientists have used fluorescent proteins to observe what’s happening inside cells for at least a couple of...earlier described. “Until our proteins, there were lots of fluorescent proteins made from jellyfishes and ...decades. Green is the classic color, but fluorescent proteins are available in a variety of hues. While those... applications, Verkhusha and his lab at Albert Einstein College of Medicine in New York recognized their... The key to their bacterial phytochome-derived proteins, iRFP670, iRFP682, iRFP702, iRFP713 and iRFP720... The challenge then was to develop fluorescent proteins that would fall within that near-infrared range... and that’s exactly what iRFPs achieved. Those proteins allowed a signal-to-background ratio in mammalian...
  30. New CRISPR Tools: Cas7-11 and PASTE

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    ...bacterial genome, and inserted it into E. coli to express and then test for any proteins that could cut RNA...the lab instead turned to phage serine integrases, where they saw 10-20% integration of inserts up to 36...Schematic of programmable gene insertion with PASTE. The PASTEsystem involves insertion of landing sites via Cas9...single-stranded nicks instead of the double-stranded breaks used in other insertion systems. Off-target ...nonetheless a new subtype. Cas7-11 had combined all the domains into a single protein, shedding the complexity ...Cas7-11   Use The Cas7-11 targeting system contains two pieces: a single protein, computationally ...computationally described as a fusion of four Cas7 proteins and a putative Cas11-like protein, and a guide RNA. The ...
  31. Choosing the B(right)est Fluorescent Protein: Aggregation Tendency

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    ..., the red fluorescent proteins form tetramers. In general, fluorescent proteins have a natural affinity...true monomeric fluorescent proteins. Concluding remarks Many fluorescent proteins are available, and their...aggregation The tendency of purified fluorescent proteins to form homodimers or higher order oligomers can...-PAGE under non-denaturing conditions separate proteins based on size. Whether higher molecular weight...protein, reflect the likelihood that fluorescent proteins interact or oligomerize in cells? This question...question is largely unanswered. Ideally, fluorescent proteins should act as inert modules that fail to homodimerize...homodimerize in cells. To understand how well fluorescent proteins approach this ideal situation, cellular assays...
  32. Viral Vectors 101: Parts of the AAV Packaging Plasmid

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    ...Rep78 and Rep68 contains a DNA-binding and endonuclease domains, all four Rep proteins share a common ...which contains the AAV structural and packaging genes, the adenoviral helper plasmid which contains the ...the proteins needed for the virus to replicate,  and the transfer plasmid which contains the viral genome...Rep proteins. Alternative splicing generates the different C-terminal regions of the Rep proteins. While...common helicase and ATPase domains. To function, the Rep proteins form oligomers of Rep 78/68 or Rep52/40. ... start sites generate the three VP proteins. The three VP proteins assemble into capsid at a 1:1:10 ratio...gene of interest can be packaged into the virus instead.  Next let’s take a closer look at the rep and ...
  33. Mouse Modeling, Part 1: Genetically Engineered Mice

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    ...editing techniques. Inbred and outbred strains Mouse strains used in research can fall under one of two.... Common inbred strains include C57BL/6, Balb/c, and 129. Conversely, outbred strains were originally ...Examples of outbred strains include Swiss Webster and Harlan (Hsd) National Institutes of Health (NIH) Swiss...broad classifications: inbred or outbred. Inbred strains share a common genetic background, which means ...limited but genetically diverse gene pool. Outbred strains are strategically bred to maintain maximum genetic...genetic diversity of the human population. Outbred strains of mice are useful for comparing dominant and recessive...Genetically engineered mice Mice can be engineered by inserting a targeting vector containing the gene of interest...
  34. The Golden Stopwatch Award: Recognizing Facilitators of Research

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    ...Hospital  Brandeis University  Broad Institute  California Institute of Technology Cold Spring Harbor Laboratory...Laboratory  Dana-Farber Cancer Institute  Fred Hutchinson Cancer Research Center Memorial Sloan-Kettering...  National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK)  National Institute of Genetics...Rockefeller University  Salk Institute for Biological Studies The Scripps Research Institute St. Jude Children's...University and Medical Center  Weizmann Institute of Science Whitehead Institute for Biomedical Research Glossary...intellectual property, and to help requesting institutions safeguard themselves from undue liability. Before...materials? If so, you should always talk to your institution’s TTO or legal office first. Generally, Addgene...
  35. Delivery Methods for Generating iPSCs

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    ...could be affected by the location of insertion. Lentiviral insertion can also disrupt the expression of ...Low Efficient and Stable Genome integration Insertional mutagenesis, transgene reactivation, residual...Low Efficient and Stable Genome integration Insertional mutagenesis, residual expression piggyBac ... inefficient Difficult to purify reprogramming proteins. Table 1: Key Features of Different Methods...of iPSC generating methods due to the risk of insertional mutagenesis. Random integration also creates ...potential. Finally, retroviruses are prone to insertional mutagenesis and random integration creates variation...Addgene. Another drawback is that lentiviral vectors insert in different genetic locations in each transduced...
  36. Antibodies 101: Single Chain Fragment Variables (scFvs)

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    ...generations of scFvs against two antigens that are impossible to generate scFvs against in vivo: antigens...the sequences for the variable domains of the selected scFvs are inserted into a vector encoding the antibody... are often the building blocks for engineering proteins. So let’s get acquainted with scFvs. What is an...variable heavy chain (VH) of an antibody. These two chains are connected by a flexible linker peptide that...scFv. While you might assume that the variable domains of an scFv would mirror that of an antibody (VL-linker-VH...antigens found in the body or self antigens, and toxins that are lethal to animals.  In the clinic, scFvs’ size...to produce scFvs in mammalian, yeast, plant, and insect cells, they are most often expressed from a plasmid...
  37. Antibodies 101: Affinity Reagents

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    ...ankyrin repeat proteins, or DARPins, are genetically engineered small affinity proteins, around 14-15 ...antibodies. Instead, they are derived from a class of binding proteins known as ankyrin repeat proteins. DARPins...and heavy chains made by immune systems. But here, we're not interested in antibodies. Instead, we're going...engineered fusion proteins similar to a Fab fragment but created through engineering instead of cleavage. ...synthetic binding proteins which use the Fibronectin type III domain as their scaffolding instead of the antibody...the ability to specifically recognize and bind proteins. They’re used in a number of research and clinical...these alternative reagents are created in the lab, instead of generated in vivo, they have higher reproducibility...
  38. Lambda Red: A Homologous Recombination-based Technique for Genetic Engineering

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    ...  The best applications for dsDNA inserts include: large insertions or deletions, including selectable...note* not all linked strains contain the Lambda Red system).  In some of these strains, expression of exo... used to make an assortment of modifications: insertion and deletion of selectable and non-selectable ...of the experiment. dsDNA substrate is best for insertions or deletions greater than approximately 20 nucleotides... only a few base pairs.  dsDNA Substrate dsDNA inserts can be made by PCR using primers that amplify the... with 50 base pairs of homology to the targeted insert site (Figure 2, top).  These primers are typically...not determine the direction of replication and instead design oligos that target both strands. One of ...
  39. Plasmids 101: Optimizing Plasmid Yields

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    ...high quality DNA that contains these elements. Be aware of endA+ strains Strains like Stbl3 have been ...incomplete. Protein expression strains are not good for cloning Bacterial strains adapted for protein purification...bacterial strain Differences between E. coli host strains can impact plasmid yield. Check the bacterial strain...an example). Look out for carbohydrates Certain strains, including HB101 and derivatives, release large...have previously reviewed many common lab E. coli strains on the blog, and also recommend this handy guide...for a more extensive listing of common E. coli strains. Increase the volume Starting with a larger culture... be affected by the plasmid size, nature of the insert, propagation strain, growth conditions, and the...
  40. Plasmids 101: Protein tags

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    ...tags and fusion proteins to aid in the expression and purification of recombinant proteins. Tags for stability...recombinant proteins for one-step purification with glutathione, can also protect against proteolysis....one form of instability. Prokaryotes can also have a hard time folding eukaryotic proteins. You can get...101 has covered GFP and its related fluorescent proteins, which are sometimes used as tags for detection... biologists who need to overexpress and purify proteins can face any number of technical challenges depending...protein (MBP). Overexpression can also lead to insolubility, and aggregated protein is not useful protein... but scientists may also choose to add smaller proteins, such as Thioredoxin A (TrxA) that improve disulfide...
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