Newsletter Hot Articles
Tool for Proteomic Mapping of Mitochondria in Living Cells
Alice Ting's lab has designed a new technology for creating a spatially and temporally resolved proteomic map of large numbers of proteins in living cells. The method works by targeting ascorbate peroxidase (APEX) within the cell, resulting in biotinylation of nearby proteins. The biotinylated proteins are then analyzed by mass spectrometry, providing a readout of colocalized proteins from live cells.
The Ting Lab validated this technique by localizing APEX to the mitochondrial matrix with the plasmid pcDNA3-mito-APEX. This resulted in the identification of 495 proteins within the human mitochondrial matrix, including 31 which were not previously linked to the mitochondria. Browse the relevant plasmids.
Rhee et al., Science 2013 Mar 15; 339(6125):1328-31.
Gateway-compatible Cloning and Expression Vectors
Have you ever wished that your favorite empty vector or tag was available in a Gateway-compatible version? We may have exactly what you are looking for already in our repository.
Image from Dubin et al., Plant Methods (Biomed Central), 2008 Jan 22; 4:3.
The lab of Giovanna Benvenuto created a series of twelve Gateway Entry vectors with six commonly used tags for either N- or C-terminal fusions. The available tags (STREP, HA, MYC, GST, ECFP and EYFP) are present within the attachment sites, avoiding any extra linker amino acids between the tag and insert. Traditional restriction enzyme cloning is used to insert a gene of interest into these Entry vectors, followed by recombination with a Gateway-compatible Destination vector of your choice for bacterial, insect, mammalian, plant or yeast expression. All of the vectors utilize the same cloning sites and contain a stop codon before the final attachment site in the entry cassette.
Converting existing vectors to Gateway-compatible vectors that can be used with recombination-based cloning can be a tedious process. Fortunately, the Yu-Zhu Zhang laboratory has developed a method using site-specific recombination to convert non-Gateway based vectors to Gateway-compatible vectors. This process was then used to create eleven Gateway-compatible Destination vectors from commonly used conventional empty vectors containing His, hemoglobin, EGFP, Flag, Myc-His tags or from other empty vectors used in adenoviral, bacterial, mammalian or yeast systems. An Entry vector containing your gene of interest can be recombined with one of these Gateway-compatible Destination vectors to generate an expression-ready construct.
More empty backbones can be found at Addgene’s Guide for Empty Backbones.
New NIR Fluorescent Probes: iRFPs, PAiRFPs, and iSplit
Several types of new near-infrared fluorescent proteins derived from bacterial phytochrome photoreceptors (BphPs) have been developed by Vladislav Verkhusha’s lab and can be used for deep-tissue optical in vivo imaging. They fluoresce in mammalian cells and tissues without adding exogenous biliverdin. The four new spectrally distinct permanently fluorescent iRFP variants (iRFP670, iRFP682, iRFP702, and iRFP720) described by Shcherbakova et al., along with the group’s original iRFP (iRFP713), were shown to have high effective brightness and allowed multicolor imaging. Next, Piatkevich et al. described the engineering of photo-activatable iRFPs (PAiRFP1 and PAiRFP2), which can be ‘turned on’ by non-phototoxic far-red light and used for spatially selective imaging of tissues in living animals. Most recently, further development of the original iRFP resulted in a split fluorescence complementation probe, iSplit, by Filonov et al. iSplit was tested both in vitro and in vivo as a biomolecular fluorescence complementation (BiFC) reporter to detect protein-protein interactions.
Looking for other fluorescent proteins? Check out Addgene’s Fluorescent Protein Guide.
The Open Source Wnt Project
Wnt signalling pathways play essential roles in embryonic development as well as tissue homoeostasis in adults, and their aberrant regulation has been linked to diseases in man including diabetes, neurodegeneration and cancer. In order to allow direct side by side comparison of the various mammalian Wnts and their function, the labs of Marian Waterman and David Virshup have developed a standardized set of Wnt expression plasmids. The kit contains the ORFs of all 19 human Wnts in the same expression backbone. Each ORF is cloned into 2 entry backbones, pENTR/D-TOPO with and without a STOP codon, and 2 mammalian expression backbones, with and without a C-terminal V5 tag. In addition, the Xi He lab has contributed a fifth set containing a modified version of each tagged ORF that enables epitope tagging without loss of Wnt signaling activity.
Learn more about how the Open Source Wnt Kit was developed using crowd-sourcing in our interview with Dr. Marian Waterman.
Genome Engineering in hPSCs: New Musunuru/Cowan TALEN Kit
Developed by the labs of Kiran Musunuru and Chad Cowan, the newest TALEN kit allows for the quick and easy delivery of TALENs into human pluripotent stem cells and other difficult-to-transfect mammalian cell types. TALEN construction can be completed in 1-2 days without PCR amplification.
Ding et al., Cell Stem Cell 2013 Feb 7;12(2):238-51.
Do you want to edit plant, fly, worm, or fish genomes? We now have CRISPRs for that! Are you interested in activating your gene of interest? New CRISPR technology lets you selectively activate your gene of choice!
Don't see the CRISPR/Cas system you're looking for here? Find more CRISPR/Cas9 plasmids at Addgene.
New Plasmid Kit: Fluorescent Proteins
Organizing your fluorophore combinations at the start of a research project can be a tricky task. Many times, having access to additional colors or combinations can be a big asset. The Hamdoun lab constructed a number of fluorescent plasmids for their recent JBC publication, and the fluorescent protein- containing empty vectors have wide applications for use in Zebrafish, Sea urchin, Xenopus, and C. elegans. The following 9 plasmids have been bundled together to provide a useful “starter kit” for screening fluorescent protein fusion expression in organisms or cells in which an exogenous mRNA can be injected and expressed. The utility of this kit is that it enables the user to generate N and C terminal fusions to mCherry, Cerulean, mCitrine, or EGFP, and could also be employed for many types of multicolor experiments or assays with fluorescent small organic molecules.
Gokirmak et al., J Biol Chem 2012 Dec 21; 287(52):43876-83E.
Additional plasmids for fluorescent protein tagging can be found on Addgene's Fluorescent Protein Guide.
CRISPRi: Repurposing of the CRISPR/Cas Genome-Editing Technology for Transcriptional Silencing
The CRISPR/Cas system is quickly becoming well known as an effective genome-editing technology, and a simple alternative to TALENs. With only two components, CRISPR systems utilize Cas9 nuclease to cleave DNA and chimeric guide RNA (gRNA) to target the Cas9 to a specific region of the genome. The system has been optimized for DNA editing in a variety of different species and cell types. The current technology utilizes Cas9’s nuclease abilities to destroy a specific locus in DNA through directed cleavage followed by non-homologous end joining (NHEJ). Alternatively, a modified Cas9 can be made to nick the DNA, cutting only one of the DNA strands to facilitate DNA replacement by homologous recombination. This requires the transfection of an additional plasmid that contains a complimentary sequence.
The Stanley Qi lab has created a new function of the CRISPR/Cas system called CRISPR Interference. CRISPRi is the latest tool available to scientists looking to manipulate the genome of their favorite organism. CRISPRi utilizes a catalytically inactive Cas9 nuclease in complex with a gRNA to interfere with transcription of the DNA downstream of its binding site. The mechanism of the interference is believed to involve physically impairing the RNA polymerase progression past the Cas9:gRNA complex. These CRISPRi plasmids are optimized for use in human cells and an additional set of CRISPRi plasmids are optimized for use in bacteria.
Qi et al., Cell 2013 Feb 28;152(5):1173-83.
Alternative TALEN Assembly and Validation Vectors for Golden Gate TALEN Kit
Recent advances in genome editing technology, such as transcription activator-like effector nuclease (TALEN) systems, have reduced the barrier to studying gene function. With a focus on efficiency, the laboratory of Takashi Yamamoto has developed optimized array and destination vectors for use in combination with original vectors from the Golden Gate TALEN and TAL Effector kit, deposited by the labs of Dan Voytas and Adam Bogdanove. The modified pFUS array vectors are designed for six-module assembly to improve the assembly success rate and efficiency of the first Golden Gate cloning step, while reducing the number of necessary RVD module vectors. An optional ligation with pre-digested RVD and array vectors for the first module assembly step is reportedly more robust than the typical Golden Gate assembly method. The mammalian destination vectors offer the choice of a CMV/T7 or CAG promoter with codon-optimized FokI and Flag tag, ready for use in mammalian cells without additional cloning.
A novel TALEN evaluation system utilizing the pGL4-SSA vector included in the Yamamoto Lab TALEN Accessory Pack allows for validation of TALEN plasmids in mammalian cells using a luciferase reporter containing custom oligonucleotides corresponding to the TALEN target sequence in a single-strand annealing (SSA) assay. The Yamamoto lab has provided a step-by-step protocol describing the use of their array and destination vectors, as well as this universal TALEN validation assay in mammalian cells.
Sakuma et al., Genes Cells 2013 Apr;18(4):315-26.
FREQ-Seq: a rapid method to determine specific allele frequencies from mixed populations.
To help scientists track the frequencies of specific alleles in microbial populations through time Christopher Marx's lab has engineered and validated a new method called FREQ-Seq. This strategy allows scientists to construct barcoded, locus-spe cific libraries compatible with Illumina next generation sequencing in order to study evolutionary dynamics. By counting DNA sequence reads, FREQ-Seq can quantitatively determine allele frequencies across timepoints or populations. This kit consists of a 48 plasmid adaptor library, with each plasmid carrying a unique barcoded Illumina-M13F bridging primer. These bridging primers are amplified and used to generate Illumina sequencing libraries using a 2-step PCR-based protocol and are compatible with single-end or paired-end read flow cells. FREQ-Seq is an open source platform and the libraries can be generated in a cost-effective manner with minimal bias.
Chubiz et al., PLoS One 2012; 7(10): e47959. doi:10.1371/journal.pone.0047959.
Experimental dose–response data for htetR::NLS::eGFP and mCherry expression in the two gene mammalian linearizer system plotted on log-log scale after background subtraction (defined as the fluorescence at 0 ng/mL of doxycycline).
Linearly Tunable Gene Expression Systems
Gábor Balázsi’s lab has developed a series of systems that allow for tunable gene expression. The group first developed the system in yeast by creating a synthetic linearizer gene circuit that controlled gene expression with a linear dependency on the extracellular concentration of an inducer (anhydrotetracycline). The use of a negative feedback circuit also resulted in gene expression that was homogenous across the cell population. Plasmids for the various reporter and regulator parts of the circuits are available at Addgene.
Using computational modeling as a guide, the circuit was further adapted for use in mammalian cells. Enhancements to the mammalian gene expression system were sequentially made by identifying additions to the circuit that would improve transcription, translation, and nuclear localization (including addition of an intron, use of a nuclear localization sequence, generation of new TetR-repressible promoters, and more). Gene circuits were successfully developed that showed a linearly tunable expression response to the doxycycline inducer when tested in MCF-7 cells, both for a one- and two-gene linearizer system. The related constructs can be found here.
Nevozhay et al., PNAS 2009 Mar 31; 106(13): 5123-8.
Nevozhay et al., Nat Commun 2013 Feb 5; 4: 1451.
PCR-mediated Modification of Chromosomal Genes in Yeast
PCR-mediated modification and deletion of chromosomal genes is a tried-and-tested technique for analyzing gene function in S. cerevisiae.
Peter Philippsen's and John Pringle's laboratories have created a set of plasmids that serve as templates for the PCR synthesis of fragments used for a variety of gene modifications. The modifications, based on the groundbreaking work by Baudin et al., include gene deletion, gene overexpression (using the regulatable GAL1 promoter), and tagging with a variety of epitopes and fusion proteins. Browse a table of these plasmids here.
Tim Formosa's lab has constructed 36 plasmids that can also be used to generate linear PCR products. The PCR products can easily be fused to the 3' end of an ORF in the yeast genome, thereby adding a variety of tags preceded by a TEV or PreScission protease site. Browse these plasmids here.
Longtine et al., Yeast 1998 Jul;14(10):953-61.
New Optogenetic Tool Derived from Box Jellyfish - JellyOp
Optogenetics, a recent technological breakthrough in neuroscience, combines the fields of optics and genetics to allow for precise spatial and temporal control of individual neurons. Photons stimulate cells expressing microbial light-gated ion channels, such as channelrhodopsin-2 and halorhodopsin, to modulate neuronal firing. The laboratory of Robert Lucas designed a new optogenetic tool incorporating an opsin from the box jellyfish to achieve improved sensitivity and reproducibility in signaling. JellyOp is more bleach resistant than existing variants of mammalian rod opsin and allows for sustained signaling under conditions of repeated light exposure. The present JellyOp construct is ideally suited for mimicking the activity of Gs-coupled G protein coupled receptors, while further structural modifications could permit coupling of JellyOp to additional signaling pathways.
Bailes et al., PLoS ONE 7(1): e30774. doi:10.1371/journal.pone.0030774.
Additional plasmids for optogenetics research can be found on Addgene's Optogenetics Guide.
Optimized Glutamate-sensing Fluorescent Reporter
Glutamate signaling is important in many species and biosensors are allowing scientists to study this process with greater ease and resolution. The Looger lab has created a new intensity-based glutamate sensing fluorescent reporter and has validated it in a wide variety of neurological systems. To learn more and browse these plasmids, click here.
Marvin et al., Nat Methods 2013 Feb; 10(2):162-70.
FLuc-P2A-RLuc - A New Reporter System for High Throughput Screening
High throughput screening (HTS) with a single reporter-gene is a convenient method for rapidly assaying diverse compounds (such as small molecules) to identify those that may modulate a specific biomolecular pathway. Reporter-gene HTS identifies the ‘active’ compounds by measuring the amount of the reporter-gene activity compared to controls and thus provides a great starting point for downstream experiments. Unfortunately, direct interactions between compounds and the reporter-gene itself can cause misleading, false-positive results that complicate data interpretation.
To overcome this problem, James Inglese’s lab has devised a “coincidence reporter biocircuit” system that expresses two unique bioluminescent genes (firefly and renilla lucifereases) at equivalent levels in order to efficiently distinguish compounds with active biological activity from those that are interfering with the reporter-gene itself. Because the two luciferase genes are nonhomologous, any compound that shows activity from both reporters has higher probability of being biologically relevant.
Cheng KC, et al. Nat Methods 2012 Oct;9(10):937.
RGB-Marking with LeGO Vectors
The lab of Boris Fehse initially described their lentiviral "gene ontology" (LeGO) vectors as a system "that allows simultaneous expressing and/or suppression of several genes in a single cell to facilitate the analysis of gene networks." These 3rd-generation lentivectors consist of various combinations of fluorescent markers, promoters/enhancers, and shRNA expression cassettes, all of which can be used in conjunction with each other to visualize complex systems.
The Fehse lab recently published a new application for the LeGO vectors: Red, Green, Blue (RGB) Marking. The fluorescent protein marking system is based on the same principle as TV screens, which combine red, green, and blue beams of light at different intensities to make all colors (see the layman's explanation here). The applications go beyond making pretty images--the ability to produce an almost limitless number of colors allows researchers to identify and track single cell clones. For example, all pink cells in a pink cell cluster are derived from a single pink cell.
This unique marker system gives scientists the means to follow tumor clonalities and to investigate the development of monoclonal or polyclonal metastases. Also, in a setting of organ regeneration after transplantation of stem cells, RGB marking enables the visualization of what individual cells are doing after engraftment. The number of cell clusters with different colors shows the number of engrafted cells, and the size of each cell cluster shows how often the cell has divided after engraftment. There are multiple LeGO vectors available, but all you need to get started with RGB marking is a standard fluorescence microscope and the following three LeGO vectors: LeGO-Cer2, LeGO-C2, and LeGO-V2.
Weber et al., Nat Protoc 2012 Apr 5;7(5):839-49.
Weber et al., Nat Med 2011 Apr;17(4):504-9.
Weber et al., Gene Ther 2010 Apr;17(4):511-20.
Newest pLX Lentiviral Expression Vectors
From the laboratory of David Root, these newest '300' series pLX vectors (pLEX) are similar in function to the previous 300s, but with new promoters and selectable markers. For example, while pLX301 - 4 utilize the CMV promoter, which is known to be silenced in ES cells, pLEX_307 contains the EF1a promoter which is strongly expressed in ES cells.
The '400' series provides all-in-one doxycycline inducibility. These vectors show almost no leakiness in the off-state, allowing the user to titrate expression by varying the levels of doxycycline. This is ideal for avoiding spurious phenotypes caused by expression far above endogenous levels, such as when performing RNAi rescue experiments or when trying to compare activities of gene variants. Available new pLX plasmids include:
Constitutive Lentiviral Expression
Inducible Lentiviral Expression
New TALEN Destination Vectors – pc-GOLDYTALEN & RCIscript-GoldyTALEN
Transcription activator-like effector nucleases (TALENs) consist of assembled DNA binding motifs coupled to FokI nuclease monomers that can dimerize and introduce a DNA double strand break. In the past year TALENs have become the tool for genome editing primarily due to their simple and straightforward design and assembly strategies. The laboratory of Dan Carlson and Stephen Ekker designed a new and improved TALEN scaffold, GoldyTALEN, truncated at both the N and C terminus and inducing higher mutation rates than the parental pTAL vector. Dan Carlson deposited 2 destination vectors containing the GoldyTALEN compatible with the Voytas lab Golden Gate TALEN kit. pC-GoldyTALEN directs expression of TALENs from a truncated CAGs promoter. RCIscript-GoldyTALEN is designed for in vitro synthesis of TALEN mRNAs. Both 5’ and 3’ Xenopus β-globin UTRs are included in the vector to enhance expression of the message.
Carlson et al., PNAS 2012 Oct; 109(43):17382-7.
Improved Genetically Encoded Calcium Indicators - GCaMP6 Variants
The capacity to image and measure neuronal activity in vivo has been improved by the development of various calcium (Ca2+) indicators. Such indicators bind Ca2+ and induce a change in fluorescence signal, allowing scientists to measure action potentials and other receptor activation events which trigger Ca2+ fluxes. Genetically encoded calcium indicators (GECIs), such as GCaMP, express indicators in specific tissues or cells.
Douglas Kim’s lab at Janelia Farm recently developed and deposited novel GCaMP6 variants. pGP-CMV-GCaMP6s, pGP-CMV-GCaMP6m, and pGP-CMV-GCaMP6f have increased ΔF/F0 and faster kinetics compared to previous GCaMP3 and GCaMP5G.
Live Visualization of Single mRNAs with MS2 and PP7 Systems
Fluorescent in situ hybridization (FISH) has been considered to be the gold standard for labeling nucleic acids in their native environment; however, the technique lacks spatiotemporal resolution available in living cells. An alternative imaging technique has been developed in the laboratory of Robert Singer that permits live detection of single mRNAs by tagging mRNAs of interest with a repeated MS2- or PP7-derived nucleotide sequence. These binding site sequences form hairpin loops that can subsequently bind to the corresponding MS2 or PP7 coat proteins tagged with a fluorescent protein. Modified MS2 and PP7 coat protein constructs, tdMCP and tdPCP respectively, improve labeling and imaging of target mRNAs by reducing fluorescent background to allow for more intricate investigation of mRNA processing.
Wu et al., Biophys J 2012 Jun 20;102(12):2936-44.
Enhanced FRET Pairing using Clover and mRuby 2
Förster (or Fluorescence) Resonance Energy Transfer (FRET) is an important tool for determining whether two fluorophores are within a certain distance of each other, and is widely utilized to observe and quantify dynamic biological processes. Historically, CFP and YFP have been the most common FRET fluorophore duo; however, limitations such as emissions overlap between the donor-acceptor pair, sub-optimal FRET efficiency/dynamic range, and low photostability make constructing improved fluorophores desirable.
Michael Lin’s group at Stanford University has recently engineered the novel Clover-mRuby2 FRET pair which shows not only the brightest fluorescence for their respective colors (green and red), but also improves FRET efficiency, dynamic range, and photostability while limiting emissions overlap. The Clover-mRuby2 couple was tested in 4 established FRET reporters (Camuiα-CR, AKAR2-CR, VSFP-CR, and Raichu-RhoA-CR) with noticeable improvement, making these updated sensors more useful in detecting rapid cellular processes in real-time. This new FRET pair has great potential not only for enhancing existing sensors, but also for the construction of new, more sensitive FRET reporters.
Lam et al., Nat Methods 2012 Oct; 9(10):1005-12.
A New Split GFP for Studying in vivo Protein-Protein Interaction – spGFP
A new superpositive split GFP (spGFP) construct for detecting protein-protein interactions in vivo at room temperature was develop by Brian McNaughton's lab. The superpositive split GFP has a greater reassembly speed than previous split GFP constructs. The increased positive charge significantly reduces protein aggregates. This new design also shows robust signal at room temperature making this ideal for studying protein-protein interactions in vivo. The pET11a-Z-NspGFP and pMRBad-Z-CspGFP plasmids are available through Addgene.
Blakeley et al., Mol Biosyst 2012 Aug; 8(8):2036-40.
EM Imaging in all Cellular Compartments Using APEX
A key component of creating high-resolution electron microscopy (EM) images is contrast. Existing genetic tags designed to increase EM contrast, such as horseradish peroxidase (HRP), are helpful in some cellular locales, but have restrictions. In their recent Nature Biotechnology article, the MIT laboratory of Alice Ting describes the engineering of ascorbate peroxidase (APX) to make a new genetic tag that overcomes the shortcomings of previous EM reporters. The Ting lab introduced a series of mutations to APX to change it from monomeric to dimeric, as well as more highly active towards DAB, thus creating enhanced APX (APEX).
APEX offers the following advantages as a genetic tag EM reporter:
APEX plasmids are now available at Addgene.
Martell et al., Nat Biotechnol 2012 Nov; 30(11):1143-8.
Improved Mos-1-mediated Transgenesis Reagents for C. elegans
Erik Jorgensen's lab had previously created a set of plasmids for targeted transgene insertions (Mos1-mediated single-copy transgene insertions; MosSCI) and targeted deletions (Mos1-mediated deletions; MosDEL) in C. Elegans. In their 2012 Nature Methods paper, they add to this collection, making it even easier to use.
First, they have created a Mos-1 expression vector under the eft-3 promoter that significantly increases the insertion and deletion frequencies. Second, they introduce a set of plasmids to facilitate selection of transgenic strains with antibiotic markers and additional transgene insertion sites. Plasmids from the paper are available from Addgene.
Frokjaer-Jensen et al., Nat Methods 2012; 9(2):117-8.
A Brighter ECFP Variant – mTurquoise2
Cyan based fluorescent proteins suffer from low quantum yield and hence are mostly used as the acceptor, rather than donor, in FRET assays. Using site-directed mutagenesis and fluorescent lifetime-based screening, the Dorus Gadella lab identified mTurquoise2, a variant of ECFP (enhanced cyan fluorescent protein). mTurquoise2 has the highest quantum yield of any monomeric fluorescent protein. In vivo studies in mammalian cells show a 20% gain of brightness, high photostability and better performance in FRET studies.
Addgene distributes several mTurquoise2 vectors with various targeting sequences - mitochondria, nucleus, ER, etc.
Goedhart et al., Nat Commun 2012; 3: 751.
Drosophila phiC31 Transgenesis Vectors – pBID and pMartini Gate
Advanced genetic tools available for examining gene function in Drosophila have strongly contributed to its widespread use as a model organism in the genomics era. Integration of transgenes into the Drosophila genome via phiC31 integrase permits efficient and site-specific targeting.
The laboratory of Brian McCabe at Columbia University has recently improved upon phiC31 transgenesis by creating a series of vectors for expressing transgenes in Drosophila. The pBID series of plasmids incorporates several design enhancements, including: (1) gypsy insulator sequences to permit uniform expression levels independent of genomic integration site; (2) backwards compatibility with pUAST cloning sites; (3) Gateway cloning compatibility; (4) DSCP promoter with 10 UAS binding sites to improve expression while eliminating leaky expression in the absence of GAL4; and (5) a variety of fluorescent protein or epitope tagged constructs. The pMartini-Gateway series of plasmids, a set of intermediate vectors, was generated concurrently with the pBID series to assist in Gateway cloning and in developing novel destination vectors.
Wang et al., PLoS ONE 2012; 7(7): e42102.
Drosophila transcription factor ORFs
Drosophila melanogaster, one of the best-known model organisms, has been used to advance our knowledge of genetics and developmental biology since first employed over 100 years ago. The complete sequence of the fly genome, published back in 2000, opened many doors to investigating not only the 15,000+ genes, but also the >60% of functional, non-coding DNA found within it. Over the course of the last decade, many methodologies have been employed to identify some of the regulatory elements found within the non-coding DNA; however, the specific functions of these have not been deeply explored as this requires not only identifying the elements, but also the transcription factors that bind to them.
Bart Deplancke’s group from the Laboratory of Systems Biology and Genetics at the Swiss Federal Institute of Technology has recently deposited a nearly complete collection of Drosophila transcription factor open reading frames (ORFs) comprised of 692 plasmids. These ORFs were cloned open-ended into Gateway compatible Entry vectors, permitting easy and efficient subcloning for a variety of downstream applications. Using this clone library, the authors developed and validated a gene-centered, high-throughput yeast 1-hybrid system by which they identified some previously uncharacterized direct interactions between transcription factors and Drosophila cis-regulatory elements. This ORF library will be a significant resource for many scientists studying the biological importance of specific DNA-protein interactions within the Drosophila regulatory gene network.
Browse this whole collection of Drosophila transcription factor ORFs available through Addgene.
Hens et al., Nat Methods 2011; 8(12): 1065-70.
Add-Ons for the Golden Gate TALEN Kit
The Golden Gate TALEN kit, deposited by the Voytas and Bogdanove labs, has proven to be Addgene's most popular kit. Due to its popularity, a number of labs designed new plasmids to be used in conjunction with this powerful tool. In the summer of 2012, three new Addgene depositors contributed destination vectors compatible with this kit:
pCS2TAL3-DD and pCS2TAL3-RR
Developed in the lab of David Grunwald, pCS2TAL3-DD and pCS2TAL3-RR are next generation TALEN backbone vectors in place of pTAL1, 2, 3, or 4 from the Golden Gate TALEN kit. For both plasmids, sequence positions 1214–2210 of pTAL3 were cloned into a pCS2 expression vector resulting in shorter N- and C-terminal tal protein segments (136AA and 63AA, respectfully). This next generation architecture has been shown to increase mutation induction when using TALENs. The FokI domains (DD, RR) used are obligate heterodimers that require cloning of left and right TALEN monomer proteins into opposite vectors.
Dahlem et al., PLoS Genet 2012; 8(8): e1002861.
pTAL5-BB and pTAL6-BB
Plasmids pTAL5-BB and pTAL6-BB were created in Tom Ellis’ lab and function as alternative destination vectors to generate TAL Orthongal Repressors (TALORs). TALORs can be used to custom repress gene expression in yeast. They consist of the DNA-binding domain of a TALE and strong nuclear localization tags. TALORs repress transcription initiation when targeted to DNA sequences within core promoter regions. pTAL5-BB contains the GAL1 promoter, placing TALORs built into this vector under galactose-inducible expression. pTAL6-BB contains the TEF1 promoter, resulting in constitutive expression of TALORs built into this vector.
Blount et al., PLoS One 2012; 7(3): e33279.
pCAG-T7-TALEN(Sangamo)-Destination with homo- and heterodimeric FokI domains
pCAG-T7-TALEN(Sangamo)-Destination constructs were designed by Pawel Pelczar’s lab for the purpose of optimal mammalian expression of Voytas Golden Gate-assembled TALENs, both in microinjected embryos and transfected cells. TALEN expression is driven by the strong CAG promoter or can be achieved by in vitro mRNA synthesis from the T7 promoter. Truncations were introduced to the N- and C-terminus of the pTAL3 TALEN backbone, which were initially published by Sangamo BioSciences (N153AA, C63AA) and showed robust cleavage activity in several later studies. pCAG-T7-TALEN(Sangamo)-Destination vectors are available with homodimeric or enhanced heterodimeric (ELD, KKR mutations) FokI domains.
Promiscuous Biotin Ligases
In recent years there has been a significant focus on finding a protein’s “interactome”, identifying neighboring and potentially interacting partners of your protein of interest. Current means of identifying one’s network are limited and have several drawbacks, for example biochemical approaches encounter problems with insolubility of expressed proteins and in Y2H systems the interactions are tested outside of the natural environment.
In his recent paper, Kyle Roux developed a simply and quick technique for identifying interacting proteins. The system relies on promiscuous biotin protein ligase fused to a protein of interest; once the culture media is supplemented with biotin, the ligase will biotinylate proteins that are in close proximity. Biotinylated proteins can then be captured by affinity purification and identified using mass spec.
Specifically, Roux et al utilize a mutated form of the E. coli DNA-binding biotin protein ligase, BirA. BirA* (with R118G mutation) lacks the specificity of BirA and has been shown to promiscuously biotinylate proteins in a proximity dependent fashion. Roux et al test their system on lamin-A, a structural element of the nuclear envelope, thus identifying proteins that interact and/or are in close proximity to lamin-A.
Roux et al., J Cell Biol. 2012 Mar 19;196(6):801-10. Epub 2012 Mar 12.
Expression Vectors from the QB3 MacroLab
Finding the right empty vector for your purification technique of choice is often challenging. Finding a vector with the right tags and the right fluorescent fusion protein is even more challenging. What are the chances that someone has a backbone with just the right combination of tags and fusion proteins?
Actually, if you look at Addgene's collection of backbones from QB3 MacroLab, your chances are pretty good. This core facility for the California Institute for Quantitative Biosciences (QB3) designed these backbones to offer different combinations of the following TEV-cleavable N-terminal tags: His6, MBP, FLAG, NusA, Mocr, proteingG, StrepII, Sumo, gCrystallin, N10, and Biotin. The N-terminal tags can be found in various combinations with the C-terminal fusions that include mCherry, mOrange, mCitrine, msfGFP, and mCerulean. Most of the vectors were designed for bacterial expression, but there are also baculovirus and mammalian expression backbones.
The vectors were designed for ligation independent cloning (LIC), for which there are convenient protocols on the MacroLab website. You can also download a full expression vector list in Excel format from their website.
GCaMP5: Out With the Old and In With the New
The very popular calcium sensor GCaMP3 has been updated. GCaMP5G, a.k.a. GCaMP3-T302L R303P D380Y, has improved deltaF/F0 and lower F0 as compared to GCaMP3. Addgene now offers pCMV-GCaMP5G from Loren Looger's lab or the membrane targeted version, Lck-GCaMP5G, from Baljit Khakh's lab.
Zinc Finger Arrays Targeting Endogenous Zebrafish Genes
Gene targeting is a powerful technique that induces specific DNA stand breaks followed by stand rejoining to modify genes of interest. Engineered zinc-finger nucleases (ZFNs) are widely used for targeted genome modification in Drosophila, C. elegans, D. rerio, plants and humans. ZFNs function as dimmers and consist of a DNA-binding zinc finger domain that is covalently linked to a non-specific DNA cleavage domain of a restriction endonuclease, such as FokI. When the two zinc finger DNA binding domains bind to the target sites, the cleavage domains are able to dimerize and cleave at the desired target site. In order to provide researchers with easy-to-use zinc finger arrays, the laboratories of Keith Joung, Randall Peterson and Joanna Yeh at Massachusetts General Hospital have produced 49 pairs of zinc finger arrays targeting a variety of zebrafish genes.
Methods for engineering zinc finger domains:
Maeder et al., Mol Cell 2008 July 25; 31(2): 294-301 Oligomerized Pool Engineering (OPEN)
Sander et al., Nat Methods 2011 Jan; 8(1): 67-69 Context-dependent Assembly (CoDA)
New Retroviral Vectors for Cellular Reprogramming
Alzheimer’s disease is a neurodegenerative disorder for which there is no known cure. The disease most often arises sporadically, but familial forms can also be genetically inherited. The majority of research to date has focused on the less prevalent familial form, as this is more easily modeled in the lab. A new technology used to reprogram primary cells into induced pluripotent stem cells (iPSCs) has been successfully utilized in the study of some neurological diseases; however, it is not known whether this approach would be effective for studying both the sporadic and familial forms Alzheimer’s disease. Steven Dowdy and Larry Goldstein at UCSD have developed retroviral plasmids to generate iPSCs from the primary cells of Alzheimer’s patients. The resulting data provides evidence that iPSCs are effective for studying pathogenesis at the early stages of sporadic and familial Alzheimer’s disease, and can be successfully used in patient-specific cells. This technology not only provides a means to study the mechanisms of disease pathogenesis, but may also prove to be a useful tool for Alzheimer’s disease diagnosis.
Israel et al., Nature. 2012 Jan 25;482(7384):216-20.
Engineering Phosphoproteins in E. Coli
Protein kinases post-translationally phosphorylate specific residues as a means of regulating cell-signaling cascades. O-phosphoserine (Sep) being, by far, the most common phosphorylation modification. Phosphorylation events often require specific stimuli or conditions that are difficult to experimentally replicate, limiting investigations into the functional roles of these phosphoamino acids. Jesse Rinehart’s group at Yale has devised a system to incorporate Sep directly into the genetic code of E. coli using a re-engineered tRNA (tRNAsep). This process requires not only the orthogonal tRNAsep:Sep-tRNA synthetase pair, but also a modified EF-Tu, which allows tRNAsep to be incorporated during protein synthesis. This study elegantly deduces the minimal requirements for genetic code expansion as well as provides a unique tool for protein engineering and research.
Park et al., Science 2011 Aug 26;333(6046):1151-4.
See details on the Rinehart & Söll Phosphoprotein Synthesis Kit here.
Genome-wide shRNA Knockdown Screens Made Easier with DECIPHER
In 2011, Addgene began collaborating with Dr. Alex Chenchik of Cellecta, Inc. and Dr. Gus Frangou of the Fred Hutchinson Cancer Research Center to distribute Cellecta's DECIPHER pooled lentiviral shRNA libraries. The DECIPHER Project was designed to make high-throughput RNAi genetic screening accessible to academia.
Each pooled shRNA library (or module) targets approximately 5,000 genes/transcripts, with 5 to 6 bar-coded shRNAs per target gene to maximize screening efficiency. The library modules were constructed as a series with non-overlapping sets of target genes. There are currently three modules for human and two modules for mouse available which target 15,000 and 10,000 genes, respectively. The first two library modules for human and mouse target mostly well characterized pathway-associated and disease-associated genes. The third human module targets cell surface and DNA-binding proteins, and other conserved genes. Just like Cellecta's custom libraries, the DECIPHER Project libraries are constructed with shRNA expression cassette oligonucleotides containing unique sequence tags ("bar-codes") synthesized on Agilent's array-based platform. Cellecta also offers free bar-code analyzer/deconvoluter software to assist scientists in processing Illumina HT Sequencing data generated from their RNAi screens. For more information about this powerful new screening tool, visit http://www.addgene.org/decipher/.
MiniPromoters for Brain-Specific Gene Expression
Region and cell-specific expression of a gene of interest is a critical experimental consideration, especially when studying the human brain which by some estimates contains 100 billion cells and possibly 100 trillion cellular connections. In order to address the lack of tools available for brain-region specific gene expression, a team of investigators joined forces to create the Pleiades Promoter Project (www.pleiades.org). Using a novel design pipeline, they produced MiniPromoters derived from endogenous human gene promoter sequences and combined them with reporter genes such as EGFP, EGFP/Cre or LacZ in constructs designed for knock-in insertion of transgenes to yield region specific expression as verified by in vivo experiments in mouse brain. Some MiniPromoters produced neuron or glia specific expression, as expected based on the gene the promoter was taken from, while others produced interesting, but unrelated expression patterns. The MiniPromoters available in the Pleiades Plasmids offer researches a more refined tool to obtain localized gene expression in the brain than previously available.
Portales-Casamar et al., Proc Natl Acad Sci USA 2010 Sep 21; 107(38):16589-94.
Cyclin D1 Reporters
Regulated progression through the cell cycle requires sequential expression of a family of proteins called cyclins. Frank McCormick's group at UCSF recently deposited a series of human cyclin D1 promoter constructs from his Nature 1999 publication with Addgene. Cyclin D1 is over-expressed in many colon carcinomas and has been identified as a target of β-catenin mediated transcription via the core TCF/LEF-binding consensus sites in the promoter region. The McCormick group demonstrates this regulation using Cyclin D1 luciferase reporter constructs containing mutated TCF-binding sites.
Tetsu O, McCormick F. Nature 1999 Apr 1;398(6726):422-6.
New Flavors for Genetically Encoded Ca2+ Indicators (GECOs)
Fluorescent indicators have long been used to measure intracellular Ca2+ levels, an important process in many signaling activities. In a recent Science paper, Robert Campbell’s laboratory at the University of Alberta describe an improved screening method for detecting changes in Ca2+ dependent fluorescence that they used to develop improved genetically encoded Ca2+ indicators, dubbed GECOs. The green (G-GECOs) demonstrate a two-fold improvement in Ca2+-dependent change in fluorescence over earlier fluorescent protein Ca2+ indicators. Blue-shifted (B-GECO) and red-shifted (R-GECO) Ca2+ indicators fill a void in the spectrum of available colors for genetically encoded Ca2+ indicators. By recombining these newly created constructs, additional ratiometric GECOs, GEM-GECO and GEX-GECO, were developed. The GECO plasmids offer researchers additional choice and flexibility when selecting fluorescent Ca2+ indicators.
Zhao et al., Science 2011 Sep 30;333(6051):1888-91.
Transcription Factor Mediated Reprogramming of Fibroblasts into Motor Neurons (iMNs)
Studying cellular subtypes of the central nervous system (CNS) has proven to be challenging. For one, isolating subtypes of the human CNS can be strategically limiting in terms of supply and attainability. Moreover, differentiating embryonic stem cells (ESCs) into neuronal sub-populations has been fairly unsuccessful to date. Kevin Eggan's group at Harvard recently showed that they could use transcription factor-mediated expression to induce mouse and human fibroblasts into spinal motor neurons. This particular subset of neurons controls the contraction of muscle fibers involved in movement. Characterization of these reprogrammed cells showed they exhibit a distinct motor neuron identity . The complete set of reprogramming transcription factors are available at Addgene cloned into a retroviral backbone.
Son EY et al., Cell Stem Cell 2011 Sep 2;9(3):205-18.
Zinc Finger Nuclease Assembly in ZebrafishZinc Finger Nucleases (ZFNs), chimeric fusions between a zinc-finger protein and the nuclease domain of FokI, are used in a wide range of model organisms for gene inactivation. Gene disruption occurs by imprecise repair of a ZFN-induced double-strand break within the coding sequence of a target gene. Using the modular assembly-based approach to ZFNs construction, the Lawson and Wolfe labs from UMass Worcester created a library of over 70 different zinc-finger cassettes. In parallel, the labs assembled a new publicly available database of zebrafish genes that can be targeted by ZFNs. The Lawson and Wolfe labs also demonstrate that ZFNs are a viable tool for creating an heritable gene inactivation in vertebrates by creating several germline mutations in zebrafish.
Zhu et al., Development 2011 Oct;138(20):4555-64.
Vectors for Simplified Multicistronic Expression in
Techniques to produce stable mammalian cell lines have been around for years; however, the ability to stably transform insect cells is especially limited. Because of these limitations, cell-culture based approaches are generally disregarded when attempting to validate chemical/RNAi library screens or produce recombinant protein. The Sutherland Lab has developed two Droshophila vectors, pAc5-STABLE1-Neo and pAc5-STABLE2-Neo, which facilitate the multicistronic expression of proteins without relying on co-transfection with a second vector (for antibiotic selection) or the need for dual-promoters. Both of these versatile vectors allow for either N- or C-terminal tagging with a fluorescent protein and pAc5-STABLE2-Neo gives the additional option of co-expressing a separate fluorescent tag, that can by used for FACS analysis.
Gonzalez et al., Scientific Reports 2011 Aug; 1, Article: 75.
PSmOrange- a Novel Photoswitchable Protein
Photoconvertible proteins are widely used in tracking the migration, fate, and dynamics of cells, organelles, and proteins. Photoconvertible proteins can be divided into those that are photoactivatable- that can be turned on or off; or those that are photoswitchable- that can switch from one color to another. In a recent Nature Methods publication by Vladislav Verkhusha’s group at Albert Einstein, a novel photoswitchable protein, PSmOrange was characterized. PSmOrange is initially Orange (excitation, 548 nm; emission, 565 nm) but becomes far-red (excitation, 636 nm; emission, 662 nm) after irradiation with blue-green light. The photoconverted or the far-red version of PSmOrange is brighter than conventional far-red fluorescent proteins and can be imaged in deep tissues. PSmOrange is in an easy to clone vector and has been used to generate numerous fusion proteins.
Subach et al., Nat Methods. 2011 Jul 31;8(9):771-7.
Golden Gate TALEN and TAL Effector Kit
TAL effector nucleases (TALENs) are fusion proteins containing transcription activator-like (TAL) DNA binding domains fused to the FokI nuclease. TALENs have shown to be robust tools for DNA targeting in a variety of species. Binding specificity is determined by customizable arrays of polymorphic amino acid repeats in the TAL effectors. The Voytas laboratory at the University of Minnesota recently published a system for custom TALEN design and assembly. The Golden Gate TALEN and TAL Effector Kit and accompanying documentation allow one to efficiently assemble TALEN constructs with custom repeat arrays, containing anywhere between 12 and 31 of these repeats. The reagents include a plasmid construct for making custom TAL effectors and one for TAL effector fusions to additional proteins of interest.
Cermac et al., Nucleic Acids Res. 2011 Jul;39(12):e82.
GLI Transcription Factor Improves iPSC Generation
Generating induced pluripotent stem cells (iPSCs) from somatic cells involves finding the “right” combination of factors. The transcription factor Myc has been used successfully in producing iPSCs (in combination with other proteins)- although these mice have been shown to develop cancer. The Yamanaka lab at Kyoto University recently performed a screen to find a transcription factor that could improve efficiency of iPSC generation and potentially improve the viability of iPSC mice. Glis1 (Glis family zinc finger 1) was shown to promote iPSC generation in combination with Oct3/4, Sox2, and Klf4 in both mouse and human fibroblasts- replacing the requirement of Myc in generating iPSCs. Since the beginning of the summer, Glis1 has been requested by over 60 laboratories and continues to be a gene of interest for many researchers. Additional reprogramming factors are also available at Addgene.
Maekawa et al., Nature. 2011 Jun 8;474(7350):225-9.
New Recombinases for Animal Genomes
Site-specific recombination is a robust tool used for controlling gene expression. Site-specific recombinases can be used in animal models to turn expression of a gene on or off, create conditional mutants, or introduce novel genetic material. Gerald Rubin’s lab at the Janelia Farm Research Campus has characterized a set of novel recombinases from yeast- KD, B2, B3, and R. All recombinases were shown to be active in Drosophila and do not cross-react. In addition, KD and B3 were shown to be non-toxic and active in mice. Increasing the number of functional, specific recombinases allows for greater flexibility when performing experiments that involve multiple recombination events. Addgene houses the standard recombinases Flp and Cre, and we’re excited to also host this new set characterized by the Rubin lab.
Nern et al., Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14198-203.
RNAi vectors for improved detection and inducible expression
To improve the efficiency of shRNA delivery and expression, specifically in targeting genes involved in proliferation and survival, Scott Lowe’s laboratory at Cold Spring Harbor has designed a set of plasmids that can be used for tracking and induction of retroviral-mediated shRNA expression. The retroviral plasmids express two transcripts. The first transcript, driven by a tetracycline response element (TRE)-encodes for a dsRed tagged miR-embedded shRNA, while the second transcript encodes for Venus and a mammalian antibiotic resistance cassette or Tet-inducible transactivator (rtTA3). The dual fluorescent system adds sensitivity to detection and the TRE allows for targeted knockdown, helping mimic in vivo therapeutic strategies. The TRMPV vectors, as they’re called, come in a variety of flavors- with different antibiotic resistance cassettes- and make up part of Addgene’s collection of inducible shRNA plasmids.
Zuber et al., Nat Biotechnol. 2011 Jan;29(1):79-83.
STAG2 and Aneuploidy
Todd Waldman’s lab at Georgetown recently showed that mutations in STAG2 can result in aneuploidy. Aneuploidy-- an abnormal number of chromosomes-- is often seen in cancer cells. STAG2 is a member of the cohesin complex, which regulates the separation of sister chromatids during cell division. In the Waldman lab’s recent Science paper (Solomon et al., 2011)- they identify specific STAG2 mutations found in cancer cells- that result in chromosomal disruption. STAG2 plasmids, wild-type and these aneuploidy-associated mutant forms, are now available through Addgene; along with a set of shRNAs targeting STAG2.
Solomon et al., Science. 2011 Aug 19;333(6045):1039-43.
Hot Article Contributors:
Addgene's Hot Article page is a compilation of summaries describing new plasmids available at Addgene and their related journal articles. These summaries were written by: Andy Baltus, Melina Fan, Matthew Ferenc, Melanie Herscovitch, Caroline LaManna, Jason Niehaus, Marcy Patrick, Eric Perkins, and Lianna Swanson.