Skip to main content
Addgene

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

In Category

We narrowed to 43 results for: stem loop

Showing: 1 - 20 of 43 results

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

    Type
    Blog Post
    Published
    June 4, 2024, 1:15 p.m.
    ...separating it into two strands: the stem loops and the guide region. The stem loops bind along the outside of the...doubles back on itself at the bottom of the image. Stem loops 1 and 2 extend horizontally across both lobes... guide RNA in this structure does not include stem loop 3, and guide RNA nucleotides 11-20 are not resolved... the protein, spanning both lobes. Stem loop 1, nestled between the REC and CTD domains, is required for... for Cas9 nuclease function. Stem loops 2 and 3 are not strictly necessary for in vitro cleavage, but ...strand are not resolved due to disorder. All three stem loops and all 20 guide bases of the RNA are shown. ...stabilizes the last base pair with an end-capping loop (Nishimasu et al., 2014). This cap is where the ...

  2. Hot Plasmids - September 2019 - CRISPR, Auxin Inducible Degradation, MerMAID Channelrhodopsins, and Genome Looping

    Type
    Blog Post
    Published
    Sept. 3, 2019, 1:15 p.m.
    ...synthetic looping, the Phillips-Cremins lab developed the light-activated-dynamic-looping (LADL) system. The...our chromatin is comprised of thousands of loops. These loops not only provide a 3-D structure for packing... endogenous looping on distal promoters and enhancers, or have attempted to engineer loops to create genomic...Communications, 2019. PubMed PMID: 31346176. Using LADL to loop with light Article contributed by Eric Perkins Mammalian...interactions that wouldn’t normally occur. The synthetic looping factors developed thus far for these latter experiments... are over 500kB apart, they were able to observe loop formation as well as increased Zfp462 expression...the dynamic nature of genomic looping due to it’s briefer time scale and its inducible and reversible nature...

  3. Opto-Nanobodies: Using Light to Manipulate Cell Signaling and Protein Purification

    Type
    Blog Post
    Published
    Nov. 19, 2019, 2:08 p.m.
    ... eight surface-exposed loops of an mCherry nanobody. Only insertion into loops 1 and 6 resulted in light...opposite effects: insertion into loop 1 caused dark-induced binding while loop 6 insertion caused blue-light...AsLOV2 into loop 1 always generated OptoNBs with dark-induced binding, but insertion into loop 6 generated...mCherry #1 mCherry #2 GFP Loop 1 dark-induced dark-induced dark-induced Loop 6 blue-light induced dark-induced...binding of their target proteins. The surface-exposed loops of nanobodies seemed like a good place to put AsLOV2...membrane-localized mCherry or GFP protein. With this system, if the OptoNB can bind, it co-localizes with its...

  4. All in a Twist: dsRNA

    Type
    Blog Post
    Published
    Feb. 2, 2023, 2:15 p.m.
    ...prone to persistent R-loop formation, presumably due to their abundance of R-loops and repetitive sequence...the 3-stranded structure produced is known as an R-loop. During transcription, RNA is synthesized from ...intermediates in the process. These transcription-coupled R-loops are transient in nature and will dissociate when...these nucleic acid hybrids are always around. R-loops are particularly enriched in highly transcribed ...sequence. All of the R-loops described above play distinct roles in promoting cellular processes and functions...DNA strand. A ssDNA molecule exists within the R-loop that is now vulnerable to various forms of DNA damage...strike a balance between productive levels of R-loops and putting DNA at risk. Consequences of duplexed...

  5. Multiplexed Capture of Promoter-enhancer 3D Chromatin Structures Using CRISPR

    Type
    Blog Post
    Published
    July 2, 2020, 12:40 p.m.
    ...of gene regulation, but enhancers and chromatin looping play important supporting roles. Enhancers are ... regulate, but are brought in proximity by the looping of chromatin, the complex of DNA and proteins that...of 3C methods as taking a snapshot of chromatin looping with the photo “developed” by analyzing DNA sequencing...ends created are then ligated together to create loops of DNA. This is key to linking pieces of DNA that... populations. Key components of the CAPTURE 2.0 system To improve upon the original CAPTURE method, the...enzyme BirA Endogenous biotin ligases Expression system Stable cell line expressing 1) FLAG-biotin-tagged...

  6. Beyond the Blood Brain Barrier: PHP.B Enters the Central Nervous System Via the LY6A Receptor

    Type
    Blog Post
    Published
    July 23, 2019, 12:46 p.m.
    ...Stanford. "Concise review: stem cell antigen‐1: expression, function, and enigma." Stem cells 25.6 (2007): 1339...AAV9 mutants that had a small randomized peptide loop inserted in the AAV9 capsid. This mutant library...Deverman and Wilson labs determined LY6A, also known as stem cell antigen-1 (SCA-1), is the receptor used by ...commonly used to enrich adult mouse hematopoietic stem cells. Its ligand(s) has not been identified. While...of LY6A, but a mutation in PHP.B’s unique capsid loop disrupted binding. Collectively these results suggest...barriers to gene therapy treatment of central nervous system (CNS) diseases is the blood brain barrier (BBB)...delivery to the central and peripheral nervous systems." Nature neuroscience 20.8 (2017): 1172. PubMed...

  7. Lighting Up Cell Signaling with Photoswitchable Kinases

    Type
    Blog Post
    Published
    July 25, 2017, 1:20 p.m.
    ...Studying negative feedback loops of signaling pathways Negative feedback loops are a common feature of signal...potentially be created by inserting pdDronpa domains into loops of a protein of interest. If you plan to try this...kinases and use MEK1 as a model kinase. In this system, light is used to turn “on” and “off” MEK1 activity...cytoplasm. This all-optical psMEK1 + ERK KTR-mRuby2 system has several advantages over existing methods. First... or growth factors are used as a stimulus. This system also allows precise modulating of a particular ... kinases could possibly be used in other model systems, but they need to be expressed in a tissue or organism...

  8. Pooled CRISPR Libraries Offer Genome-Wide Control for Large-Scale Functional Screens

    Type
    Blog Post
    Published
    Feb. 24, 2015, 7:50 p.m.
    ...incorporating two MS2 RNA aptamers at the tetraloop and stem-loop 2; 3. The MS2-P65-HSF1 plasmid which expresses...The structural details revealed two exposed RNA loops, which Konermann recognized as an ideal spot to ...activation in mind. “We had not managed to create a system to allow us to reliably activate essentially any... to selectively activating them with the CRISPR system was a large one.  The question for her then was...it’s working. You can only do that screen with a system you are really confident about working for most...colleagues in Feng Zhang’s lab describe just such a system, which they call CRISPR/Cas9 Synergistic Activation... RefSeq database. The key to developing the new system, Konermann explained, was new knowledge about Cas9...

  9. Fluorescent Proteins 101: Aptamer Fluorophores

    Type
    Blog Post
    Published
    April 11, 2017, 2:30 p.m.
    ...the stem in an RNA stem-loop structure (see Fig. 1a). When the aptamer binds its ligand, the stem loop...to target molecules. Using a technique called systematic evolution of ligands by exponential enrichment...fluorescence to create an improved fluorescent aptamer system. Knowing that GFP’s  structure stabilizes a 4-hydroxybenzylidene...8. Sassolas, Audrey, et al. “Optical detection systems using immobilized aptamers.” Biosens Bioelectron...

  10. CRISPR 101: Homology Directed Repair

    Type
    Blog Post
    Published
    Jan. 26, 2023, 2:15 p.m.
    ...DNA structure referred to as the displacement loop (D loop). The recombination intermediates can then ... Unlike in DSBR, following strand invasion and D loop formation, the newly synthesized portion of the ...based on your locus of interest and experimental system.  Synthesizing ssODNs longer than 200 bases can...efficiency varies across loci and experimental systems, ssODN templates generally provide the highest ...References: Genome engineering using the CRISPR-Cas9 system. Ran FA, et al. Nature Protocols Nov;8(11):2281...Genome Engineering Approaches with the CRISPR/Cas9 System. Li, K et al. PLoS ONE 9(8); (2014). PubMed. ...

  11. Hot Biosensors 2022: Year-End Roundup

    Type
    Blog Post
    Published
    Dec. 6, 2022, 2:15 p.m.
    ...region-to-IntrAcellular loop linkers” (MTRIA for short), where a fluorescent protein is inserted into one of the loop regions... a circularly-permuted GFP into an intracellular loop of various G-protein-coupled receptors. Image adapted...Toettcher and colleagues describe pYtags, a modular system for monitoring specific RTK activation in vivo ...

  13. Antibodies 101: Reading a Flow Plot

    Type
    Blog Post
    Published
    Feb. 6, 2024, 3:13 p.m.
    ... which can send you in an endless loop. Let’s break out of the loop with all you need to know on how to...Evaluation of in vitro chondrocytic differentiation: A stem cell research initiative at the King Abdulaziz University...

  14. Build Your CRISPR Vocabulary

    Type
    Blog Post
    Published
    July 2, 2024, 1:15 p.m.
    ...antirepeat duplex. tracrRNAs also contain multiple stem loops that are recognized by the Cas9 protein from ...biology, too. CRISPR is an elegant bacterial immune system and an efficient gene editing tool… but boy does...bacterial chromosome encodes a tracrRNA (in some systems including Cas9), Cas proteins, and a CRISPR array...nontarget strand. Protein Cas: Different CRISPR systems involve different proteins, but many of them are... of DNA to be cut, which varies between CRISPR systems. Cas proteins won’t cut DNA that doesn’t have their...folds back on itself, simplifying the CRISPR-Cas9 system for laboratory applications. At Addgene, we sometimes...

  15. No Llamas Required - Synthetic Nanobodies Against Membrane Proteins

    Type
    Blog Post
    Published
    June 18, 2020, 1:15 p.m.
    ...structures (concave, loop, and convex). Each of these 3 mRNA libraries have a concave, loop, or convex scaffold...Sybody Generation Toolbox plasmid kit: SB_concave, SB_loop, SB_convex. These scaffolds contain serines and...to 1012 members) in comparison to other display systems using phage and yeast (109-1010 members). This ...FX Cloning: A Versatile High-Throughput Cloning System for Characterization of Enzyme Variants. In: Methods...

  16. Degrading DNA with Cascade-Cas3

    Type
    Blog Post
    Published
    Feb. 11, 2025, 2:15 p.m.
    ...unwinding of dsDNA occur simultaneously, which creates a loop in the target strand that is cut occasionally as... Taylor, D. W. (2023). Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular...editing. Class 1 CRISPR systems make up the majority of CRISPR-based immune systems in bacteria and archaea...Cascade-Cas3 plasmids in Addgene's collection! A “complex” system Cas3 is part of the Class 1 CRISPR family, which...genomic editing. Specifically, these types of CRISPR systems work using a multi-Cas complex called Cascade (...further broken down into different types, with Cas3 systems making up type I, the most abundant type in the...Cascade is an important component of the CRISPR Cas3 system. Most Cascade complexes are comprised of a combination...

  17. Using Phosphoserine to Study Protein Phosphorylation

    Type
    Blog Post
    Published
    June 23, 2016, 2:30 p.m.
    ...requisite dual phosphorylation events on its activation loop, but can be made constitutively active through phosphomimetic...mentioned, phosphomimetic mutations on the activation loop do not fully activate MEK1. In fact, replacing just...on protein phosphorylation in an array of model systems coupled with advances in mass spectrometry suggest...kinase specificity in vitro. The establishment of a system in which purified, recombinant protein could be...researchers to create an orthogonal translation system (OTS) for the incorporation of phosphoserine directly... recombinant proteins (5). Optimization of this system defined three components required for translation...open reading frame of interest. Two expression systems have been verified for use by the Rinehart lab:...

  18. CRISPR Between the Genes: How to Experiment with Enhancers and Epigenomics

    Type
    Blog Post
    Published
    Aug. 9, 2016, 2:30 p.m.
    ... the ENCODE project, find enhancers in embryonic stem cells, and conclude with a targeted CRISPR screen..., an essential transcription factor in embryonic stem cells (ESCs). Your ChIP-seq finds just over 13,000...reveals which NANOG-related genes are critical to stem cell survival. Knowing which genes influence the...screen. We start by infecting millions of embryonic stem cells (ESCs) with a lentiviral vector, an attenuated...step 2. The result is a heterogenous population of stem cells, usually housed in a single flask. Through...enhancer it targets is a “pillar of function” for our stem cells. Remove this pillar and the ESC dies. Order...of which stretches of the genome are pillars for stem cells, or metastasized tumor cells, or alzheimers-affected...

  19. Plasmids 101: Sequence and Ligation Independent Cloning (SLIC)

    Type
    Blog Post
    Published
    Sept. 26, 2024, 1:15 p.m.
    ... ssDNA secondary structure — for example, the stem-loop structure of transcriptional terminators. Another...cloning) would be a true rebel. Not only does this system not use site-specific recombination, it also doesn...’t require a ligation step. Based on the robust system of homologous recombination found in E. coli, SLIC...

  20. Supporting Rare Disease Research with the 2020 BeHEARD Awards

    Type
    Blog Post
    Published
    Sept. 8, 2020, 2 p.m.
    ...cytokines are a potent inducer of an autoinflammatory loop: keratinocytes both respond to and release IL-36...aortic disease,” Prakash says. In induced pluripotent stem cells derived endothelial cells from women who are...
Showing: 1 - 20 of 43 results