...for studying colloidal gold (1).  The method was based on using a thin plane (sheet) of light generated...microscopes, optical sectioning of a specimen is based on discriminating the out-of-focus reflected light... combining Ultramicroscopy with tetrahydrofuran-based tissue clearing (13,14). A few years later, Karl...Deisseroth’s lab developed CLARITY, which is a hydrogel-based method that also allows antibody penetration for...recently developed AAV (adeno-associated virus)-based fluorescent labeling methods that can be used with...

...microbiome studies.  Find the MAGIC plasmids here Paper-based synthetic biology approach to analyze gut microbiota...microbiome, James Collins’s lab developed a paper-based method that can be used to detect microbes and biomarkers...As mRNA expression cannot be identified with DNA-based qPCR methods, the ability to detect mRNA transcripts...Takahashi, Melissa K., et al. "A low-cost paper-based synthetic biology platform for analyzing gut microbiota...

...slightly with either a 1-7 base poly(U)tail in tRNA-gRNA constructs or a 1-4 base tail from the second tRNA... cassettes (considering the gRNA itself is ~100 bases) limit the number of gRNAs that can be packaged ...Pseudomonas aeruginosa to cleave 4 gRNAs separated by 28 base Csy4 recognition sites from a polycistronic transcript...

...LoxP (locus of X(cross)-over in P1) sites are 34-base-pair long recognition sequences consisting of two...event. This event can have three general outcomes based on the location and orientation of the loxP sites...above, a genetic modification can be restricted based on experimental constraints. This has been used ...asymmetric spacer "NNNTANNN", where "N" indicates which bases may vary from the canonical sequence. Among these...

...options come in two categories: protein-based and chemical-based. Before selecting one, check your antibody...concentration. That makes the choice easy! Protein-based blockers include dry non-fat milk or serums like... of blocker, you can also use gelatin.  Protein-based blockers are inexpensive and easily made in the ... tip! If you get a speckled image, your protein-based blocker is either degraded or not completely mixed...mixed together.   Commercially available chemical-based blockers, while much more expensive, are consistent...to another. Since antibody binding varies wildly based on proteins, and their differing amounts of available...Smaller dynamic range; no multiplexing Protein-based blocker Degrades quickly Wet transfer Increased...

...years, deaminase-mediated base editing (cytosine base editor or adenine base editor) and reverse transcriptase-mediated...in Zhu et al., 2019). Both cytosine base editors and adenine base editors have been developed for plants...Belhaj et al., 2013). Nuclease dead Cas9 (dCas9) based activators (such as dCas9-VP64) or repressors (dCas9...

...process. Each variant is assigned a functional score based on its library frequency before selection compared...libraries of DNA fragments that contain variable bases (NNN) at any given codon site of interest can be... technique described in Wrenbeck et al is a PCR-based approach for generating a customizable comprehensive...primer set contains three consecutive randomized bases (NNN) at a given codon site and multiple primer ...Keith E J Tyo, and Timothy A. Whitehead. "Plasmid-based one-pot saturation mutagenesis." Nature Methods ...contain random synthesis errors, especially single basepair deletions. Therefore, Gibson assembly is better...codons that can be mutated? 88 codons, or 264 basepairs, was the maximum length tested by Wrenbeck et ...

...scientific field-based solutions or open source solutions. In comparison to paper-based record keeping,...notebooks and researcher's needs The familiar paper-based lab notebook is still a standard approach to record-keeping... or brainstorm, but we have to admit that paper-based record keeping barely copes with the growing amounts...future? As most payable software solutions have user-based pricing, it is good to know how many of your lab...

...day, you should be happy to learn that many DNA-based reagents are named for soup ingredients! From pSOUP... intracellular RNA dynamics. Aptamers are 10-100 base nucleic acid oligos that bind with high affinity...that control the expression of coding RNA. Spinach-based riboswitches can be used as stable metabolite sensors...mimic of green fluorescent protein by fluorescence-based selection and directed evolution." Journal of the...PMC4244833. Kellenberger, Colleen A., et al. "RNA-based fluorescent biosensors for live cell imaging of ...

... modifications (~1-50 base pairs). Small edits require as little as 30-50 bases for each homology arm,...arm, but keep in mind these numbers may vary based on your locus of interest and experimental system.  Synthesizing...  Synthesizing ssODNs longer than 200 bases can be difficult, thus dsDNA plasmids are generally preferred...Learn about Non-Homologous End Joining Learn about Base Editing Read 3 Tips to Improve HDR Efficiency ...

...latency (Bialek et al., 2016). Additionally, CRISPR-based activation can be made inducible upon environmental...through all the troubleshooting required for Cas9-based activation. CRISPRa for genome-wide studies One ...larger scale of activation allows for exploratory-based research as well. For example, CRISPRa can be used... interactions. Additionally, large scale CRISPR-based screens can be used to gain insight into protein...date his group has develop several popular CRISPR-based tools for altering DNA sequence or regulating gene...

...amino acid linker to use. These decisions were made based on known functional aspects of the protein gleaned...sequence into which it is being inserted: one thousand base pairs on each side, in fact. Later, when we transfect...precautionary measure, it’s also good to make a few single base pair mutations in crRNA target sites found within...endogenous gene tagging systems. Addgene’s CRISPR-based Protein Tagging collection includes systems for ...

...developed a video-based high-throughput screen for directed evolution of biosensors based on their dynamic...says Aggarwal. This biosensor changes fluorescence based on the release of glutamate from neurons and this...has developed new redox sensitive GFP2 (roGFP2)-based biosensors for live cells. His work focuses on the...

...will focus on one of the most common, purification based on the polyhistidine tag. What is the polyhistidine...tag was developed as a means to purify a protein based on the affinity of the imidazole ring of histidine...Bornhorst 2000).  One downside of polyhistidine tag-based purification, however, is the propensity for nonspecific... tags can also be used as a target for antibody based assays. Antibodies are useful tools for studying...

...Reporter signals may be electrochemical or light-based, with luminescent and fluorescent reporters being... domain induces changes in a fluorescent signal based on ligand presence or changing cellular conditions...Method Notes Quantification of a process Plate-based assays (plate reader) Detect the average amount...

...repository for DNA-based materials, including our popular kits and libraries. This DNA-based materials repository...

...initiating a base editor-based clinical trial for SCD in 2022 and Editas Medicine starting a Cas12-based clinical... today. Below we will review some of the CRISPR-based editing therapies that are currently approved or...

...called GMAP (Gibson assembly-based modular assembly platform). GMAP is based on the Gibson Assembly method... Cas9-based AID tagging Seven years ago, Masato Kanemaki's lab successfully used the plant-based auxin-inducible...University, we are now providing a powerful CRISPR-based screening source for the Drosophila community as... it is composed of two sub-pools. The first is a base “90k library” that contains ~90,000 gRNAs that target... biosensor A pH-sensitive fluorescent biosensor-based assay system was recently deposited with Addgene...University of Zagreb, constructed a CRISPR-Cas9-based tool for targeting CpG methylation by fusing catalytically...proteins in a target cell. In addition to nucleotide-based linking strategies, post translational protein fusion...

...polymerase, the construction of specific sequences for base pair overhangs, insert and vector purification, ...specific to the insert with an additional 15-17 bases that are complementary to the overlapping vector...introduced into my inserts. However, with any PCR-based cloning technique there is a chance of introducing...

...robust protocol it does have limitations. The enzyme-based CUT&RUN method overcomes many of these limitations...interacting. The CUT&RUN method Enter CUT&RUN, an enzyme-based protocol for identifying DNA binding patterns that...sets, of which there are many readily available. Based on the success that our lab and others have had ...