Tag: NGG

Solved 33. The coding DNA sequence of a human gene contains

Transcribed image text: 33. The coding DNA sequence of a human gene contains 2001 base pairs. A CRISPR-Cas9 experiment is setting up to knock out this gene in the fibroblast cell lines. It is known that the GC content of the coding sequence of this gene is 60%. In CRISPR-Cas…

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A naturally occurring polyacetylene isolated from carrots promotes health and delays signatures of aging

Cell culture conditions Unless otherwise stated, cells were cultured with DMEM (Sigma Aldrich; #D6429) and 4.5 g/l glucose, phenol red, 10% FBS, and 1% penicillin/streptomycin with pH 7.4 and were incubated at 37 °C, 5% CO2, and 95% relative humidity. Wild-type HepG2 (#300198), HEK293 (#300192), and MCF-7 (#300273) were derived from CLS…

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Prime editing-mediated correction of the CFTR W1282X mutation in iPSCs and derived airway epithelial cells

Abstract A major unmet need in the cystic fibrosis (CF) therapeutic landscape is the lack of effective treatments for nonsense CFTR mutations, which affect approximately 10% of CF patients. Correction of nonsense CFTR mutations via genomic editing represents a promising therapeutic approach. In this study, we tested whether prime editing,…

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CRISPR Gene Editing: Cas9 and Beyond

Scientists use the CRISPR-Cas9 system to target a DNA sequence of interest near a protospacer-adjacent motif (PAM). The PAM initiates Cas9-DNA binding, a guide RNA (yellow) invades the double helix (blue) and hybridizes with the target DNA, and Cas9 (red) breaks the unwound double-stranded target DNA. iStock Meletios Verras Stay…

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IJMS | Free Full-Text | CRISPR/Cas9-Mediated Genome Editing in Cancer Therapy

1. Introduction Recently, the morbidity and mortality rates of cancer have been increasing rapidly, posing a significant threat to human health. Cancer, a refractory and multifaceted disease, fundamentally originates from a cumulative series of mutations in the cellular genome and epigenome. These mutations activate oncogenes and deactivate tumor suppressors, leading…

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CRISPR-broad: combined design of multi-targeting gRNAs and broad, multiplex target finding

CRISPR-broad framework We developed a procedural pipeline for detecting gRNAs and implemented this in Python as a standalone application (Fig. 1a). For speeding up gRNA selection, we employed multithreading and used big data Python module Pandas. This allowed splitting millions of short sequences for mapping and processing large numbers of uncompressed…

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GPP Web Portal – Gene Details

Gene: Human LOC642131 (642131) immunoglobulin IGHV1OR15-3-like pseudogene Source: NCBI, updated 2019-09-11 Taxon: Homo sapiens (human) Chromosome: 15 Wildtype Transcripts: NR_135667.1 Additional Resources: NBCI Gene record: LOC642131 (642131) NCBI Gene records for discontinued versions of this gene: LOC102724835 (102724835) sgRNA constructs originally intended to target this gene (CRISPRko, NGG PAM) NOTE:…

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Amerigo Scientific Unveils CRISPR/Cas Enzymes to Expand

Amerigo Scientific, as a distributor focused on providing critical products and services to biomedical and life science communities, announced the release of a groundbreaking selection of CRISPR/Cas enzymes to its extensive life science portfolio, aimed at further expanding the vast potential of the CRISPR toolbox. This addition brings cutting-edge genetic…

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IJMS | Free Full-Text | CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis

1. Introduction Camellia sinensis is an important perennial cash crop and one of the most widely consumed non-alcoholic beverages in the world, with health benefits [1]. Camellia sinensis enriched with secondary metabolites that provide aroma, freshness, and astringent flavour are key determination factors contributing to its quality hence, it is…

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Optimized minimal genome-wide human sgRNA library

sgRNA collection and enzyme cut site annotation All sgRNAs corresponding to potential NGG-containing target sites on the human (GRCh38/hg38) genome were calculated by a customized Perl script. The enzyme cut site was set at the 17 position from 5’ to 3’ of each sgRNA sequence. These sgRNAs have more than…

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CRISPR-Cas Gene Editing Teaching Resources | Bio-Rad / Free Group Study Rooms with Timer & Music

One of the most exciting recent developments in genetic engineering is CRISPR-Cas9 (CRISPR). CRISPR derives its name from “clustered regularly interspaced short palindromic repeats,” genomic sequences that microbiological used to defending themselves vs viral attacks. Along with CRISPR associated (Cas) bio, bacteria use the sequences toward recognize and disarm future…

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GSK gonorrhea vaccine fast tracked

The US Food and Drug Administration (FDA) has granted a Fast Track designation for GSK plc’s Neisseria gonorrhoeae investigational vaccine (NgG). The vaccine candidate is currently in an ongoing phase II trial and aims to demonstrate proof of concept by assessing the efficacy of the NgG vaccine in healthy adults,…

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Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects

Amino acid sequence comparisons between GAS and GBS Cas9 identify orthologous active sites Relationships between the amino acid sequence of GBS Cas9 endonuclease and its molecular functions can be deduced from detailed studies of its GAS ortholog, SpyCas9 (Supplementary Fig. 1). As a first step in locating DNA complementary to a…

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acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens

acCRISPR framework acCRISPR performs essential gene identification by calculating two scores for each sgRNA, namely the cutting score (CS) and the fitness score (FS). CS and FS are the log2-fold change of sgRNA abundance in the appropriate treatment sample with respect to that in the corresponding control sample (see Supplementary…

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Optimized metrics for orthogonal combinatorial CRISPR screens

Plasmid design The information on each plasmid for combinatorial libraries is indicated in Supplementary Table S1. Plasmids used in this study to generate combinatorial libraries for SpCas9, enAsCas12a, CHyMErA, enAsCas12a (dual-gRNA), CHyMErA.v2, multiSPAS were deposited to Addgene (IDs: 189632, 189633, 189634, 189635, 189636, 189637, respectively). 3Cs oligonucleotide design The protocol…

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Ex vivo prime editing of patient haematopoietic stem cells rescues sickle-cell disease phenotypes after engraftment in mice

Optimizing prime editing systems for HSPCs We previously reported the use of prime editing to correct HBBS by plasmid transfection in HEK293T cells containing the SCD mutation, reaching up to 58% efficiency (Fig. 1a)24. In contrast to HEK293T cells, HSPCs are difficult to transfect with plasmid DNA but are amenable…

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PCR detection of the pKM.19/ScrfI RFLP (D7S23), a marker closely linked to the cystic fibrosis mutation

Please use this identifier to cite or link to this item: hdl.handle.net/2445/42445 Title:  PCR detection of the pKM.19/ScrfI RFLP (D7S23), a marker closely linked to the cystic fibrosis mutation Author:  Nunes Martínez, VirginiaChillón, MiguelLench, N.Ramsay, M.Estivill, Xavier,…

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IJMS | Free Full-Text | High-Efficiency CRISPR/Cas9-Mediated Correction of a Homozygous Mutation in Achromatopsia

1. Introduction Achromatopsia (ACHM) is an inherited retinal dystrophy (IRD) affecting approximately 1 in every 30,000 individuals [1,2]. It is an autosomal-recessive disorder associated with a loss of cone photoreceptor function [1,2,3,4]. ACHM usually shows an early onset presenting pendular nystagmus, poor visual acuity, lack of color vision, and photophobia…

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The CRISPR/Cas9 syst…

The CRISPR/Cas9 system is made of Cas9 nuclease and single-guide RNA (sgRNA). The sgRNA is an engineered single RNA molecule containing crispr RNA and tracr RNA parts. The sgRNA recognizes the target sequence by standard Watson-Crick base pairing. It has to be followed by a DNA motif called a protospacer…

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Single and multiplexed gene repression in solventogenic Clostridium via Cas12a-based CRISPR interference

. 2022 Dec 24;8(1):148-156. doi: 10.1016/j.synbio.2022.12.005. eCollection 2023 Mar. Affiliations Expand Affiliation 1 Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, 70118, United States. Free PMC article Item in Clipboard Rochelle Carla Joseph et al. Synth Syst Biotechnol. 2022. Free PMC article Show details Display options Display options…

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CRISPR-SpRYgests Enable Precise Cleavage of DNA Bases In Vitro

NEW YORK — A CRISPR-Cas variant engineered to no longer need a protospacer adjacent motif (PAM) can be harnessed to make cuts at any DNA base in vitro, a new study reports. Its ability to make precise breaks anywhere could be applied to a number of DNA engineering applications. Researchers…

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Bio-informatic analysis of CRISPR protospacer adjacent motifs (PAMs) in T4 genome | BMC Genomic Data

The clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) defensive system is an acquired mechanism in prokaryotes which is analogous to RNAi in eukaryotes [1]. The CRISPR machinery is a complex immune strategy that is continually evolving in the bacterial genome to accommodate the rapid changes in the nucleic acids of…

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GPP Web Portal – Transcript Details

Transcript: Human XR_933717.2 PREDICTED: Homo sapiens uncharacterized LOC105371334 (LOC105371334), ncRNA. Source: NCBI, updated 2019-09-08 Taxon: Homo sapiens (human) Gene: LOC105371334 (105371334) Length: 321 CDS: (non-coding) sgRNA constructs matching this transcript (CRISPRko, NGG PAM) This list includes CRISPRko constructs with 100% (20mer + NGG) sequence match to the exonic sequence of…

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Industrializing CRISPR

Sponsored content brought to you by Kevin Holden, PhD Kevin Holden, PhD, Head of Science at Synthego, discusses the importance of industrializing CRISPR as the technology matures and makes inroads in the clinic. GEN: What’s new and interesting to you in the world of CRISPR? HOLDEN: Some of the most…

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CRISPR Applications in Medicine Depend on Minimizing Off-Target Editing

By Rolf Turk, PhD Genome editing technologies, such as CRISPR, are being applied to better understand basic biological systems as well as to research new kinds of gene and cell therapies. The CRISPR-Cas9 system comprises a Cas9 endonuclease protein that forms a complex with a guide RNA (gRNA) molecule, which…

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High-purity production and precise editing of DNA base editing ribonucleoproteins

Abstract Ribonucleoprotein (RNP) complex–mediated base editing is expected to be greatly beneficial because of its reduced off-target effects compared to plasmid- or viral vector–mediated gene editing, especially in therapeutic applications. However, production of recombinant cytosine base editors (CBEs) or adenine base editors (ABEs) with ample yield and high purity in…

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CRISPR: Guide to gRNA design

Introduction to CRISPR in SnapGene Genome editing technology has been evolving for many years. The Holy Grail of genome engineering has always been to introduce a specific genetic change that affects only the genomic target and leaves no undesired changes in the DNA. The discovery and application of the bacterial…

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