scholarly journals Improving the efficiency of precise genome editing with site-specific Cas9-oligonucleotide conjugates

2020 ◽  
Vol 6 (15) ◽  
pp. eaaz0051 ◽  
Author(s):  
Xinyu Ling ◽  
Bingteng Xie ◽  
Xiaoqin Gao ◽  
Liying Chang ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Genome Editing ◽  
Therapeutic Potential ◽  
Chemical Reactivity ◽  
Specific Chemical ◽  
Site Specific ◽  
Additional Tool ◽  
Homology Directed Repair ◽  
Chemically Modified ◽  
Dna Template ◽  
Oligonucleotide Conjugates

Site-specific chemical conjugation of proteins can enhance their therapeutic and diagnostic utility but has seldom been applied to CRISPR-Cas9, which is a rapidly growing field with great therapeutic potential. The low efficiency of homology-directed repair remains a major hurdle in CRISPR-Cas9–mediated precise genome editing, which is limited by low concentration of donor DNA template at the cleavage site. In this study, we have developed methodology to site-specifically conjugate oligonucleotides to recombinant Cas9 protein containing a genetically encoded noncanonical amino acid with orthogonal chemical reactivity. The Cas9-oligonucleotide conjugates recruited an unmodified donor DNA template to the target site through base pairing, markedly increasing homology-directed repair efficiency in both human cell culture and mouse zygotes. These chemically modified Cas9 mutants provide an additional tool, one that is complementary to chemically modified nucleic acids, for improving the utility of CRISPR-Cas9–based genome-editing systems.

scholarly journals Genome Editing With Targeted Deaminases

2016 ◽  
Author(s):  
Luhan Yang ◽  
Adrian W. Briggs ◽  
Wei Leong Chew ◽  
Prashant Mali ◽  
Marc Guell ◽  
...  
Keyword(s):  
Genome Editing ◽  
Dna Cleavage ◽  
Zinc Finger Nucleases ◽  
Human Stem Cells ◽  
Site Specific ◽  
Cytidine Deaminases ◽  
Genetic Modifications ◽  
Reduced Toxicity ◽  
A Site ◽  
Dna Template

Precise genetic modifications are essential for biomedical research and gene therapy. Yet, traditional homology-directed genome editing is limited by the requirements for DNA cleavage, donor DNA template and the endogenous DNA break-repair machinery. Here we present programmable cytidine deaminases that enable site-specific cytidine to thymidine (C-to-T) genomic edits without the need for DNA cleavage. Our targeted deaminases are efficient and specific in Escherichia coli, converting a genomic C-to-T with 13% efficiency and 95% accuracy. Edited cells do not harbor unintended genomic abnormalities. These novel enzymes also function in human cells, leading to a site-specific C-to-T transition in 2.5% of cells with reduced toxicity compared with zinc-finger nucleases. Targeted deaminases therefore represent a platform for safer and effective genome editing in prokaryotes and eukaryotes, especially in systems where DSBs are toxic, such as human stem cells and repetitive elements targeting.

Reactive Nanopattern in a Triple Structured Bio-Inspired Honeycomb Film as a Clickable Platform

2018 ◽  
Author(s):  
Pierre Marcasuzaa ◽  
Samuel Pearson ◽  
Karell Bosson ◽  
Laurence Pessoni ◽  
Jean-Charles Dupin ◽  
...  
Keyword(s):  
Self Assembly ◽  
Double Porosity ◽  
Surface Groups ◽  
Specific Chemical ◽  
Site Specific ◽  
Surface Functionality ◽  
Wenzel State ◽  
Breath Figure ◽  
Responsive Surfaces ◽  
Secondary Population

A hierarchically structured platform was obtained from spontaneous self-assembly of a poly(styrene)-<i>b</i>-poly(vinylbenzylchloride) (PS-<i>b</i>-PVBC) block copolymer (BCP) during breath figure (BF) templating. The BF process using a water/ethanol atmosphere gave a unique double porosity in which hexagonally arranged micron-sized pores were encircled by a secondary population of smaller, nano-sized pores. A third level of structuration was simultaneously introduced between the pores by directed BCP self-assembly to form out-of-the-plane nano-cylinders, offering very rapid bottom-up access to a film with unprecedented triple structure which could be used as a reactive platform for introducing further surface functionality. The surface nano-domains of VBC were exploited as reactive nano-patterns for site-specific chemical functionalization by firstly substituting the exposed chlorine moiety with azide, then “clicking” an alkyne by copper (I) catalyzed azide-alkyne Huisgen cycloaddition (CuAAC). Successful chemical modification was verified by NMR spectroscopy, FTIR spectroscopy, and XPS, with retention of the micro- and nanostructuration confirmed by SEM and AFM respectively. Protonation of the cyclotriazole surface groups triggered a switch in macroscopic behavior from a Cassie-Baxter state to a Wenzel state, highlighting the possibility of producing responsive surfaces with hierarchical structure.

scholarly journals AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Liyang Zhang ◽  
John A. Zuris ◽  
Ramya Viswanathan ◽  
Jasmine N. Edelstein ◽  
Rolf Turk ◽  
...  
Keyword(s):  
T Cells ◽  
Nk Cells ◽  
Genome Editing ◽  
Nk Cell ◽  
Basic Research ◽  
Cell Recognition ◽  
Site Specific ◽  
Editing Efficiency ◽  
Rapid Generation ◽  
Therapeutic Cell

AbstractThough AsCas12a fills a crucial gap in the current genome editing toolbox, it exhibits relatively poor editing efficiency, restricting its overall utility. Here we isolate an engineered variant, “AsCas12a Ultra”, that increased editing efficiency to nearly 100% at all sites examined in HSPCs, iPSCs, T cells, and NK cells. We show that AsCas12a Ultra maintains high on-target specificity thereby mitigating the risk for off-target editing and making it ideal for complex therapeutic genome editing applications. We achieved simultaneous targeting of three clinically relevant genes in T cells at >90% efficiency and demonstrated transgene knock-in efficiencies of up to 60%. We demonstrate site-specific knock-in of a CAR in NK cells, which afforded enhanced anti-tumor NK cell recognition, potentially enabling the next generation of allogeneic cell-based therapies in oncology. AsCas12a Ultra is an advanced CRISPR nuclease with significant advantages in basic research and in the production of gene edited cell medicines.

IL-4 Analogues with Site-Specific Chemical Modification at Position 121 Inhibit IL-4 and IL-13 Biological Activities

2013 ◽  
Vol 25 (1) ◽  
pp. 52-62 ◽  
Author(s):  
Viswanadham Duppatla ◽  
Maja Gjorgjevikj ◽  
Werner Schmitz ◽  
Heike M. Hermanns ◽  
Carmen M. Schäfer ◽  
...  
Keyword(s):  
Chemical Modification ◽  
Biological Activities ◽  
Specific Chemical ◽  
Site Specific ◽  
Specific Chemical Modification

scholarly journals Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification

2006 ◽  
Vol 34 (17) ◽  
pp. 4900-4911 ◽  
Author(s):  
Sujiet Puthenveetil ◽  
Landon Whitby ◽  
Jin Ren ◽  
Kevin Kelnar ◽  
Joseph F. Krebs ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Chemical Modification ◽  
Dependent Protein Kinase ◽  
Specific Chemical ◽  
Site Specific ◽  
Specific Chemical Modification ◽  
Dependent Protein

Targeted chemical nucleases have a wide range of untapped applications in biological fields, including gene therapy

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Metal Complex ◽  
Dna Cleavage ◽  
Therapeutic Potential ◽  
Chemical Reactivity ◽  
Major Groove ◽  
Sequence Recognition ◽  
Wide Range ◽  
Chemical Nucleases

A feasible alternative to state-of-the-art enzymatic nucleases was created by regulating the cleavage activity of metal complexes using (covalent or non-covalent) homing agents. Targeted AMNs, unlike enzymatic nucleases, break DNA by an oxidative mechanism and can therefore permanently knock off genes. Compared to larger enzymatic nucleases, the modest size of the metal complex may aid cellular transfection. Furthermore, the painstaking construction of the sequence-specific probe permits a metal complex to be directed to dsDNA's minor or major groove. To direct the chemical reactivity of several small-molecule compounds to dsDNA's minor groove, covalently bonded polyamide samples were used. PNA and DNA were also used to construct antisense and antigen hybrids, with Watson–Crick or Hoogsteen base pairing with major groove nucleobases giving sequence recognition. Click chemistry created chimeric AMN-TFOs with desirable focused effects and negligible off-target cleavage. Clip-Phen-modified TFOs, 230 polypyridyl-modified TFOs, 232 and intercalating phenanthrene-modified TFOs are three contemporary instances of copper AMN–TFOs. All three systems have distinct advantages in maintaining the desired 2:1 phenthroline/copper ratio for DNA cleavage (clip-Phen TFOs), caging the copper center and facilitating efficient ROS-mediated strand scission (polypyridyl-modified TFO) and improving triplex stability (polypyridyl-modified TFO) (phenanthrene-TFOs). Cerium (IV)/EDTA complexes, recently shown to bind and hydrolytically cleave ssDNA/dsDNA junctions and used in conjunction with PNA to successfully introduce genome changes in vitro and in vivo, are another important class of targeted chemical nucleases. The chemical reactivity and wide flexibility of metal complex design, combined with their coupling to sequence specific samples for directed applications, show that these compounds have a wide range of untapped applications in biological fields such as chemotherapy, protein engineering, DNA footprinting, and gene editing. Parallel advancements in cell and tissue targeting will be essential to maximise their therapeutic potential, either by using specific ligands or creating new targeting modalities.

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