Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases

2021 ◽  
Author(s):  
Louise Moyle
Keyword(s):  
Dna Cleavage ◽  
Drag And Drop

scholarly journals Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases

2021 ◽  
Author(s):  
Eleonora I. Ioannidi ◽  
Matthew T. N. Yarnall ◽  
Cian Schmitt-Ulms ◽  
Rohan N. Krajeski ◽  
Justin Lim ◽  
...  
Keyword(s):  
Genome Editing ◽  
Dna Cleavage ◽  
High Efficiency ◽  
End Joining ◽  
Differentiated Cells ◽  
Dividing Cells ◽  
Gene Integration ◽  
Fluorescent Tagging ◽  
Non Homologous End Joining ◽  
Drag And Drop

Programmable and multiplexed genome integration of large, diverse DNA cargo independent of DNA repair remains an unsolved challenge of genome editing. Current gene integration approaches require double-strand breaks that evoke DNA damage responses and rely on repair pathways that are inactive in terminally differentiated cells. Furthermore, CRISPR-based approaches that bypass double stranded breaks, such as Prime editing, are limited to modification or insertion of short sequences. We present Programmable Addition via Site-specific Targeting Elements, or PASTE, which achieves efficient and versatile gene integration at diverse loci by directing insertion with a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase. Without generating double stranded breaks, we demonstrate integration of sequences as large as ~36 kb with rates between 10-50% at multiple genomic loci across three human cell lines, primary T cells, and quiescent non-dividing primary human hepatocytes. To further improve PASTE, we discover thousands of novel serine integrases and cognate attachment sites from metagenomes and engineer active orthologs for high-efficiency integration using PASTE. We apply PASTE to fluorescent tagging of proteins, integration of therapeutically relevant genes, and production and secretion of transgenes. Leveraging the orthogonality of serine integrases, we engineer PASTE for multiplexed gene integration, simultaneously integrating three different genes at three genomic loci. PASTE has editing efficiencies comparable to or better than those of homology directed repair or non-homologous end joining based integration, with activity in non-dividing cells and fewer detectable off-target events. For therapeutic applications, PASTE can be delivered as mRNA with synthetically modified guides to programmably direct insertion of DNA templates carried by AAV or adenoviral vectors. PASTE expands the capabilities of genome editing via drag-and-drop gene integration, offering a platform with wide applicability for research, cell engineering, and gene therapy.

In Silico Appraisal, Synthesis, Antibacterial Screening and DNA Cleavage for 1,2,5-thiadiazole Derivative

2019 ◽  
Vol 15 (5) ◽  
pp. 445-455 ◽  
Author(s):  
Suraj N. Mali ◽  
Sudhir Sawant ◽  
Hemchandra K. Chaudhari ◽  
Mustapha C. Mandewale
Keyword(s):  
Molecular Docking ◽  
Dna Cleavage ◽  
In Silico ◽  
Oral Absorption ◽  
Inhibition Mechanism ◽  
Hydrogen Binding ◽  
Docking Score ◽  
Antibacterial Screening ◽  
Mycobacteria Tuberculosis

Background: : Thiadiazole not only acts as “hydrogen binding domain” and “two-electron donor system” but also as constrained pharmacophore. Methods:: The maleate salt of 2-((2-hydroxy-3-((4-morpholino-1, 2,5-thiadiazol-3-yl) oxy) propyl) amino)- 2-methylpropan-1-ol (TML-Hydroxy)(4) has been synthesized. This methodology involves preparation of 4-morpholino-1, 2,5-thiadiazol-3-ol by hydroxylation of 4-(4-chloro-1, 2,5-thiadiazol-3-yl) morpholine followed by condensation with 2-(chloromethyl) oxirane to afford 4-(4-(oxiran-2-ylmethoxy)-1,2,5-thiadiazol- 3-yl) morpholine. Oxirane ring of this compound was opened by treating with 2-amino-2-methyl propan-1- ol to afford the target compound TML-Hydroxy. Structures of the synthesized compounds have been elucidated by NMR, MASS, FTIR spectroscopy. Results: : The DSC study clearly showed that the compound 4-maleate salt is crystalline in nature. In vitro antibacterial inhibition and little potential for DNA cleavage of the compound 4 were explored. We extended our study to explore the inhibition mechanism by conducting molecular docking, ADMET and molecular dynamics analysis by using Schrödinger. The molecular docking for compound 4 showed better interactions with target 3IVX with docking score of -8.508 kcal/mol with respect to standard ciprofloxacin (docking score= -3.879 kcal/mol). TML-Hydroxy was obtained in silico as non-carcinogenic and non-AMES toxic with good percent human oral absorption profile (69.639%). TML-Hydroxy showed the moderate inhibition against Mycobacteria tuberculosis with MIC 25.00 μg/mL as well as moderate inhibition against S. aureus, Bacillus sps, K. Pneumoniae and E. coli species. Conclusion: : In view of the importance of the 1,2,5-thiadiazole moiety involved, this study would pave the way for future development of more effective analogs for applications in medicinal field.

Pharmacological Uses of the Plants Belonging to the Genus Commiphora

2020 ◽  
Vol 18 ◽  
Author(s):  
Subbiah Latha ◽  
Palanisamy Selvamani ◽  
Thangavelu Prabha
Keyword(s):  
Secondary Metabolites ◽  
Plant Species ◽  
Dna Cleavage ◽  
Structural Information ◽  
Chemical Constituents ◽  
Future Research ◽  
Pharmacological Properties ◽  
Chemical Structures ◽  
Indigenous Uses ◽  
Available Information

: Natural products have a unique place in the healthcare industry. The genus Commiphora emerged as a potential medicinal with huge benefits as evidenced through its use in various traditional and modern systems of medicine. Therefore, we aimed to prepare a concise review on the pharmacological activities and the indigenous uses of various plant species belonging to the genus Commiphora along with the structural information of various active botanical ingredients present in these plants based on the published literatures and scientific reports. To collect the various published literatures on Commiphora in various journals; to study and classify the available information on the pharmacological uses and chemical constituents; and to present the gathered information as a precise review to serve as a potential reference for future research. Pharmacological and phytochemical data on Commiphora plant species were collected from various journals, books, reference materials, websites including scientific databases, etc for compilation. This review article describes the various pharmacological properties of plants of Commiphora species viz., Anti-arthritic and anti-inflammatory, Anti-atherogenic, Antibacterial, Anti-coagulant, Anti-dicrocoeliasis, Anti-epileptic, Anti-fascioliasis, Anti-fungal, Anti-heterophyidiasis, Anti-hyper cholesterolemic, Anti-hyperlipidemic, Anti-hypothyroidism, Anti-obesity, Anti-osteoarthritic, Anti-osteoclastogenesis, Anti-oxidant, Anti-parasitic, Anti-pyretic, Anti-schistosomiasis, Anti-septic, Anti-thrombotic, Anti-ulcer, Cardioprotective, COX enzyme inhibitory, Cytotoxic /Anti-carcinogenic/Anti-cancer, DNA cleavage, Hypotensive, Inhibits lipid peroxidation, Inhibits NO and NO synthase production, Insecticidal, Local anesthetic, Molluscicidal, Smooth muscle relaxant, Tick repellent activities along with toxicity studies. Furthermore, the review also included various secondary metabolites isolated from various species of Commiphora genus along with their chemical structures serve as a ready resource for researchers. We conclude that the plant species belonging to the genus Commiphora possesses abundant pharmacological properties with a huge treasure of diverse secondary metabolites within themselves. This review indicates the necessity of further in-depth research, pre-clinical and clinical studies with Commiphora genus which may help to detect the unidentified potential of the Commiphora plant species.

scholarly journals Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin

2021 ◽  
Vol 7 (11) ◽  
pp. eabd6030
Author(s):  
Isabel Strohkendl ◽  
Fatema A. Saifuddin ◽  
Bryan A. Gibson ◽  
Michael K. Rosen ◽  
Rick Russell ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Dna Cleavage ◽  
Genome Engineering ◽  
Eukaryotic Cells ◽  
Loop Formation ◽  
Chromatin Compaction ◽  
Dna Targeting ◽  
Genomic Regions ◽  
Dna Bendability ◽  
Nucleosome Arrays

Genome engineering nucleases must access chromatinized DNA. Here, we investigate how AsCas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome arrays. Using quantitative kinetics approaches, we show that dynamic nucleosome unwrapping regulates target accessibility to Cas12a and determines the extent to which both steps of binding—PAM recognition and R-loop formation—are inhibited by the nucleosome. Relaxing DNA wrapping within the nucleosome by reducing DNA bendability, adding histone modifications, or introducing target-proximal dCas9 enhances DNA cleavage rates over 10-fold. Unexpectedly, Cas12a readily cleaves internucleosomal linker DNA within chromatin-like, phase-separated nucleosome arrays. DNA targeting is reduced only ~5-fold due to neighboring nucleosomes and chromatin compaction. This work explains the observation that on-target cleavage within nucleosomes occurs less often than off-target cleavage within nucleosome-depleted genomic regions in cells. We conclude that nucleosome unwrapping regulates accessibility to CRISPR-Cas nucleases and propose that increasing nucleosome breathing dynamics will improve DNA targeting in eukaryotic cells.

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