High-throughput biochemistry in RNA sequence space: predicting structure and function
RNAs are central to fundamental biological processes in all known organisms. The set of
possible intramolecular interactions of RNA nucleotides defines the range of alternative …
possible intramolecular interactions of RNA nucleotides defines the range of alternative …
Systems-Level Modeling for CRISPR-Based Metabolic Engineering
The CRISPR-Cas system has enabled the development of sophisticated, multigene
metabolic engineering programs through the use of guide RNA-directed activation or …
metabolic engineering programs through the use of guide RNA-directed activation or …
Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints
Q Chen, G Chuai, H Zhang, J Tang, L Duan… - Nature …, 2023 - nature.com
The powerful CRISPR genome editing system is hindered by its off-target effects, and
existing computational tools achieved limited performance in genome-wide off-target …
existing computational tools achieved limited performance in genome-wide off-target …
Massively parallel kinetic profiling of natural and engineered CRISPR nucleases
Engineered SpCas9s and AsCas12a cleave fewer off-target genomic sites than natural
SpCas9. However, understanding their fidelity, mechanisms and cleavage outcomes …
SpCas9. However, understanding their fidelity, mechanisms and cleavage outcomes …
Negative DNA supercoiling induces genome-wide Cas9 off-target activity
CRISPR-Cas9 is a powerful gene-editing technology; however, off-target activity remains an
important consideration for therapeutic applications. We have previously shown that force …
important consideration for therapeutic applications. We have previously shown that force …
The energy landscape for R-loop formation by the CRISPR–Cas Cascade complex
Clustered regularly interspaced short palindromic repeats (CRISPR) sequences and
CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have …
CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have …
Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin
Genome engineering nucleases must access chromatinized DNA. Here, we investigate how
AsCas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome …
AsCas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome …
Titrating CD47 by mismatch CRISPR-interference reveals incomplete repression can eliminate IgG-opsonized tumors but limits induction of antitumor IgG
Phagocytic elimination of solid tumors by innate immune cells seems attractive for
immunotherapy, particularly because of the possibilities for acquired immunity. However, the …
immunotherapy, particularly because of the possibilities for acquired immunity. However, the …
Coordinated actions of Cas9 HNH and RuvC nuclease domains are regulated by the bridge helix and the target DNA sequence
CRISPR-Cas systems are RNA-guided nucleases that provide adaptive immune protection
in bacteria and archaea against intruding genomic materials. Cas9, a type-II CRISPR …
in bacteria and archaea against intruding genomic materials. Cas9, a type-II CRISPR …
Guide-target mismatch effects on dCas9–sgRNA binding activity in living bacterial cells
As an effective programmable DNA targeting tool, CRISPR–Cas9 system has been adopted
in varieties of biotechnological applications. However, the off-target effects, derived from the …
in varieties of biotechnological applications. However, the off-target effects, derived from the …