Genomic manipulation has advanced from stochastic nuclease‐mediated disruption toward programmable, deterministic precision. Early clustered regularly interspaced short palindromic repeats (CRISPR) strategies enabled targeted mutagenesis through double‐strand breaks; however, their therapeutic application is limited by genotoxicity, chromosomal instability, and dependence on endogenous repair pathways that are difficult to predict. In this review, we examined the transition from gene editing to genome writing, an approach that decouples genomic modification from host repair pathways to better balance efficiency, precision, and payload delivery. We also discussed the principles of precision technologies, including base and prime editors, and described emerging large‐scale writers, such as CRISPR‐associated transposases and recombinase‐based bridge RNAs, which enable the integration of multi‐kilobase synthetic modules. Beyond enzymatic mechanisms, we further considered the combined use of generative artificial intelligence, structural biology, and novel delivery architectures as potential strategies to overcome current biological limitations. Taken together, these developments point toward Generative Biology, in which computational design and high‐throughput screening transform the genome from a static substrate into a more dynamic model for complex, synthetic functional design.
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute adaptive immune systems in prokaryotes and have transformed life sciences, precision medicine, and synthetic biology as programmable genome-editing tools. Despite their broad utility, naturally occurring DNA-targeting Cas effectors remain constrained by several intrinsic limitations, including large protein size that complicates delivery, stringent protospacer adjacent motif (PAM) requirements that restrict targetable genomic space, and mismatch tolerance that can lead to off-target activity and potential genotoxicity. These challenges have made Cas protein engineering and the discovery of novel CRISPR and CRISPR-like systems from metagenomic resources central to the development of next-generation genome-editing platforms. This Review places recent advances within an integrated synthetic biology engineering continuum that links natural effector discovery, structure-guided hypothesis generation, high-throughput functional screening, machine learning-enabled model construction, and iterative redesign. This Review summarizes progress in the screening, optimization, and functional engineering of DNA-targeting CRISPR and CRISPR-like effectors, with emphasis on structure-guided rational design, directed evolution coupled with high-throughput screening, bioinformatics- and evolution-guided mining of novel systems from large-scale sequence databases, and artificial intelligence-assisted development. By integrating these strategies, we highlight how CRISPR effector engineering is moving toward design-build-test-learn (DBTL)-inspired workflows that expand the functional landscape of genome-editing technologies and advance genome editing toward improved efficiency, safety, and programmability.
Lingwei She, Zeyu Liang, Qin Zou et al.· ACS Synthetic Biology· 1 citation
An RNA-guided bridge recombinase system is engineered through rational mutagenesis and AI-assisted directed evolution, enabling programmable chromosomal rearrangements in both plant and mammalian cells and achieving up to a 29.8-fold increase in activity.
Rui Gao, Jingjing Wei, Chao Sun et al.· Trends in Biotechnology· 0 citations
This review compares Cas9-mediated homology-directed repair (HDR) with generations of cytosine base editors (CBE1–CBE3), adenine base editors (ABE1-ABE7), and prime editors (PE1–PE3b), focusing on their mechanistic distinctions, efficiencies, delivery challenges, and therapeutic applications.
Anoushka Sinha· American Journal of Student...· 0 citations
This article synthesizes contemporary advancements in CRISPR-mediated mammalian genome modification, detailing core mechanisms – such as guide RNA and the Cas9 endonuclease – alongside next-generation modalities, including base and prime editing.
Olga Aldoshina, Dmitriy Lazarev, E. Smirnova· Veterinariya, Zootekhniya i...· 0 citations
This review details the optimization of carbon flux in microbial cell factories to circumvent production bottlenecks, alongside the elucidation of protective multigenic networks against severe environmental stress, and provides a comprehensive guide for decoding complex traits and driving rational designs of next-generation cell factories.
Xiaofei Zhu, Weiwen Zhang, Tao Sun et al.· Microbiology Research· 0 citations
The convergence of CRISPR-Cas9 genome editing and nanozyme engineering is revolutionizing synthetic biology, biotechnology, and medical science. CRISPR-Cas9, a precise and programmable tool, enables targeted genetic modifications that enhance nanozyme functionality, stability, and catalytic efficiency. Through the site-specific mutagenesis, metabolic pathway regulation, and synthetic biology strategies, researchers have significantly improved nanozyme performance for diverse applications, including environmental remediation, biomedical diagnostics, and industrial catalysis. This article explores the fundamental mechanisms of CRISPR-based genome editing, its role in nanozyme optimization, and the latest breakthroughs in enzyme engineering. It also critically examines challenges such as off-target effects, biosafety concerns, and ethical implications associated with gene-edited nanozymes. As advancements in AI-driven predictive modeling and next-generation gene-editing tools emerge, CRISPR-Cas9 is poised to unlock unprecedented possibilities in bioengineering. The integration of genetic precision with catalytic innovation marks a transformative era, redefining the frontiers of molecular biotechnology and paving the way for groundbreaking applications in medicine, industry, and sustainable technology.
Modamori I.O, Okanlawon T.S, Ebhomienlen J.O et al.· Biological and Environmental...· 0 citations