Next-Generation CRISPR Editing: Base Editing, Prime Editing, and the Transition Beyond Double-Strand Breaks

Abstract

Genome editing technologies have advanced rapidly since the introduction of CRISPR-Cas9, which enables targeted genetic modification through double-strand DNA breaks. Despite its effectiveness, double-strand break–dependent editing is limited by imprecise repair outcomes, off-target effects, and activation of DNA damage responses, raising concerns regarding precision, reproducibility, and long-term genomic stability. These constraints have driven the development of next-generation CRISPR-based strategies that enable precise genome modification without inducing DNA cleavage. Among these approaches, base editing and prime editing represent major conceptual advances. Base editing enables efficient single-nucleotide conversion through programmable chemical modification of DNA bases, whereas prime editing expands editing scope by facilitating precise insertions, deletions, and substitutions via reverse transcription–mediated DNA rewriting. This review provides a mechanism-centered comparison of base editing and prime editing, synthesizing their molecular architectures, editing capabilities, efficiencies, and technical limitations. By explicitly contrasting break-dependent and break-free editing strategies, this review highlights emerging applications across biomedical research, plant biotechnology, and functional genomics, while outlining remaining technical and translational challenges that inform context-dependent selection of precision genome engineering approaches.