人工智能生成的MLH1小分子结合剂提高了碱基编辑效率。

AI-generated MLH1 small binder improves prime editing efficiency.

作者信息

Park Ju-Chan, Uhm Heesoo, Kim Yong-Woo, Oh Ye Eun, Lee Jang Hyeon, Yang Jiyun, Kim Kyoungmi, Bae Sangsu

机构信息

Genomic Medicine Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.

Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.

出版信息

Cell. 2025 Aug 1. doi: 10.1016/j.cell.2025.07.010.

DOI:10.1016/j.cell.2025.07.010

PMID:40769155

Abstract

The prime editing (PE) system consists of a Cas9 nickase fused to a reverse transcriptase, which introduces precise edits into the target genomic region guided by a PE guide RNA. However, PE efficiency is limited by mismatch repair. To overcome this limitation, transient expression of a dominant-negative MLH1 (MLH1dn) has been used to inhibit key components of mismatch repair. Here, we designed a de novo MLH1 small binder (MLH1-SB) that binds to the dimeric interface of MLH1 and PMS2 using RFdiffusion and AlphaFold 3. The compact size of MLH1-SB enabled its integration into existing PE architectures via 2A systems, creating a PE-SB platform. The PE7-SB2 system significantly improved PE efficiency, achieving an 18.8-fold increase over PEmax and a 2.5-fold increase over PE7 in HeLa cells, as well as a 3.4-fold increase over PE7 in mice. This study highlights the potential of generative AI in advancing genome editing technology.

摘要

碱基编辑（PE）系统由与逆转录酶融合的Cas9切口酶组成，该酶在PE引导RNA的引导下将精确编辑引入目标基因组区域。然而，PE效率受到错配修复的限制。为了克服这一限制，已使用显性负性MLH1（MLH1dn）的瞬时表达来抑制错配修复的关键成分。在这里，我们设计了一种全新的MLH1小分子结合物（MLH1-SB），它利用RFdiffusion和AlphaFold 3与MLH1和PMS2的二聚体界面结合。MLH1-SB的紧凑尺寸使其能够通过2A系统整合到现有的PE架构中，创建了一个PE-SB平台。PE7-SB2系统显著提高了PE效率，在HeLa细胞中比PEmax提高了18.8倍，比PE7提高了2.5倍，在小鼠中比PE7提高了3.4倍。这项研究突出了生成式人工智能在推进基因组编辑技术方面的潜力。