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Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms

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Published on: May 25, 2018

Search-and-remove genome editing allows selection of cells by DNA sequence.

Luise Fast¹, Madina Omar¹, Philipp Kanis¹

¹Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

Nature Communications

|December 8, 2025

Summary

Introducing SNIPE, a marker-free cell selection method for gene editing. This technique enables precise selection based on single nucleotide differences, avoiding unintended physiological effects and enabling nucleotide-level edits.

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Area of Science:

Molecular Biology
Genetics
Biotechnology

Background:

Traditional cell selection relies on marker genes (drug resistance, fluorophores).
Marker genes can cause unintended physiological effects.
Existing methods are incompatible with single nucleotide edits.

Purpose of the Study:

To present SNIPE, a novel marker-free cell selection method.
To enable selection of cells with precise single nucleotide edits.
To overcome limitations of current marker-based selection techniques.

Main Methods:

SNIPE utilizes single nucleotide differences to distinguish edited from unedited cells.
The method was validated using Cas9 and Cas12a gene editing tools.
Experiments were conducted across diverse cell types and species.

Main Results:

SNIPE achieves significant enrichment of precisely edited cells (median 7-fold).
The approach was successfully validated for 42 distinct gene edits.
SNIPE was used to revert modern human missense mutations to ancestral states.

Conclusions:

SNIPE offers a powerful marker-free approach for precise gene editing selection.
The method has broad applicability in various cell types and species.
SNIPE demonstrates potential for therapeutic applications, including tumor cell ablation and mutation repair.