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Updated: Nov 21, 2025

Mouse Genome Engineering Using Designer Nucleases

Mouse Genome Engineering Using Designer Nucleases

Published on: April 2, 2014

Mutation Maker, An Open Source Oligo Design Platform for Protein Engineering.

Kaori Hiraga¹, Petr Mejzlik², Matej Marcisin³

¹Protein Engineering, MRL, Merck & Co. Inc., Rahway, New Jersey 07065, United States.

ACS Synthetic Biology

|January 12, 2021

Summary

This summary is machine-generated.

Mutation Maker is a new open-source software that designs mutagenic oligos for protein engineering. It enables efficient, large-scale generation of diverse mutant protein libraries for research and industry.

Keywords:

PCR-based accurate synthesis directed evolution gene synthesis multi site-directed mutagenesis protein design protein engineering site-scanning saturation mutagenesis synthetic biology

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Last Updated: Nov 21, 2025

Mouse Genome Engineering Using Designer Nucleases

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Protein engineering
Molecular biology
Bioinformatics

Background:

Protein engineering aims to create novel proteins for research, therapeutics, and industry.
Current methods for generating mutant protein libraries face limitations in scale, complexity, and automation.
Existing automated library design tools are often functionally restricted or inaccessible.

Purpose of the Study:

To develop an open-source software tool for designing mutagenic oligonucleotides for large-scale protein engineering.
To address the limitations of current automated tools in terms of functionality, availability, and scalability.
To facilitate efficient and accurate generation of diverse mutant protein libraries.

Main Methods:

Development of Mutation Maker, an open-source software for mutagenic oligonucleotide design.
Implementation of a novel combination of heuristics, optimization, constraint-satisfaction, and backtracking algorithms.
Tailoring the software for multisite random and directed mutagenesis, as well as de novo gene synthesis workflows.
Validation through in silico simulations and experimental data.

Main Results:

Mutation Maker provides a versatile toolbox for gene diversification at an industrial scale.
The software supports both multisite random/directed mutagenesis and de novo gene synthesis.
Oligonucleotides designed by Mutation Maker yield diverse gene libraries with high success rates across various genes and vectors.
Experimental validation confirms the efficacy and accuracy of the designed libraries.

Conclusions:

Mutation Maker is an effective and accessible solution for large-scale protein engineering library design.
The software enhances efficiency and accuracy in generating diverse mutant protein libraries.
Mutation Maker serves as an extensible platform, poised to support future advancements in directed evolution techniques.