Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates

• Published in: Applied Microbiology and Biotechnology
• Main Authors: Sanchis, Joaquin, Fernandez, Layla, Daniel Carballeira, J., Drone, Jullien, Gumulya, Yosephine, Höbenreich, Horst, Kille, Sabrina, Lohmer, Renate, Jp Peyralans, Jérôme, Podtetenieff, John, Prasad, Shreenath, Soni, Pankaj, Wu, Sheng, E Zilly, Felipe, Reetz, Manfred
• Other Authors: Max-Planck-Institut für Kohlenforschung (Coal Research), Max-Planck-Gesellschaft, Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2008
• Subjects: Directed evolution; Saturation mutagenesis; PCR; Megaprimer; Antiprimer; Difficult-to-amplify templates; [SDV.BIO]Life Sciences [q-bio]/Biotechnology; [SDV.BBM]Life Sciences [q-bio]/Biochemistry; Molecular Biology; Antarc*; Antarctica
• Online Access: https://hal.science/hal-00354234; https://doi.org/10.1007/s00253-008-1678-9

International audience Saturation mutagenesis constitutes a powerful method in the directed evolution of enzymes. Traditional protocols of whole plasmid amplification such as Stratagene's QuikChange sometimes fail when the templates are difficult to amplify. In order to overcome such restrictions, we have devised a simple two-primer, two-stage polymerase chain reaction (PCR) method which constitutes an improvement over existing protocols. In the first stage of the PCR, both the mutagenic primer and the antiprimer that are not complementary anneal to the template. In the second stage, the amplified sequence is used as a megaprimer. Sites composed of one or more residues can be randomized in a single PCR reaction, irrespective of their location in the gene sequence.The method has been applied to several enzymes successfully, including P450-BM3 from Bacillus megaterium, the lipases from Pseudomonas aeruginosa and Candida antarctica and the epoxide hydrolase from Aspergillus niger. Here, we show that megaprimer size as well as the direction and design of the antiprimer are determining factors in the amplification of the plasmid. Comparison of the results with the performances of previous protocols reveals the efficiency of the improved method.