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Patch Cloning Method for Multiple Site-Directed and Saturation Mutagenesis Naohiro Taniguchi, Sayumi Nakayama, Takashi Kawakami and Hiroshi Murakami*

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Patch Cloning Method for Multiple Site-Directed and Saturation Mutagenesis Naohiro Taniguchi, Sayumi Nakayama, Takashi Kawakami and Hiroshi Murakami* Taniguchi et al. BMC Biotechnology 2013, 13:91 http://www.biomedcentral.com/1472-6750/13/91 METHODOLOGY ARTICLE Open Access Patch cloning method for multiple site-directed and saturation mutagenesis Naohiro Taniguchi, Sayumi Nakayama, Takashi Kawakami and Hiroshi Murakami* Abstract Background: Various DNA manipulation methods have been developed to prepare mutant genes for protein engineering. However, development of more efficient and convenient method is still demanded. Homologous DNA assembly methods, which do not depend on restriction enzymes, have been used as convenient tools for cloning and have been applied to site-directed mutagenesis recently. This study describes an optimized homologous DNA assembly method, termed as multiple patch cloning (MUPAC), for multiple site-directed and saturation mutagenesis. Results: To demonstrate MUPAC, we introduced five back mutations to a mutant green fluorescent protein (GFPuv) with five deleterious mutations at specific sites and transformed Escherichia coli (E. coli) with the plasmids obtained. We observed that the over 90% of resulting colonies possessed the plasmids containing the reverted GFPuv gene and exhibited fluorescence. We extended the test to introduce up to nine mutations in Moloney Murine Leukemia Virus reverse transcriptase (M-MLV RT) by assembling 11 DNA fragments using MUPAC. Analysis of the cloned plasmid by electrophoresis and DNA sequencing revealed that approximately 30% of colonies had the objective mutant M-MLV RT gene. Furthermore, we also utilized this method to prepare a library of mutant GFPuv genes containing saturation mutations at five specific sites, and we found that MUPAC successfully introduced NNK codons at all five sites, whereas other site remained intact. Conclusions: MUPAC could efficiently introduce various mutations at multiple specific sites within a gene. Furthermore, it could facilitate the preparation of experimental gene materials important to molecular and synthetic biology research. Background The most commonly used method for site-directed Site-directed and saturation mutagenesis are widely used to mutagenesis is the QuikChange® method (Stratagene, La prepare mutant genes for studying a protein function in Jolla, CA, USA), which employs mutagenic plasmid basic research and for preparation of engineered proteins amplification to introduce single site-directed muta- for industrial and pharmaceutical applications. For example, tions. Using a more complicated protocol, this method protein function is studied by comparing the wild-type pro- was extended to introduce up to five site-directed muta- tein with the corresponding mutant proteins produced tions, although the complete mutagenesis efficiency from genes with single or multiple mutations. Site-directed decreased to 32% [14]. To improve this efficiency, saturation mutagenesis combined with directed evolu- OmniChange was developed and was used to success- tion strategies were also used to modify protein proper- fully introduce five site-directed saturation mutations ties [1-4], such as altering substrate specificity [5-7], [15]. Although this method demonstrated high effi- enhancing activity [8-11], or improving thermal stability ciency for complete multiple mutagenesis, synthesis of [12,13]. To facilitate the preparation of mutant genes, vari- phosphorothioate nucleotides is necessary to generate ous methods of multiple site-directed and saturation mu- 3′-overhanging DNA fragments. tagenesis have been developed. Since 1990, several homologous DNA assembly methods [16-21] have been developed; one method in * Correspondence: [email protected] particular, one-step isothermal in vitro recombination Department of Life Sciences, Graduate School of Arts and Sciences, The (the ISO method) [20], was used to introduce multiple University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan © 2013 Taniguchi et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Taniguchi et al. BMC Biotechnology 2013, 13:91 Page 2 of 8 http://www.biomedcentral.com/1472-6750/13/91 site-directed mutations [22]. In this method, termed as multiple sites in GFPuv gene. Because MUPAC is a cost multichange isothermal in vitro recombination (the effective and efficient method for the DNA manipulation, MISO method), multiple DNA fragments were first pre- this method would be a useful tool to prepare various mu- pared using polymerase chain reaction (PCR) followed tant genes to study and improve protein’s functions. by gel purification. The DNA fragments possess 40-base pair (bp) sequences homologous to the adjacent DNA Results fragments on either side. Because the ISO reaction em- Multiple patch cloning method ploys T5 exonuclease, DNA fragments are degraded in MUPAC is an optimized mutagenesis/cloning method a5′–3′ direction, exposing a 3′ overhanging sequence that allows the assembly of multiple dsDNA using short complementary to the adjacent DNA fragment. The 16-bp assembly sequences (Figure 1). MUPAC employs DNA fragments are annealed, and the gaps are filled T5 exonuclease, Klenow fragment (exo−), and T4 DNA using Phusion DNA polymerase, and the resulting ligase. In the reaction mixture, T5 exonuclease degraded nicks are sealed by Taq DNA ligase. This method per- the DNA in a 5′–3′ direction and exposed 3′ overhang mits highly efficient assembly of up to six DNA frag- in the assembly regions at the ends of each fragment. ments and is used to successfully introduce eight point When the DNA fragments annealed at the exposed mutations in a gene. However, because the ISO method complementary single-strand region, Klenow fragment was originally generated to assemble DNA fragments (exo–) filled the gaps and T4 DNA ligase joined the nick several hundred kilobases in length, the reaction condi- to assemble dsDNA. The difference between MUPAC tion was not necessary suitable for multiple site- and the ISO method was the enzymes that were used directed mutagenesis. in the reaction mixture. Because the ISO method In this study, we developed an optimized DNA assembly employed thermostable DNA polymerase (Phusion DNA method, termed multiple patch cloning (MUPAC), which polymerase) and DNA ligase (Taq DNA ligase) instead could assemble up to 11 DNA fragments to introduce of the Klenow fragment (exo−) and T4 DNA ligase, the nine site-directed mutations (Figure 1). The MUPAC reac- optimum temperature for the ISO reaction was 50°C tion mixture is easily prepared from commercially avail- [20,22], which favored a long assembly sequence, typic- able common enzymes, including T5 exonuclease, Klenow ally 40 bp. When the method was applied to a multiple fragment (exo−), and T4 DNA ligase. We also utilized site-directed mutagenesis in MISO, this feature became MUPAC to introduce site-directed saturation mutations at drawback because the preparation of relatively long oligo-DNAs was required to introduce each point muta- tion. In contrast, MUPAC required an assembly se- quence of only 16 bp because the optimal reaction temperature for the enzymes used was 37°C. This differ- ence also made it easy to prepare a saturation mutant gene pool using short oligonucleotides as mentioned in the section below. GFPuv single site-directed mutagenesis To evaluate the performance of new enzyme mixture in a point mutagenesis, we first tested its ability to mutate Tyr 66 in the mutant GFPuv to Asp. Because the Tyr 66 residue is key to the formation of the GFPuv chromo- phore (Figure 2a), the mutation from Tyr to Asp abol- ished fluorescence. Two PCR fragments were prepared using wild-type GFPuv gene template and two sets of PCR primers (1 and 2 in Additional file 1: Table S2), one of which had a sequence that corresponded to the muta- tion from the Tyr (TAT) codon to the Asp (GAT) codon. The two fragments were assembled with the NheI– Figure 1 Schematic illustration of the multiple patch cloning procedure. DNA fragments are amplified by polymerase chain EcoRI-digested pBAD plasmid using MUPAC, and the reaction using two sets of oligo-DNA primers (shown in red and colonies of the E. coli JM109 transformed by the assem- blue). The star on the primer indicates the site of mismatch. The bled plasmid were exposed to a UV light to observe resultant DNA fragments and digested vector DNA containing 16 bp fluorescence. As expected, none of the colonies exhibited homologous regions (shown in yellow) were assembled at 37°C by fluorescence, indicating that no detectable wild-type T5 exonuclease, Klenow fragment and T4 DNA ligase. GFPuv gene persisted through MUPAC (Figure 2b vs. 2c). Taniguchi et al. BMC Biotechnology 2013, 13:91 Page 3 of 8 http://www.biomedcentral.com/1472-6750/13/91 Figure 2 Multiple site-directed mutagenesis of GFPuv. (a) Three-dimensional structure of GFP (PDB ID: 1GFL) depicted using the ribbon model. Molecular graphics was created with the program UCSF Chimera (http://www.cgl.ucsf.edu/chimera/). The five residues, indicated by yellow balls, were selected as mutation sites because each was essential for GFPuv fluorescence. (b) Wild-type GFPuv in the pBAD vector was used to transform E. coli JM109. The tenth aliquot of each transformant was spread on the right half of an LB agar plate, and the remainder on the left half. The percentage frequency of fluorescent colonies is indicated
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