Proc. NatL Acad. Sci. USA Vol. 79, pp. 1588-1592, March 1982 Genetics Gap misrepair mutagenesis: Efficient site-directed induction of transition, transversion, and frameshift mutations in vitro (site-specific mutagenesis/base substitutions/DNA polymerase/fidelity of DNA synthesis/thiophosphate nucleotides) DAVID SHORTLE*, PAULA GRISAFI*, STEPHEN J. BENKOVICt, AND DAVID BOTSTEIN* *Department of Biology, Massachusetts Institute ofTechnology, Cambridge, Massachusetts 02139; and tDepartment of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 Contributed by David Botstein, November 13, 1981 ABSTRACT Short single-stranded gaps can be constructed by tagenesis to within afewbase pairs, the degree ofsite-specificity limited exonuclease action at single-stranded breaks (nicks) placed is determined by which ofseveral endonucleolytic reactions are at predetermined sites on closed circular DNA molecules. As ef- used to generate the nick (5-11). ficient primer-templates for DNA polymerase, single-stranded gaps can be repaired in vitro to regenerate an intact DNA duplex. MATERIALS AND METHODS In this report two in vitro reaction schemes are described that produce a high frequency oferrors during repair ("misrepair") of Strains. The Escherichia coli strains HB101 (thr- leu- pro- gaps and thereby allow the efficient recovery ofmutations limited recA- thi- hsdR- hsdMf supE-), BD-1528 (F' met- hsdR- to the nucleotide sequence at or near the original gap. In the first hsdM+ supE supF ungi-1 nadB7; obtained from B. Duncan), and of these misrepair schemes, nucleotide misincorporations are DB4906 (thr- leu- thi- supE lacY tonA ara- hsdR- hsdMf stimulated by omission of one of the four deoxynucleoside tri- uvrD::Tn5) were used as recipients for transformation with the phosphates; the misincorporations are trapped by the presence of small plasmid pBR322. excess DNA ligase in the reaction mixture. The second misrepair Materials. Micrococcus luteus DNA polymerase I was ob- scheme involves the misincorporation of an excision-resistant a- tained from Miles; restriction endonuclease Cla I was obtained thiophosphate nucleotide, followed by gap filling in the presence from Boehringer Mannheim; all other enzymes were obtained ofall four conventional deoxynucleoside triphosphates. When ap- from New England BioLabs. Units ofenzyme activity are those plied to short gaps constructed at one ofseveral unique restriction ofthe manufacturer. Deoxynucleoside triphosphates were pur- sites on the small plasmid 'pBR322, both gap misrepair methods chased from Schwartz/Mann. The Sp diastereomers of thymi- yielded mutations within the targeted restriction site at high fre- dine 5'-O-(l-thiotriphosphate) (dTTP[aS]) and 2'-deoxyaden- quency (6-42%). A majority of the sequence changes identified osine were prepared were base substitutions; transversions and transitions are approx- 5'-O-(1-thiotriphosphate) (dATP[aS]) imately equally represented. The remaining sequence changes according to Bryant and Benkovic (12). were an insertion of a single base pair and deletions ofone to four Restriction Enzyme Nicking Reactions. Covalently closed base pairs. circular pBR322 DNA (13) was nicked with restriction endo- nucleases HindIII, Cla I, or BamHI by incubating 10 pkg of In the past few years, several methods of site-specific muta- plasmid DNA in a 100-Al solution of20 mM Tris'HCl, pH 7.8/ genesis have been developed to facilitate recovery ofmutations 7 mM MgClJ7 mM 2-mercaptoethanol/gelatin (100 Ag/ml) in genes carried on small circular DNA molecules (1-3). Per- and -a concentration of ethidium bromide (150 ,ug/ml, 75 pig/ haps the most direct of these methods involves the use of syn- ml, or 100 Ag/ml, respectively) determined by titration to give thetic oligonucleotides as primers for DNA synthesis after an- an optimal level of nicking. An amount of restriction endonu- nealing to a single-stranded' circle of wild-type DNA (2, 4). clease was added sufficient to convert ==50-90% of the input Because the nucleotide sequence of the synthetic oligonucleo- DNA to an open circular form on incubation at room temper- tide replaces the homologous wild-type sequence, in principle ature for 2-4 hr. The nicking reaction with the EcoRI enzyme any mutation-base substitution, insertion, or deletion-can consisted of 100 mM Tris'HCl, pH 7.6/50 mM- NaCV5 mM be induced at any site via synthesis of the appropriate oligo- MgCl2/gelatin (100 ug/ml)/ethidium bromide (150 ,ug/ml). nucleotide. However, when the exact nucleotide sequence Reactions were stopped by addition of excess EDTA followed change necessary to create a mutant allele with a particular phe- by phenol extraction and ethanol precipitation. notype is unknown, synthesis of the many different oligonu- Gapping Reaction and Purification of Gapped-Circular cleotides required to cover all possibilities becomes inefficient DNA. To convert restriction enzyme-induced nicks into short and laborious. In such situations, the optimal strategy for mu- single-stranded gaps, 5 ug of nicked pBR322 was added to 25 tagenesis is one that induces a variety of point mutations scat- 1.d of70 mM Tris-HCl, pH 8.0/7 mM MgCl2/1 mM 2-mercap- tered over a specificed region of the gene. toethanol containing 0.5 unit of M. luteus DNA polymerase I Methods have been developed (5-7) that allow the direction per Ag of DNA (10). After incubation at room temperature for of mutagenesis to unique nucleotide positions or to sites dis- 60 min, the reaction was stopped with excess EDTA, phenol tributed within a defined segment of DNA. These methods are extraction, and ethanol precipitation. From this mixture of based on the introduction ofa single-stranded break (nick) into DNA forms, circular DNA with single-stranded gaps was se- a DNA molecule, followed by enlargement to a small gap that lectively purified by first ligating linear and nicked-circular can serve as a specific target for an in vitro mutagenic reaction. molecules to a relaxed, covalently closed form in a 50-.ul re- Because the position of the nick determines the region of mu- action consisting of 66 mM Tris HCl, pH 7.6/6.6 mM M'gClJ 5 mM dithiothreitol/gelatin (100 ug/ml)/0.5 mM ATP/150 The publication costs ofthis article were defrayed in part by page charge units of T4 DNA ligase; the reaction was incubated overnight payment. This article must therefore be hereby marked "advertise- at 00C. After phenol extraction and ethanol precipitation, this ment" in accordance with 18 U. S. C. §1734 solely to indicate this fact. DNA mixture was dissolved in 0.2 ml of 10 mM sodium citrate, 1588 Downloaded by guest on September 28, 2021 Genetics: Shortle et al. Proc. Natl. Acad. Sci. USA 79 (1982) 1589 pH 6.0/0.5 mM EDTA/0.2 M NaCVethidium bromide (2 ,ug/ 1.Endonuclease ml) and passed over a 0.2-ml column of acridine yellow ED 2. Exonuclease beads (Boehringer Mannheim). After washing the column-first 5'-- A-T-C-G-A-T -- 3' with the loading solution and then with 10 mM sodium citrate, 3'-- T-A-G-C-T-A --5' pH 6.0/0.5 mM EDTA/0.2 M NaCl without ethidium bro- A-T P04 mide-the open-circular (i.e., gapped) DNA fraction was eluted T-A-G-C-T-A with the same buffer containing 0.5 M NaCl and was concen- Misincorporation Excision trated by ethanol precipitation in the presence of carrier tRNA. of dNTP t 1Ecso Gap Misrepair: Method 1. A typical reaction consisted of 100-200 ng ofgapped pBR322 DNA in 20 ,ul of60 mM Tris HCl, _ A-TN Po= pH 8.0/20 mM 2-mercaptoethanol/1 mM MgAc2/2 mM T-A-G -C-T-A MnCl2/gelatin (100 tWg/ml)/0.5 mM ATP and three deoxynu- Gap filling+ cleoside triphosphates at a concentration of 125 ,uM each. To ligation this mixture was added 150 units ofT4 DNA ligase plus 0.2 unit A-TNG -A-T ofM. luteus DNA polymerase I, and incubation was carried out T-AG-C -T-A at 26°C for 16-18 hr. The percentage ofmolecules that had been Replication /A Ah converted to a covalently closed form was assayed by electro- phoresis ofan aliquot on a 1.2% agarose gel containing ethidium -A-T-N-G-A-T- - A-T-C-G-A-T- bromide at 0.5 ,ug/ml in both the gel and the running buffer. -T- A-N'- C-T-A - T-A-G-C-T-A- runs as a On such gels, circular DNA closed by ligation faintly MUTANT WILD - TYPE fluorescent band with a mobility slightly greater than that of ( ClaI resistant) (ClaI sensitive) negatively supercoiled pBR322. Gap Misrepair: Method 2. In the first reaction, an a-thio- FIG. 1. Outline of steps used to induce point mutations within a was onto the unique restriction site (Cla I is used as an example) by gap misrepair. phosphate deoxyribonucleotide misincorporated In method 1, misincorporation of a dNTP and gap filling plus ligation 3' terminus of a single-stranded gap in a 15-p1 reaction con- all occur in a single reaction mixture; in method 2, a single a-thio- sisting of 130 mM Hepes, pH 7.5/0.2 mM MnCl2/2 mM 2- phosphate nucleotide is misincorporated (essentially irreversibly) in mercaptoethanol/gelatin (100 ,ug/ml)/100 uM dTTP[aS] (or one reaction, followed by gap filling and ligation in a second reaction. dATP[aS])/50-100 ng of DNA. In some reactions, either dTTP or dGTP was also present at a concentration of 20 ,M. After ditions used, an average offive or six nucleotides were removed addition of0.3 unit ofKlenow fragment polymerase, incubation from the nicked strand, predominantly in the 5' -- 3' direction. was carried out at 26°C for 14-16 hr. The reaction was stopped Circular DNA gapped at a particular restriction site was purified by making the mixture 10 mM in EDTA, followed by phenol and used as substrate for an in vitro "gap misrepair" reaction extraction and ethanol precipitation.