# Patent

## Title
High fidelity restriction endonucleases

## Abstract

Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

## Background
CROSS REFERENCE
This application is a divisional of U.S. Ser. No. 12/172,963 filed Jul. 14, 2008, now U.S. Pat. No. 8,372,619, which claims priority from U.S. provisional application Ser. No. 60/959,203 filed Jul. 12, 2007, herein incorporated by reference.


BACKGROUND
Restriction endonucleases are enzymes that cleave double-stranded DNAs in a sequence-specific manner (Roberts, R. J., Proc Natl Acad Sci USA, 102:5905-5908 (2005); Roberts, et al., Nucleic Acids Res, 31:1805-1812 (2003); Roberts, et al., Nucleic Acids Res, 33:D230-232 (2005); Alves, et al., Restriction Endonucleases, “Protein Engineering of Restriction Enzymes,” ed. Pingoud, Springer-Verlag Berlin Heidelberg, New York, 393-407 (2004)). They are ubiquitously present among prokaryotic organisms (Raleigh, et al., Bacterial Genomes Physical Structure and Analysis, Ch. 8, eds. De Bruijin, et al., Chapman & Hall, New York, 78-92 (1998)), in which they form part of restriction-modification systems, which mainly consist of an endonuclease and a methyltransferase. The cognate methyltransferase methylates the same specific sequence that its paired endonuclease recognizes and renders the modified DNA resistant to cleavage by the endonuclease so that the host DNA can be properly protected. However, when there is an invasion of foreign DNA, in particular bacteriophage DNA, the foreign DNA will be degraded before it can be completely methylated. The major biological function of the restriction-modification system is to protect the host from bacteriophage infection (Arber, Science, 205:361-365 (1979)). Other functions have also been suggested, such as involvement in recombination and transposition (Carlson, et al., Mol Microbiol, 27:671-676 (1998); Heitman, Genet Eng (NY), 15:57-108 (1993); McKane, et al., Genetics, 139:35-43 (1995)).
The specificity of the approximately 3,000 known restriction endonucleases for their greater than 250 different target sequences could be considered their most interesting characteristic. After the discovery of the sequence-specific nature of the first restriction endonuclease (Danna, et al., Proc Natl Acad Sci U S A, 68:2913-2917 (1971); Kelly, et al., J Mol Biol, 51:393-409 (1970)), it did not take long for scientists to find that certain restriction endonucleases cleave sequences which are similar but not identical to their defined recognition sequences under non-optimal conditions (Polisky, et al., Proc Natl Acad Sci USA, 72:3310-3314 (1975); Nasri, et al., Nucleic Acids Res, 14:811-821 (1986)). This relaxed specificity is referred to as star activity of the restriction endonuclease. It has been suggested that water-mediated interactions between the restriction endonuclease and DNA are the key differences between specific complexes and star complexes (Robinson, et al., J Mol Biol, 234:302-306 (1993); Robinson, et al., Proc Natl Acad Sci USA, 92:3444-3448 (1995), Sidorova, et al., Biophys J, 87:2564-2576 (2004)).
Star activity is a problem in molecular biology reactions. Star activity introduces undesirable cuts in a cloning vector or other DNA. In cases such as forensic applications, where a certain DNA substrate needs to be cleaved by a restriction endonuclease to generate a unique fingerprint, star activity will alter a cleavage pattern profile, thereby complicating analysis. Avoiding star activity is also critical in applications such as strand displacement amplification (Walker, et al., Proc Natl Acad Sci USA, 89:392-396 (1992)) and serial analysis of gene expression (Velculescu, et al., Science, 270:484-487 (1995)).
SUMMARY
In an embodiment of the invention, a composition is provided that includes a restriction endonuclease having at least one artificially introduced mutation and an overall fidelity index (FI) improvement factor of at least two, the restriction endonuclease being capable of cleaving a substrate with at least a similar cleavage activity to that of the restriction endonuclease absent the artificially introduced mutation in a predetermined buffer, the artificially introduced mutation being the product of at least one of a targeted mutation, saturation mutagenesis, or a mutation introduced through a PCR amplification procedure.
In a further embodiment of the invention, at least one of the artificially introduced mutations is a targeted mutation resulting from replacement of a naturally occurring residue with an oppositely charged residue. An Alanine or a Phenylalanine may replace the naturally occurring residue at the target site.
In a further embodiment of the invention, a composition of the type described above includes a restriction enzyme absent the artificially introduced mutation selected from the group consisting of: BamHI, EcoRI, ScaI, SalI, SphI, PstI, NcoI, NheI, SspI, NotI, SacI, PvuII, MfeI, HindIII, SbfI, EagI, EcoRV, AvrII, BstXI, PciI, HpaI, AgeI, BsmBI, BspQI, SapI, KpnI and BsaI.
Further embodiments of the invention include compositions listed in Table 4.
In a further embodiment of the invention, a DNA encoding any of the enzymes listed in Table 4 is provided, a vector comprising the DNA and a host cell for expressing the protein from the vector.
In an embodiment of the invention, a method is provided having the steps of (a) identifying which amino acid residues in an amino acid sequence of a restriction endonuclease having star activity are charged amino acids; (b) mutating one or more codons encoding one or more of the charged residues in a gene sequence encoding the restriction endonuclease; (c) generating a library of gene sequences having one or more different codon mutations in different charged residues; (d) obtaining a set of proteins expressed by the mutated gene sequences; and (e) determining an FI in a predetermined buffer and a cleavage activity for each expressed protein.
An embodiment of the method includes the step of determining an overall FI improvement factor for proteins belonging to the set of proteins in a defined set of buffers where for example, the set of buffers contains NEB1, NEB2, NEB3 and NEB4 buffers.
An embodiment of the method includes the steps described above and additionally mutating codons encoding hydroxylated amino acids or amide amino acids in a same or subsequent step to that of mutating codons for the charged amino acids.
In an embodiment of the invention described above, the codons are mutated to an Alanine except for Tyrosine which is mutated to a Phenylalanine.
In a further embodiment, the overall FI improvement factor is improved using saturation mutagenesis of one or more of the mutated codon.



BRIEF DESCRIPTION OF THE DRAWINGS
In each of the reactions described in FIGS. 1-2A-B, the reaction mixture contains a volume of 3 μl unless otherwise specified of a buffer from New England Biolabs, Inc. (NEB), Ipswich, MA, (see Table 1 and NEB catalog), 3 μl unless otherwise specified of a specified restriction endonuclease in a diluent from NEB, Ipswich, Mass. (See Table 1 and NEB catalog) as well as variable volumes of specified substrate (containing 0.6 μg) substrate and a volume of water to bring the reaction mixture to a total of 30 μl. Reactions were conducted at 37° C. for an incubation time of 1 hour. The results are analyzed on a 0.8% agarose gel. Where the overall volume of the reaction mix, amount of substrate, temperature of the reaction or incubation time varies from above, values are provided in the description of the figures.
FIG. 1 shows the determination of the FI for wild type (WT) ScaI by digesting 1.2 μl lambda DNA substrate (0.6 μg) with a two-fold serial dilution using diluent A of a preparation of WT ScaI (1,200 U) in NEB3 buffer and examining the digestion products on an agarose gel. The highest concentration of a restriction endonuclease with no star activity is shown with a solid arrow; and the minimum concentration giving rise to complete digestion of substrate is shown with a hollow arrow.
FIGS. 2A-B show cleavage of 1.2 μl pXba DNA substrate using 2-fold serial dilutions of NheI-HF (287,200 U and 76.8 U) and 2-fold serial dilutions of WT NheI (9,600 U and 300 U) in NEB3 and NEB4 buffers, respectively. Serial dilutions were performed in diluent A.
FIG. 2A shows cleavage by NheI-HF in NEB4 buffer (upper panel) and NEB3 buffer (lower panel).
FIG. 2B shows cleavage by WT NheI in NEB4 buffer (upper panel) and NEB3 buffer (lower panel).
The theoretical digestion pattern is provided on the right side of the gel for FIGS. 1-2A-B. Those substrates with only one restriction endonuclease site should be digested into one linear band from supercoiled form.
For FIG. 2A-B “U” denotes units of enzyme.



DETAILED DESCRIPTION OF THE EMBODIMENTS
Embodiments of the invention provide a general method for selecting for restriction endonucleases with desired characteristics. The general method relies on a suitable assay for determining whether the desired restriction endonuclease has been created. In particular an embodiment of the general method provides a systematic screening method with a set of steps. This method has been deduced by performing many hundreds of reactions using many restriction endonucleases. The example provided herein relates to identifying a restriction endonuclease with reduced star activity but with cleavage activity that is at least similar to the WT restriction endonuclease. However, it is expected that the same methodology can be applied successfully to modifying other properties of the restriction endonucleases relating, for example, to improved cleavage activity in desired buffers, thermostability, rate of reaction in defined conditions, etc.
As discussed above, an end point of interest is to transform restriction endonucleases with star activity into high fidelity restriction endonucleases with significantly reduced star activity. Star activity refers to promiscuity in cleavage specificity by individual restriction endonucleases. The terms “reduction in star activity” and “increase in fidelity” are used interchangeably here. Although restriction endonucleases are characterized by their property of cleaving DNA at specific sequences, some restriction endonucleases additionally cleave DNA inefficiently at secondary sites in the DNA. This secondary cleavage may occur consistently or may arise only under certain conditions such as any of: increased concentrations, certain buffers, temperature, substrate type, storage, and incubation time.
It is generally acknowledged that little is known about the complex environment generated by the hundreds of amino acids that constitute a protein and determine specificity. One approach in the prior art has been to utilize crystallography to identify contact points between an enzyme and its substrate. Nonetheless, crystallography has limitations with respect to freezing a structure in time in an unnatural chemical environment.
The rules that determine the contribution of amino acids at any site in the protein and the role played by the structure of the substrate molecule has proved elusive using existing analytical techniques. For example, it is shown here that mutating an amino acid in a restriction endonuclease can cause all or partial loss of activity.
In this context, no structural explanation has been put forward to explain why star activity could increase with high glycerol concentration (>5% v/v), high enzyme to DNA ratio (usually >100 units of enzyme per μg of DNA), low ionic strength (<25 mM salt), high pH (>8.0), presence of organic solvent (such as DMSO, ethanol), and substitution of Mg2+ with other divalent cations (Mn2+, Co2+). It was here recognized that because of the diversity of factors affecting star activity, it would be necessary to conduct comparisons of WT and mutant star activity under the same reaction conditions and in the same predetermined buffer and to develop a standard reaction condition in which any high fidelity enzyme must be capable of showing the described characteristics even if these characteristics were also observed in other reaction conditions.
Present embodiments of the invention are directed to generating modified restriction endonucleases with specific improved properties, namely enhanced cleavage fidelity without significant reduction in overall cleavage activity or significant loss of yield from the host cells that make the protein. The methods that have been developed here for finding mutants with improved properties have resulted from exhaustive experimentation and the properties of the resultant enzymes have been defined in the context of specified conditions. The methods described herein may be used for altering the enzymatic properties of any restriction endonuclease under predetermined conditions, but are not limited to the specific defined conditions.











Restriction
Steps Used to Generate a High Fidelity Restriction


Endonuclease
Endonuclease







BamHI
Comparison of isoschizomer



Targeted 22 residues to mutate to Ala. 14 mutants obtained, 3



had improved fidelity



Saturation mutagenesis on 2 residues-K30 and E86



Recovered E86P as preferred mutant with greatest reduced star



activity in selected buffers. Added mutations to E86P.



Second round of mutation (Arg, Lys, His, Asp, Glu, Ser, Thr) to



Ala and Tyr to Phe. Selected E167 and Y165 for saturation



mutagenesis and selected E167T and Y165F.



E163A/E167T was selected as preferred high fidelity mutant



(BamHI-HF).


EcoRI
Comparison of isoschizomer



Targeted 42 charged residues to mutate to Ala. No high fidelity



mutants



Second round of mutation: Target additional 32 charged residues



to mutate to Ala: Identified K62A.



Saturation mutagenesis on K62A. EcoRI(K62E) was selected as



a preferred high fidelity mutant (EcoRI-HF).


ScaI
Comparison of isoschizomers.



Targeted 58 charged residues to mutate to Ala. Identify 4



mutants



Preferred mutant of 4 is (H193A/S201F). This is selected as a



preferred high fidelity mutant (ScaI-HF)


SalI
Target 86 charged residues and mutate to Ala. SalI (R107A) was



preferentially selected as a preferred high fidelity mutant (SalI-



HF).


SphI
Target 71 charged residues and mutate to Ala. SphI (K100A) was



preferentially selected as a preferred high fidelity mutant (SphI-



HF)


PstI
Target 92 charged amino acids and mutate to Ala. PstI (D91A)



was preferentially selected as a preferred high fidelity mutant



(PstI-HF)


NcoI
Target 66 charged residues and mutate to Ala. NcoI (A2T/R31A)



was preferentially selected as a preferred high fidelity mutant



(NcoI-HF).


NheI
Target 92 charged residues and mutate to Ala. NheI (E77A) was


(Ex. 1)
preferentially selected as a preferred high fidelity mutant (NheI-



HF)


SspI
Target 81 charged residues and mutate to Ala. No preferential



mutants obtained.



Target 95 residues to additional charged residues and



hydroxylated residues to Ala except Tyr. Tyr mutated to Phe. SspI



(Y98F) was preferentially selected as a preferred high fidelity



mutant (SspI-HF)


NotI
Target 97 charged residues and mutate to Ala. K150A was



preferentially selected as a preferred high fidelity mutant (NotIHF)


SacI
Target 101 charged residues and mutate to Ala. SacI



(Q117H/R200A) was preferentially selected as a preferred high



fidelity mutant (SacI-HF) where Q117H was a carry over mutation



from template with no affect on activity


PvuII
Target 47 charged residues and mutate to Ala. No preferred



mutants obtained



Target 19 hydroxylated residues—Ser/Thr and Tyr. Select T46A



for further improvement



Saturation mutagenesis results in a preferred mutant T46G, T46H,



T46K, T46Y. PvuII(T46G) was preferentially selected as a



preferred high fidelity mutant (PvuII-HF)


MfeI
Target 60 charged residues and mutate to Ala. No preferred



mutants obtained



Target 26 hydroxylated residues and mutate to Ala except for Tyr



which was changed to Phe.



Target 38 residues (Cys, Phe, Met, Asn, Gln, Trp) and mutate to



Ala



Identify Mfe (Q13A/F35Y) as a preferred high fidelity mutant



(MfeI-HF) where F35Y is carried from the template


HindIII
Target 88 charged residues and mutate to Ala. No preferred



mutants obtained



Target 103 residues (Cys Met Asn, Gln, Ser Thr Trp) and mutate



to Ala and Tyr changed to Phe.



Identify HindIII (K198A) as a preferred high fidelity mutant



(HindIII-HF)


SbfI
Target 78 charged residues mutated to Ala



Target 41 residues (Ser Thr) mutated to Ala/Tyr to Phe



Target 55 residues of Cys, Phe, Met Asn, Gln, Trp to Ala



SbfI (K251A) was selected as a preferred high fidelity mutant



(SbfI-HF)


EagI
Target 152 residues (Asp, Glu, His, Lys, Arg, Ser, thr, Asn, and



Gln changed to Ala and Tyr changed to Phe).



EagI H43A was selected as a preferred high fidelity mutant (EagIHF)


EcoRV
Target 162 residues (Cys, Asp, Glu, Phe, his, Lys, Met, Asn, Gln,



Arg, Ser, Thr, to Ala and Trp to Phe)



EcoRV (D19A/E27A) was selected as a preferred high fidelity



mutant (EcoRV-HF)


AvrII
Target 210 residues (Cys, Asp, Glu, Phe, his, Lys, Met, Asn, Gln,



Arg, Ser, Thr, to Ala and Trp to Phe)



AvrII (Y104F) was selected as a preferred high fidelity mutant



(AvrII-HF)


BstXI
Target 237 residues (Cys, Asp, Glu, Phe, his, Lys, Met, Asn, Gln,



Arg, Ser, Thr, to Ala and Trp to Phe)



BstXI (N65A) was selected as a preferred high fidelity mutant



(BstXI-HF)


PciI
Target 151 residues (Cys, Asp, Glu, Phe, his, Lys, Met, Asn, Gln,



Arg, Ser, Thr, to Ala and Trp to Phe)



PciI (E78A/S133A) was selected as a preferred high fidelity



mutant. (PciI-HF) This was spontaneous and not one of the 151



separate mutations


HpaI
Target 156 residues (Cys, Asp, Glu, Phe, his, Lys, Met, Asn, Gln,



Arg, Ser, Thr, to Ala and Trp to Phe)



HpaI (E56A) was selected as a preferred high fidelity mutant



(HpaI-HF)


AgeI
Target 149 residues (Cys, Asp, Glu, Phe, his, Lys, Met, Asn, Gln,



Arg, Ser, Thr, to Ala and Trp to Phe)



AgeI (R139A) was selected as a preferred high fidelity mutant



(AgeI-HF)


BsmBI
Target 358 residues (Cys, Asp, Glu, Phe, his, Lys, Met, Asn, Gln,



Arg, Ser, Thr, to Ala and Trp to Phe)



BsmBI(N185Y/R232A) was selected as a preferred high fidelity



mutant (BsmBI (HF)


BspQI
Target 122 residues (Arg, Lys, His, Glu, Asp, Gln, Asn, Cys)



Replace R at position 279 with Phe, Pro, Tyr, Glu, Asp or Leu.



Preferred mutations were R388F and K279P.



Created a double mutant BspQI(K279P/R388F) as preferred high



fidelity mutant (BspQI-HF)


SapI
Find K273 and R380 in SapI corresponding to R388 and K279 in



BspQI.



SapI (K273P/R380F) was selected as a preferred high fidelity



mutant (SapI-HF)


KpnI
Target all residues (Asp, Glu, Arg, Lys, His, Ser, Thr, Tyr, Asn,



Gln, Phe, Trp, Cys, Met) to Ala.



More mutation was done on site D16 and D148.



A combined D16N/E132A/D148E was selected as a preferred high



fidelity mutant (KpnI-HF).


BsaI
Find 11 amino acids corresponding to the site in BsmBI.



BsaI (Y231F) was selected as a preferred high fidelity mutant



(BsaI-HF).









The method follows from the realization that amino acids responsible for cognate activity and star activity are different. The engineering of high fidelity restriction endonucleases described herein demonstrates that cognate activity and star activity can be separated and there are different critical amino acid residues that affect these different activities. The locations of amino acids that are here found to affect star activity are not necessarily found within the active site of the protein. The cleavage properties of any restriction endonuclease has been determined here for the first time by developing a criterion of success in the form of determining a FI (see also Wei, et al. Nucleic Acid Res., 36, 9, e50 (2008)) and an overall fidelity index improvement factor.
An “overall fidelity index improvement factor” refers to the highest FI for a mutant with maximum cleavage activity divided by the highest FI of the corresponding WT endonuclease with maximum cleavage activity within a selected set of buffers. The selected set may be of any size greater than one but practically will contain less than 10 different buffers and more preferably contains 4 buffers. The set may also include less than 4 buffers. The overall FI improvement factor of at least two should preferably be applicable for any mutant restriction endonuclease in the claimed invention additionally but not exclusively to the set of buffers consisting of NEB1, NEB2, NEB3 and NEB4.
A “similar cleavage activity” can be measured by reacting the same amount of enzyme with the same amount and type of substrate under the same conditions and visually comparing the cleavage profiles on a gel after electrophoresis such that the amount of cleavage product appears to be the same within a standard margin of error and wherein the quantitative similarity is more than 10%.
“Artificial” refers to “man-made”.
“Standard conditions” refers to an overall FI improvement factor calculated from results obtained in NEB1-4 buffers.
The general method described herein has been exemplified with 27 restriction endonucleases: AgeI, AvrII, BamHI, BsaI, BsmBI, BspQI, BstXI, EagI, EcoRI, EcoRV, HindIII, HpaI, KpnI, MfeI, NcoI, NheI, NotI, PciI, PstI, PvuII, SacI, SalI, SapI, SbfI, ScaI, SphI and SspI restriction endonucleases. However, as mentioned above, the method is expected to be effective for the engineering of any restriction endonuclease that has significant star activity.
Embodiments of the method utilize a general approach to create mutant restriction endonucleases with reduced star activity. For certain enzymes, it has proven useful to mutate charged residues that are determined to be conserved between two isoschizomers. In general, however, the method involves a first step of identifying all the charged and polar residues in a protein sequence for the endonuclease. For example, charged amino acids and polar residues include the acidic residues Glu and Asp, the basic residues His, Lys and Arg, the amide residues Asn and Gln, the aromatic residues Phe, Tyr and Trp and the nucleophilic residue Cys. Individual residues are targeted and mutated to an Ala and the products of these targeted mutations are screened for the desired properties of increased fidelity. If none of the mutants obtained provide a satisfactory result, the next step is to target mutations to all the hydroxylated amino acids, namely, Ser, Thr and Tyr, the preferred mutation being Ser and Thr to Ala and Tyr to Phe. It is also possible to target mutations to both classes of residues at one time. The mutation to Ala may be substituted by mutations to Val, Leu or Ile.
After these analyses, if one or more of the preferred mutants generated in the above steps still have substandard performance under the selected tests, these mutants can be selected and mutated again to each of the additional possible 18 amino acids. This is called saturation mutagenesis. Saturation mutagenesis provided the preferred high fidelity mutants for EcoRI, BamHI in part and PvuII. Depending on the results of saturation mutagenesis, the next step would be to introduce additional mutations either targeted or random or both into the restriction endonuclease. SacI-HF includes a random mutation generated fortuitously during inverse PCR. PciI-HF resulted from a random mutation and not from targeted mutations. BspQI-HF contains two mutations that were found to act synergistically in enhancing fidelity.
The use of various methods of targeted mutagenesis such as inverse PCR may involve the introduction of non-target mutations at secondary sites in the protein. These secondary mutations may fortuitously provide the desired properties. It is desirable to examine those mutated enzymes with multiple mutations to establish whether all the mutations are required for the observed effect. Q117H in the double mutant had no effect on activity.
In some cases, a mutation may provide an additional advantage other than improved fidelity.
The high fidelity/reduced star activity properties of the mutants provided in the Examples were selected according to their function in a set of standard buffers. Other mutations may be preferable if different buffer compositions were selected. However, the same methodology for finding mutants would apply. Table 4 lists mutations which apply to each restriction endonuclease and provide an overall FI improvement factor in the standard buffer.
The engineering of the high fidelity restriction endonucleases to provide an overall FI improvement factor of at least 2 involves one or more of the following steps:
1. Assessment of the Star Activity of the WT Restriction Endonuclease
In an embodiment of the invention, the extent of star activity of a restriction endonuclease is tested by means of the following protocol: the endonuclease activity is determined for an appropriate substrate using a high initial concentration of a stock endonuclease and serial dilutions thereof (for example, two-fold or three-fold dilutions). The initial concentration of restriction endonuclease is not important as long as it is sufficient to permit an observation of star activity in at least one concentration such that on dilution, the star activity is no longer detected.
An appropriate substrate contains nucleotide sequences that are cleaved by cognate endonuclease activity and where star activity can be observed. This substrate may be the vector containing the gene for the restriction endonuclease or a second DNA substrate. Examples of substrates used in Table 2 are pBC4, pXba, T7, lambda, and pBR322.
The concentration of stock restriction endonuclease is initially selected so that the star activity can be readily recognized and assayed in WT and mutated restriction endonucleases. Appropriate dilution buffers such as NEB diluent A, B or C is selected for performing the serial dilutions according to guidelines in the 2007-08 NEB catalog. The serially diluted restriction endonuclease is reacted with a predetermined concentration of the appropriate substrate in a total reaction volume that is determined by the size of the reaction vessel. For example, it is convenient to perform multiple reactions in microtiter plates where a 30 μl reaction mixture is an appropriate volume for each well. Hence, the examples generally utilize 0.6 μg of substrate in 30 μl, which is equivalent to 1 μg of substrate in 50 μl. The amount of substrate in the reaction mixture is not critical, but it is preferred that it be constant between reactions. The cleavage reaction occurs at a predetermined temperature (for example 25° C., 30° C., 37° C., 50° C., 55° C. or 65° C.) for a standard time such as one hour. The cleavage products can be determined by any standard technique, for example, by 0.8% agarose gel electrophoresis to determine the fidelity indices as defined above.
Not all restriction endonucleases have significant star activity as determined from their FI. However, if an endonuclease has a highest FI of no more than about 250 and a lowest FI of less than 100, the restriction endonuclease is classified as having significant star activity. Such endonucleases are selected as a target of enzyme engineering to increase fidelity for a single substrate. In some cases, the restriction endonucleases with both FI over about 500 and FI less than about 100 are also engineered for better cleavage activity.
Table 2 below lists the FI of some engineered restriction endonucleases before engineering. All samples were analyzed on 0.8% agarose gel.














TABLE 2






Diluent

Temp






Enzyme
(NEB)***
Substrate*
° C.
FI-1**
FI-2**
FI-3**
FI-4**


























AgeI
C
pXba
37
16
(1)
8
(1/2)
64
(1/8)
8
(1/2)


AvrII
B
T7
37
64
(1)
8
(1)
32
(1/4)
32
(1)


BamHI
A
λ
37
4
(1/2)
4
(1)
32
(1)
4
(1/2)


BsaI
B
pBC4
50
8
(1/4)
120
(1)
16
(1/4)
32
(1)


BsmBI
B
λ
55
1
(1/8)
8
(1/2)
120
(1)
4
(1/4)


BspQI
B
λ
50
2
(1/8)
16
(1)
32
(1)
4
(1/2)


BstXI
B
λ
55
2
(1/2)
2
(1/2)
2
(1/8)
4
(1)


EagI
B
pXba
37
4
(1/4)
8
(1/2)
250
(1)
16
(1)


EcoRI
C
λ
37
250
(1/2)
4
(1)
250
(1)
4
(1)


EcoRV
A
pXba
37
32
(1/16)
120
(1/2)
1000
(1)
64
(1/4)


HindIII
B
λ
37
32
(1/4)
250
(1)
4000
(1/4)
32
(1/2)


HpaI
A
λ
37
32
(1/16)
1
(1/4)
2
(1/8)
16
(1)


KpnI
A
pXba
37
16
(1)
16
(1/4)
8
(1/16)
4
(1/2)


MfeI
A
λ
37
32
(1)
16
(1/8)
8
(1/16)
32
(1)


NcoI
A
λ
37
120
(1)
32
(1)
120
(1/4)
32
(1)


NheI
C
pXba
37
32
(1)
120
(1/4)
120
(1/8)
32
(1)


NotI
C
pXba
37
≧32000
(1/16)
64
(1)
500
(1)
32
(1/4)


PciI
A
pXba
37
2000
(1/2)
16
(1/4)
120
(1)
8
(1/8)


PstI
C
λ
37
64
(1)
32
(1)
120
(1)
8
(1/2)


PvuII
A
pBR322
37
250
(1)
16
(1/4)
8
(1/32)
1/4
(1)


SacI
A
pXba
37
120
(1)
120
(1/2)
120
(1/32)
32
(1/2)


SalI
A
λ (H3)
37
8
(1/500)
1
(1/16)
32
(1)
1
(1/120)


SapI
C
λ
37
16
(1/4)
64
(1/2)
32
(1/4)
16
(1)


SbfI
A
λ
37
32
(1)
8
(1/4)
8
(1/16)
8
(1/2)


ScaI
A
λ
37
1/16
(1/32)
1/8
(1)
4
(1/2)
1/64
(1/16)


SphI
B
λ
37
64
(1)
32
(1)
64
(1/4)
16
(1/2)


SspI
C
λ
37
64
(1)
16
(1)
32
(1/4)
16
(1)





*Substrate: λ is lambda phage DNA; λ (H3) is HindIII-digested lambda phage DNA; pXba is pUC19 with XbaI-digested fragment of Adeno Virus; pBC4: a shorter version of pXba; T7: T7 DNA


**FI-1 to FI-4: fidelity index of the enzyme in NEBuffer 1, 2, 3 and 4. The number in parenthesis is a value for relative cleavage activity of the mutant restriction endonuclease in a specified buffer in a set of buffers compared with the “best” cleavage activity of the same mutant restriction endonuclease in any of the buffers in the set of buffers.


The compositions of NEB buffers follow:


NEB1: 10 mM Bis Tris Propane-HCl, 10 mM MgCl2, 1 mM dithiothreitol (pH 7.0 at 25° C.);


NEB2: 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, 1 mM dithiothreitol (pH 7.9 at 25° C.);


NEB3: 100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1 mM dithiothreitol (pH7.9 at 25° C.);


NEB4: 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol (pH7.9 at 25° C.).


***The compositions of NEB diluents follow. (Using diluents in the dilution instead of water will keep the glycerol concentration in the reaction as a constant.)


Diluent A: 50 mM KCl, 10 mM Tris-HCl, 0.1 mM EDTA, 1 mM dithiothreitol, 200 mg/ml BSA. 50% glycerol (pH7.4 at 25° C.);


Diluent B: 300 mM NaCl, 10 mM Tris-HCl, 0.1 mM EDTA, 1 mM dithiothreitol, 500 mg/ml BSA, 50% glycerol (pH7.4 at 25° C.);


Diluent C: 250 mM NaCl, 10 mM Tris-HCl, 0.1 mM EDTA, 1 mM dithiothreitol, 0.15% Triton X-100, 200 mg/ml BSA, 50% glycerol (pH 7.4 at 25° C.).






2. Construction of High Expression Host Cell Strains

It is convenient if a host cell is capable of over-expressing the mutant restriction endonuclease for which reduced star activity is sought. If the restriction enzyme is highly expressed in E. coli, the star activity can be readily detected in the crude extract, which simplifies the screening for the high fidelity restriction endonuclease. However, the mutated restriction endonuclease can be expressed in any host cell providing that the host cell is protected in some way from toxicity arising from enzyme cleavage.
This might include: the presence of a methylase; production in a compartment of the cell which provides a barrier to access to the genome (such as an inclusion body or the periplasm); in vitro synthesis; production in an emulsion (see U.S. patent application Ser. No. 12/035,872) absence of cleavage sites in the host genome; manufacture of the enzyme in component parts subject to intein mediated ligation (see U.S. Pat. No. 6,849,428), etc.
Over-expression of the mutated restriction endonucleases for purposes of production can be achieved using standard techniques of cloning, for example, use of an E. coli host, insertion of the endonuclease into a pUC19-derived expression vector, which is a high copy, and use of a relatively small plasmid that is capable of constant expression of recombinant protein. The vector may preferably contain a suitable promoter such as the lac promoter and a multicopy insertion site placed adjacent to the promoter. Alternatively, a promoter can be selected that requires IPTG induction of gene expression. If the activity in the crude extract is not sufficient, a column purification step for the restriction endonuclease in crude extract may be performed.
3. Mutagenesis of Restriction Endonuclease
DNA encoding each charged or polar group in the restriction endonuclease may be individually targeted and the mutated DNA cloned and prepared for testing. Multiple mutations may be introduced into individual restriction endonuclease genes. Targeted mutagenesis of restriction endonucleases may be achieved by any method known in the art. A convenient method used here is inverse PCR. In this approach, a pair of complementary primers that contains the targeted codon plus a plurality of nucleotides (for Example 18 nt) on both the 5′ and 3′ side of the codon is synthesized. The selection of suitable primers can be readily achieved by reviewing the gene sequence of the endonuclease of interest around the amino acid residue of interest. Access to gene sequences is provided through REBASE and GenBank. The template for PCR is a plasmid containing the restriction endonuclease gene. The polymerase is preferably a high fidelity polymerase such as Vent® or Deep VentTM DNA polymerase. By varying the annealing temperature and Mg2+ concentration, successful introduction of most mutations can be achieved. The PCR amplification product is then purified and preferably digested by DpnI. In an embodiment of the invention, the digested product was transformed into competent host cells (for example, E. coli), which have been pre-modified with a corresponding methylase. Colonies from each mutant were picked and grown under similar conditions to those in which the WT is grown (for example, using similar growth medium, drug selection, and temperature). The resulting restriction endonucleases were screened for reduced star activity.
4. Screening for Mutant Restriction Endonucleases with Reduced Star Activity
Conditions such as buffer composition, temperature and diluent should be defined for determining star activity in a mutant restriction endonuclease. Tables 2 and 3 show the FI of recombinant endonucleases before and after mutation in four different buffers using three different diluents at 37° C. Accordingly, it is possible to determine which mutants have an overall desirable improved fidelity index factor of at least 2, more than 10, at least 50 or more than 500 and to select enzymes as preferred high fidelity mutants.
In an embodiment of the invention, the mutant restriction endonucleases were screened for activity in normal buffer conditions (no more than 5% glycerol) first. For those mutants with at least about 10% of activity of WT restriction endonuclease, activity was also determined in star activity promotion conditions that promoted star activity, for example, high glycerol concentration and optionally high pH. Preferably, the mutant with the least star activity but with acceptable cognate activity in normal buffers is selected. Plasmid can then be extracted and sequenced for the confirmation of the mutant. In some cases, the star activity is not easily measured, even with high glycerol and high pH conditions. Instead, the activity in different buffers is measured and compared, and the one with the highest cleavage activity ratio in NEB4 compared with NEB3 can be tested further for star activity improvement.
5. Saturation Mutagenesis on One Single Residue
As described in the previous section, the first step is to mutate a target amino acid in the restriction endonuclease to Ala. If the results are not satisfactory, saturation mutagenesis is performed. This is preferably performed by one of two methods. One method is to change the intended codon into NNN. After mutagenesis, multiple colonies are assayed under normal conditions and under conditions that promote star activity. Alternatively, a different codon can be selected for mutagenesis of each of the targeted amino acids for example: Ala: GCT; Cys: TGC; Asp: GAC; Glu: GAA; His: CAC; Ile: ATC; Lys: AAA; Leu: CTG; Met: ATG; Asn:
AAC; Pro: CCG; Gln: CAG; Arg: CGT; Ser: TCC; Thr: ACC; Val: GTT; Trp: TGG and Tyr: TAC
6. Combination
More than one mutation can be introduced into the restriction endonuclease gene if a single mutation does not sufficiently reduce the star activity. Mutation combination and saturation mutagenesis can be performed in any order.
7. Mutant Purification and Assessment of the Improvement
The high fidelity mutants may be purified in a variety of ways including use of different chromatography columns. For normal quality assessment, one FPLC heparin column is enough to eliminate the DNA and non-specific nucleases from the preparation. Multiple columns including ion exchange, hydrophobic, size exclusion and affinity columns can be used for further purification.
Purified high fidelity restriction endonucleases are measured for FI in four NEB buffers and compared with the FIs of the WT restriction endonuclease. The ratio of FI for the high fidelity restriction endonuclease in its optimal buffer to that of WT is the overall improvement factor.







TABLE 3







FI* for exemplified restriction endonucleases















Diluent

Temp






Enzyme
(NEB)
Substrate*
° C.
FI-1**
FI-2**
FI-3**
FI-4**





















AgeI-
C
pXba
37
≧500
(1)
≧250
(1/2)
≧16
(1/16)
≧250
(1)


HF


AvrII-
B
T7
37
500
(1)
≧500
(1/2)
≧16
(1/64)
≧1000
(1)


HF


BamHI-
A
λ
37
≧4000
(1)
≧4000
(1)
≧250
(1/16)
≧4000
(1)


HF


BsaI
B
pBC4
50
≧4000
(1/2)
≧8000
(1)
120
(1)
≧8000
(1)


BsmBI
B
λ
55
2
(1)
≧500
(1)
≧64
(1/8)
≧500
(1)


BspQI-
A
pUC19
50
≧1000
(1/4)
≧1000
(1/4)
≧64
(1/64)
≧4000
(1)


HF


BstXI-
A
λ
55
≧120
(1/2)
≧250
(1)
≧16
(1/16)
≧250
(1)


HF


EagI-
C
pXba
37
250
(1/2)
250
(1)
250
(1/2)
500
(1)


HF


EcoRI-
C
λ
37
2000
(1/8)
4000
(1/4)
250
(1/250)
16000
(1)


HF


EcoRV-
A
pXba
37
≧16000
(1/4)
≧64000
(1)
≧32000
(1/2)
≧64000
(1)


HF


HindIII-
B
λ
37
≧16000
(1/4)
≧64000
(1)
≧16000
(1/4)
≧32000
(1/2)


HF


HpaI-
A
λ
37
≧32
(1/32)
≧2000
(1)
2
(1/8)
≧2000
(1/2)


HF


KpnI-
A
pXba
37
≧4000
(1)
≧1000
(1/4)
≧64
(1/64)
≧4000
(1)


HF


MfeI-HF
A
λ
37
≧1000
(1)
≧250
(1/4)
≧16
(1/64)
≧500
(1/2)


NcoI-
A
λ
37
≧4000
(1/4)
≧4000
(1/4)
≧1000
(1/16)
≧64000
(1)


HF


NheI-
C
pXba
37
≧128000
(1)
≧4000
(1/32)
≧32
(1/2000)
≧32000
(1/2)


HF


NotI-HF
C
pXba
37
≧8000
(1/16)
≧128000
(1)
≧4000
(1/64)
≧64000
(1/2)

















PciI-HF
A
pXba
37
NC
≧2000
(1)
≧2000
(1)
≧1000
(1)


















PstI-HF
C
λ
37
1000
(1/8)
4000
(1/2)
4000
(1/4)
4000
(1)


PvuII-
A
pBR322
37
≧250
(1/120)
≧2000
(1/16)
≧250
(1/120)
500
(1)


HF


SacI-
A
pXba
37
≧32000
(1)
≧16000
(1/2)
≧500
(1/64)
≧32000
(1)


HF


SalI-HF
A
λ (H3)
37
≧8000
(1/8)
≧64000
(1)
≧4000
(1/16)
≧32000
(1/2)


SbfI-HF
C
λ
37
1000
(1)
120
(1/2)
8
(1/32)
250
(1)


ScaI-
A
λ
37
4000
(1/8)
1000
(1)
2000
(1/32)
1000
(1)


HF


SphI-
B
λ
37
4000
(1/8)
2000
(1/16)
250
(1/250)
8000
(1)


HF


SspI-
C
λ
37
≧4000
(1/2)
120
(1/2)
≧32
(1/128)
500
(1)


HF





*The FI is a ratio of the highest concentration that does not show star activity to the lowest concentration that completes digestion of the substrate.


**The number in parenthesis is a value for relative cleavage activity of the mutant restriction endonuclease in a specified buffer in a set of buffers compared with the greatest cleavage activity of the same mutant restriction endonuclease in any of the buffers in the set of buffers.













TABLE 4







Mutations providing restriction endonucleases with high fidelity








Restriction



Endonuclease
Examples of mutants with overall improved FI factor ≧ 2





AgeI
R139A; S201A*


AvrII
Y104F; M29A; E96A; K106A; S127A; F142A


BamHI
E163A/E167T; K30A; E86A; E86P; K87A; K87E; K87V; K87N; P144A;



Y165F; E167A; E167R; E167K; E167L; E167I K30A/E86A;



E86A/K106A; K30A/E86A/K106A; K30A/K87A; E86P/K87E;



E86A/Y165F; K30A/E167A; E163S/E170T/P173A;



E163S/E170T/P173A; E86P/K87T/K88N/E163S/E170T/P173A;



E86P/K87R/K88G/E163S/E170T/P173A;E86P/K87P/K88R/



E163S/E170T/P173A/E211K; E86P/K87T/K88R/



E163S/E170T/P173A/N158S; E86P/K87S/K88P/



E163S/E170T/P173A; E86P/K87G/K88S/E163S/E170T/P173A;



E86P/K87R/K88Q/E163S/E170T/P173A; E86P/K87W/K88V;



E86P/P173A


BsaI
Y231F


BsmBI
N185Y/R232A; H230A; D231A; R232A;


BspQI
K279P/R388F; K279A; K279F; K279P; K279Y; K279E; K279D



R388A; R388F; R388Y; R388L; K279P/R388F; K279A/R388A;



D244A


BstXI
N65A; Y57F; E75A; N76A; K199A;


EagI
H43A


EcoRI
K62A; K62S; K62L; R9A; K15A; R123A; K130A; R131A; R183A; S2Y;



D135A; R187A; K62E


EcoRV
D19A; E27A; D19A/E27A


HindIII
S188P/E190A; K198A


HpaI
Y29F; E56A


KpnI
D148E; D16N/R119A/D148E; D2A/D16N/D148E;



D16N/E134A/D148E; D16N/E132A/D148E


MfeI
Y173F; Q13A/F35Y


NcoI
D56A; H143A; E166A; R212A; D268A; A2T/R31A


NheI
E77A


NotI
K176A; R177A; R253A; K150A


PciI
E78A/S133A


PstI
E204G; K228A; K228A/A289V; D91A


PvuII
T46A; T46H; T46K; T46Y; T46G


SacI
Q117H/R154A/L284P; Q117H/R200A


SalI
R82A; K93A; K101A; R107A


SapI
K273P; R380A; K273P/R380A


SbfI
K251A


ScaI
R18A; R112A; E119A; H193A; S201F; H193A/S201F


SphI
D91A; D139A; D164A; K100A


SspI
H65A; K74A; E78A; E85A; E89A; K109A; E118A; R177A; K197A;



Y98F





The mutations for each enzyme are separated by a semicolon.






All references cited above and below, as well as U.S. Ser. No. 12/172,963 filed Jul. 14, 2008 and U.S. provisional application Ser. No. 60/959,203, are incorporated by reference.
EXAMPLES
Where amino acids are referred to by a single letter code, this is intended to be standard nomenclature. The key to the code is provided for example in the NEB catalog 2007/2008 on page 280.
Plasmids used for cloning and as substrates have sequences as follows:
pLaczz2 (SEQ ID NO:102), pSyx20-lacIq (SEQ ID NO:105), pBC4 (SEQ ID NO:103), pXba (SEQ ID. NO:104) and pAGR3 (SEQ ID NO:106). pACYC is described in GenBank XO 6403, T7 in GenBank NC001604, pUC18 in GenBank L09136, and pRRS in Skoglund et al. Gene, 88:1-5 (1990. pSX33 was constructed by inserting lad gene into pLG339 at EcoRI site. pLG339 is described in Stoker, et al. Gene 19, 335-341 (1982).
All buffers identified as NEB buffers used herein are obtainable from New England Biolabs, Inc. (NEB), Ipswich, Mass.
Example 1
Engineering of High Fidelity NheI
1. Expression of NheI
NheI was expressed in E. coli transformed with pACYC-NheIM, and placzz1-NheIR. placzz1 is a pUC19 derivative plasmid. The cell was grown at 30° C. for overnight in the LB with Amp and Cam.
2. Mutagenesis of NheI
All 92 charged residues in NheI were mutated to Ala as the following residues: 5, 6, 7, 14, 17, 19, 22, 25, 28, 31, 38, 39, 42, 47, 49, 52, 56, 58, 59, 60, 64, 74, 75, 76, 77, 80, 91, 93, 104, 105, 110, 112, 116, 117, 123, 126, 130, 131, 133, 135, 137, 147, 149, 152, 159, 160, 165, 167, 170, 171, 174, 179, 183, 195, 202, 205, 207, 209, 210, 211, 214, 216, 218, 221, 225, 231, 241, 243, 244, 250, 252, 256, 257, 259, 264, 266, 267, 281, 285, 287, 288, 289, 291, 297, 300, 307, 313, 315, 318, 321, 324, 325.
The numbers above correspond to amino acid positions in the NheI protein sequence (SEQ ID NO:89).
The methods were the same as disclosed in the examples of parent application, U.S. Ser. No. 12/172,963, filed Jul. 14, 2008, using inverse PCR followed by DpnI digestion. The treated product was then transformed into E. coli (pACYC-NheIM).
3. Selection of NheI-HF
Selection of NheI-HF was performed according to the examples as disclosed in the parent application, U.S. Ser. No. 12/172,963 filed Jul. 14, 2008. The standard and star activity assays contained pBR322 as a substrate in NEB4 buffer and 5% glycerol and 39% glycerol, respectively. Only one mutation was found to be significant in improving the NheI. This was E77A. NheI(E77A) was selected as the NheI-HF.
4. Comparison of NheI-HF and WT NheI
The FIs of NheI-HF and WT NheI were determined separately on pXba, a plasmid substrate containing the XbaI digested piece from Adeno virus in each of NEB1-4 buffers. The comparison is shown in FIG. 2A-B, and the result is listed in Table 14 (below).







TABLE 14







Comparison of NheI-HF and WT NheI











NheI-HF
WT NheI















Fidelity

Fidelity
Improvement


Buffer
Activity
Index
Activity
Index
Factor















NEB1
100%
≧128000
100%
32
≧4000


NEB2
 3%
≧4000
 25%
120
≧32


NEB3
0.05% 
≧32
12.5% 
120
≧0.25


NEB4
 50%
≧32000
100%
32
≧1000





NheI-HF showed optimal activity in NEB1 buffer where its FI is ≧128,000. WT NheI has maximum activity in NEB1 and NEB4 buffers, where its best FI is 32. The overall FI improvement factor is ≧128,000/32 = ≧4000.

## Claims

1. A composition comprising a variant NheI restriction endonuclease having reduced star activity, wherein the variant NheI restriction endonuclease comprises an amino acid sequence that differs from the amino acid sequence of the parent NheI restriction endonuclease by a substitution at an amino acid position corresponding to position 77 of SEQ ID NO:89.

2. The composition according to claim 1, wherein the amino acid substitution is E77A.