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Applied and Environmental Microbiology, October 1998, p. 3669-3673, Vol. 64, No. 10
0099-2240/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Characterization of an Extremely Thermostable
Restriction Enzyme, PspGI, from a Pyrococcus
Strain and Cloning of the PspGI Restriction-Modification
System in Escherichia coli
Richard
Morgan,
Jian-ping
Xiao, and
Shuang-Yong
Xu*
New England Biolabs, Inc., Beverly,
Massachusetts 01915
Received 8 June 1998/Accepted 31 July 1998
 |
ABSTRACT |
An extremely thermostable restriction endonuclease,
PspGI, was purified from Pyrococcus sp. strain
GI-H. PspGI is an isoschizomer of EcoRII and
cleaves DNA before the first C in the sequence 5' ^CCWGG 3' (W is A
or T). PspGI digestion can be carried out at 65 to 85°C.
To express PspGI at high levels, the PspGI
restriction-modification genes (pspGIR and
pspGIM) were cloned in Escherichia coli.
M.PspGI contains the conserved sequence motifs of
-aminomethyltransferases; therefore, it must be an N4-cytosine
methylase. M.PspGI shows 53% similarity to (44%
identity with) its isoschizomer, M.MvaI from
Micrococcus variabilis. In a segment of 87 amino acid
residues, PspGI shows significant sequence similarity to
EcoRII and to regions of SsoII and
StyD4I which have a closely related recognition sequence (5' ^CCNGG 3'). PspGI was expressed in E. coli via a T7 expression system. Recombinant PspGI
was purified to near homogeneity and had a half-life of 2 h at
95°C. PspGI remained active following 30 cycles of
thermocycling; thus, it can be used in DNA-based diagnostic
applications.
 |
INTRODUCTION |
Since the discovery of the first
type II restriction endonuclease (24), these enzymes have
played important roles in creating recombinant DNA molecules (7,
21). Over 100 type II restriction-modification (R-M) systems have
been cloned so far (22). Among the cloned restriction
endonucleases, some enzymes with the same or related DNA recognition
sequences have similar amino acid sequences (30 to 100% identity)
(30). Weak amino acid sequence similarities (16 to 20%
identity) have been reported among some nonisoschizomers (18,
23). The methylases of different R-M systems are more conserved.
Nine conserved sequence motifs were found among the aminomethylases
(N4-cytosine and N6-adenine methylases) (14), and 10 were
found among the cytosine-5 methylases (20). The aminomethylases are separated into three groups,
,
, and
, based on the circular permutation of conserved motifs (14,
30).
Restriction enzymes BsoBI and AvaI have been used
in isothermal strand displacement amplification to detect pathogens
such as Mycobacterium tuberculosis (16, 29). Many
thermostable restriction enzymes have been isolated from
Thermus species and Bacillus stearothermophilus
(1, 22). To isolate highly thermostable restriction enzymes,
we screened extreme thermophiles living near deep-sea vents. One such
isolate, Pyrococcus sp. strain GI-H, displays restriction
enzyme activity in its cell extracts. Here we report the
characterization of this extremely thermostable restriction enzyme,
PspGI, and the cloning and expression of the pspGIR and pspGIM genes in Escherichia
coli. Recombinant PspGI was purified, and its activity
at high temperatures was determined.
 |
MATERIALS AND METHODS |
Bacterial strains.
ER1821(
DE3) is a T7 expression strain
that is also deficient in methylation-dependent restriction
(McrBC
Mrr
McrA
).
Pyrococcus sp. strain GI-H was isolated from sediments near an oceanic hydrothermal vent and provided by H. W. Jannasch, Woods Hole Oceanographic Institute, Woods Hole, Mass. (26).
Pyrococcus sp. strain GI-H cells were propagated in a medium
comprised of 0.5× Difco marine broth mixed with an equal volume of
Difco sea salts (40 g/liter), 0.01 M cysteine, 0.005 M BTP, and 10 g of sulfur per liter and incubated at 85°C in flasks without
aeration or agitation. Cells in the late log phase of growth were
collected by centrifugation and stored at
70°C until use.
Purification of PspGI, N-terminal amino acid
sequencing, and thermocycling.
Ten grams of cell paste was
resuspended in 35 ml of sonication buffer (20 mM Tris-HCl [pH 7.5], 1 mM dithiothreitol [DTT], 0.1 mM EDTA) and lysed by sonication.
PspGI was purified by chromatography through
heparin-Sepharose, Mono Q, and Mono S (Pharmacia Biotech, Piscataway,
N.J.), heparin-TSK (TosHass, Montegomeryville, Pa.), and Polycat A
(Custom LC, Inc.) fast protein liquid chromatography columns. Column
fractions were assayed for PspGI restriction activity on T7
phage DNA at 65°C for 1 h (the assay temperature of 65°C was
used before the optimal temperature for PspGI digestion was known). The peak fractions of restriction enzyme activity were pooled.
Proteins were resolved by sodium dodecyl sulfate (SDS)-10 to 20%
polyacrylamide gel electrophoresis (PAGE) and detected by Coomassie
blue staining. Purified PspGI was subjected to
electrophoresis and electroblotted in accordance with published
procedures (15). The membrane was stained with Coomassie
brilliant blue R-250, and the protein band of approximately 31 kDa was
excised and subjected to sequential degradation on an Applied
Biosystems model 407A protein sequencer.
Cell extracts containing recombinant PspGI were heated at
70°C for 30 min. Denatured proteins and insoluble materials were removed by centrifugation. PspGI was purified by
chromatography through heparin-Sepharose and Source Q columns.
The half-life of PspGI was measured by incubating the enzyme
in 1× buffer 3 (New England Biolabs, Inc. [NEB]) plus 0.1% Triton X-100 and 100 µg of bovine serum albumin per ml at 95°C for 4 h. Samples were taken every 20 min and stored at 4°C until activity assays.
To measure the thermostability of PspGI, 100 U of the
recombinant enzyme was subjected to 30 cycles of thermocycling at
95°C for 30 s, 60°C for 30 s, and 72°C for 30 s.
Following thermocycling, 1 to 10 U of the original input enzyme was
used to cleave 1 µg of T7 phage DNA at 75°C for 1 h.
Two primers were used to amplify the coding sequence from genomic DNA
by PCR. The forward primer, based on N-terminal amino acid residues 4 to 10, had the following sequence: 5' GTT GGA TCC AAC CTN GTN ATH GAY
ATH 3'. The reverse primer, based on residues 21 to 27, had the
following sequence: 5' GTT CTG CAG GCY TCR TAD ATD ATY TCR TT 3' (where
R is A or G; Y is C or T; N is A, C, G, or T; H is A, C, or T; and D is
A, G, or T). The PCR amplification conditions were as follows: 95°C
for 3 min for one cycle; four cycles of 95°C for 20 s, 38°C
for 30 s, and 72°C for 5 s; and then 20 cycles of 95°C
for 20 s, 56°C for 30 s, and 72°C for 5 s.
Mapping of PspGI cleavage sites.
PspGI
cleavage sites on T7 phage DNA were mapped by double digestion of T7
phage DNA with PspGI and endonucleases which cleave at known
positions. PspGI restriction digestion was carried out at
75°C. One unit of PspGI is defined as the amount of enzyme required to digest 1 µg of T7 phage DNA to completion at 75°C for
1 h. The activity assay buffer (high-salt buffer) contained 100 mM
NaCl, 10 mM MgCl2, 1 mM DTT, 100 µg of bovine serum
albumin per ml, and 0.1% Triton X-100. Medium-salt buffer was the same as high-salt buffer except that it contained 50 mM NaCl. Low-salt buffer contained 10 mM bis-Tris-propane-HCl, 10 mM MgCl2,
and 1 mM DTT.
DNA sequence analysis, inverse PCR, and plasmid
construction.
Plasmid DNA was sequenced by the dideoxy termination
method with an AmpliTaq DNA polymerase dideoxy terminator sequencing kit (PE Applied Biosystems, Foster City, Calif.). Inverse PCR was
carried out as described previously (19). Inverse PCR
products were gel purified and sequenced directly or cloned into pUC19 and then sequenced.
For the construction of pLG-PspGIM, two primers were used to amplify
the pspGIM gene from genomic DNA. The forward and reverse primers had the following respective sequences: 5' TAT GGA
TCC GGA GGT GAA AAA AAT GAA GTC ATG GAG AGA GTC ATT TCA 3' and 5' GGA GGA TCC TTA ACT CTT GTG TAA TAC AAC AAT GTT 3'
(BamHI sites are underlined). PCR conditions were 95°C for
1 min, 60°C for 1 min, and 72°C for 1 min with 2 U of Vent DNA
polymerase for 20 cycles. The PCR product was digested with
BamHI and ligated into BamHI-cleaved and calf
intestinal phosphatase-treated pLG339 (27). Vector pLG339
contains the pSC101 origin and is compatible with a ColE1 origin. The
Dcm
strain GM2163 was used as the host for
transformation, since Dcm methylation blocks PspGI
digestion. The level of resistance to PspGI digestion of
plasmid DNA was used as an indicator of M.PspGI
expression and modification in vivo.
For the construction of pAII17-PspGIR, the pspGIR gene was
amplified from genomic DNA by use of two primers with the following respective sequences: 5' GGA GGA GTG CAT ATG GTT AGA AAT
CTC CTT ATT GAT ATA ACA 3' and 5' GTG GGA TCC TTA CAC AAG
AGT TAA TTG TTT TCC TCT TTT 3' (NdeI and BamHI
sites are underlined). PCR conditions were the same as those used for
the amplification of the pspGIM gene. The PCR product was
digested with NdeI and BamHI and gel purified
from a low-melting-temperature agarose gel. Following
-agarase
treatment and DNA precipitation, the DNA fragment was ligated into T7
expression vector pAII17 (11) with compatible ends. The
ligated DNA was transformed into ER1821(
DE3)/pLG-PspGIM. ER1821(
DE3)/pLG-PspGIM/pAII17-PspGIR cells were cultured to the late
log phase, and PspGI production was induced by the addition of isopropyl-
-D-thiogalactopyranoside (IPTG) to a final
concentration of 0.3 to 0.5 mM for 2 h. Cell extracts were
prepared as described previously (31).
 |
RESULTS |
Purification of PspGI and mapping of PspGI
sites on T7 phage DNA.
Approximately 2,000 U of PspGI
endonuclease was purified to near homogeneity with six chromatographic
columns. This protein (~31 kDa) was electroblotted and sequenced. The
N-terminal amino acid sequence of the first 28 residues was determined
to be
(Met)-Val-Arg-Asn-Leu-Val-Ile-Asp-Ile-Thr-Lys-Lys-Pro-Thr-Gln-Asn-Ile-Pro-Pro-Thr-Asn-Glu-Ile-Ile-Glu-Glu-Ala-Ile. The amino acid sequence was used to design degenerate primers for PCR
amplification of the coding sequence (see below).
PspGI cleavage sites on T7 phage DNA were mapped to
approximate positions 2400 and 8200 by double digestion of T7 phage DNA with PspGI and with endonucleases which cleave at known
positions, such as ApaLI, BglII,
BstBI, EcoNI, MluI, NruI,
and StuI (data not shown). The sequence 5' CCWGG 3' (W is A
or T) occurs in T7 phage DNA at positions 2366 and 8188. Dideoxy
sequence analysis of the terminal base obtained from PspGI
cleavage of the DNA substrate indicated that PspGI cleaves
before the first C at 5' ^CCWGG 3' (data not shown). Thus,
PspGI is an isoschizomer of EcoRII and a
neoschizomer of BstNI (5' CC^WGG 3'). Two other
enzymes, SsoII and StyD4I, recognize a more
degenerate sequence (5' ^CCNGG 3') (9, 17).
The recognition sequence of PspGI is the same as that of the
Dcm methylase. The Dcm methylase modifies the internal C at the cytosine-5 position in 5' CCWGG 3' sites. Plasmids pBR322 and pUC19
prepared from a Dcm+ E. coli strain are mostly
resistant to PspGI digestion. Lambda DNA is partially
resistant to PspGI digestion, probably as the result of
undermethylation of Dcm sites. T7 phage DNA is susceptible to
PspGI digestion due to inhibition of Dcm methylase activity during T7 phage infection (13).
PspGI digestion can be carried out at 65 to 85°C.
PspGI is most active in a restriction buffer with 100 mM
NaCl. It has 10% relative activity in a low-salt buffer (no NaCl) and
80% relative activity in a medium-salt buffer (50 mM NaCl) (data not
shown).
Cloning of pspGIR and pspGIM genes.
Because Dcm methylase blocks PspGI digestion and the
transformation efficiency of the Dcm
strain is rather
low, the methylase selection method seemed less preferable for cloning
the pspGIM gene. The endo-blue method (5) also
failed to clone the functional pspGIR gene (17a),
probably due to the partial protection conferred by the Dcm methylase. Therefore, a PCR cloning approach was used to clone directly the N-terminal coding region of the pspGIR gene. The first 28 amino acid residues were determined by protein sequencing of the
purified PspGI protein. Degenerate primers were synthesized
based on the amino acid sequence and used to amplify codons 4 to 27. The amplified product was cloned and sequenced to confirm that it
matched the amino acid sequence derived from N-terminal protein
sequencing. Two sets of primers were used to clone the adjacent DNA by
inverse PCR. The pspGIR and pspGIM genes were
amplified by PCR and resequenced directly from PCR products in the
absence of cloning steps. The pspGIR and pspGIM
genes are 819 and 1,299 bp long, respectively, and overlap by 15 bp.
The predicted molecular mass of PspGI is 32 kDa, which
matches closely with the apparent size of 31 kDa estimated from
SDS-PAGE. The predicted mass of M.PspGI is 50.4 kDa.
The R-M genes in the PspGI and EcoRII systems are
convergent, whereas the R-M genes in the SsoII and
StyD4I systems are divergent (Fig.
1).

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FIG. 1.
Gene organization of PspGI,
EcoRII, SsoII, and StyD4I R-M systems
and of MvaI. aa, amino acids.
|
|
Comparisons of PspGI with EcoRII and
SsoII and of M.PspGI with
M.MvaI.
The EcoRII R-M system was
cloned and sequenced previously (12, 25). SsoII
and StyD4I are enzymes with a closely related recognition
sequence, 5' ^CCNGG 3'. The sequences of the SsoII and
StyD4I R-M genes were published previously (9,
17). An amino acid sequence comparison of PspGI with
EcoRII, SsoII, and StyD4I revealed
34% similarity (20% identity) over a stretch of 87 amino acid
residues (Fig. 2; the respective GenBank
accession numbers for PspGI, EcoRII,
SsoII and StyD4I are AF067805, P14633, P34880,
and D73442). The sequence of the mvaIR gene is not yet
available for comparison.

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FIG. 2.
Amino acid sequence alignment of PspGI (amino
acid residues 88 to 184), EcoRII (residues 254 to 338),
SsoII (residues 108 to 196), and StyD4I (residues
121 to 209). Identical residues are shown in bold. Similar residues are
underlined. The sequence alignment was based on the Bestfit program
(4).
|
|
Both M.PspGI and M.MvaI belong to the
group of aminomethyltransferases. M.PspGI shows
extensive homology (53% similarity and 44% identity) to its
isoschizomer M.MvaI (Fig.
3; the GenBank accession number for the
mvaIM gene sequence is X16985). Conserved or identical
residues are found throughout the proteins, even in the variable region
(target-recognizing domain). The most conserved segment lies in N4
methylase motif IV, which contains the characteristic SPPY sequence. At
the DNA level, the two methylase genes show 54% identity in their
nucleotide sequences.

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FIG. 3.
Amino acid sequence alignment of M.PspGI
and M.MvaI. Identical or similar amino acid residues
are shaded. Four plausible short segment deletions in
M.PspGI are indicated by Del1 through Del4. The
sequence alignment was made with the program MACAW. TRD,
target-recognizing domain.
|
|
Expression of PspGI in E. coli and
purification of recombinant PspGI.
We attempted to
express the pspGIR gene in E. coli in the absence
of M.PspGI modification. The pspGIR gene was
amplified by PCR and ligated into pUC-based expression vector pRRS, and
the ligated DNA was transformed into a Dcm+ RR1 variant.
After the screening of over 240 transformants, one clone that produced
a low level of PspGI in the crude cell extract was isolated.
The specific activity of this enzyme was fivefold lower than that of
the wild-type enzyme. We concluded that this isolate was probably a
mutant. It is possible that the Dcm methylase did not fully modify all
Dcm-PspGI sites in vivo, so that there was selection
pressure to yield a less active mutant of PspGI.
To construct a premodified host, a BamHI fragment containing
the pspGIM gene was cloned in low-copy-number plasmid pLG339 (27). The pspGIM gene was expressed
constitutively under the control of the Tc promoter. Four clones with
PCR inserts were isolated and shown to be partially resistant to
PspGI and BstNI digestion. It was concluded that
M.PspGI is partially active at the E. coli
growth temperature (37°C). One of the plasmids was used to transform
E. coli ER1821(
DE3) to premodify the host chromosome. A
PCR fragment containing the pspGIR gene (flanked by
NdeI and BamHI sites) was ligated into T7
expression vector pAII17 and transformed into the premodified host.
When induced with IPTG, one clone produced approximately 50,000 U of
PspGI per g of wet E. coli cells.
Recombinant PspGI was purified by heat denaturation of
E. coli proteins at 70°C for 30 min, followed by
chromatography. Recombinant PspGI was purified to >90%
homogeneity (Fig. 4). Like native
PspGI, recombinant PspGI had a specific activity
of 3 × 106 U/mg of protein on T7 DNA.

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FIG. 4.
SDS-PAGE of purified recombinant PspGI. The
apparent molecular mass of PspGI on SDS-PAGE was estimated
to be 31 kDa (indicated by an arrow). Lane 1, protein size markers;
lanes 2 and 3, E. coli cell extract containing
PspGI before and after heat treatment at 70°C,
respectively; lane 4, after heparin-Sepharose column chromatography;
lane 5, after Source Q column chromatography. The protein gel was
scanned with MicroTek ScanMaker and analyzed with the NIH Image
analysis program.
|
|
PspGI temperature optimum for digestion and half-life
at 95°C.
One unit of PspGI was used to cleave 1 µg
of T7 phage DNA for 1 h at 25, 37, 50, 65, 75, 80, and 85°C. The
DNA products were separated on an agarose gel (Fig.
5). PspGI did not cleave DNA at room temperature (Fig. 5, lane 1). It displayed partial activity at
37 to 65°C (Fig. 5, lanes 2 to 4). One unit of PspGI
resulted in a complete digestion pattern at 75 to 85°C (Fig. 5, lanes
5 to 8). The optimum temperature for PspGI digestion is in
the range of 75 to 85°C.

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FIG. 5.
DNA cleavage activity at different temperatures. One
unit of PspGI was used to cleave 1 µg of T7 phage DNA for
1 h at the specified temperatures. Lanes 1 through 7, 25, 37, 50, 65, 75, 80, and 85°C, respectively; lane 8, native PspGI
digestion of T7 phage DNA at 85°C.
|
|
To measure the enzyme half-life, 1 U of recombinant PspGI
was preheated at 95°C for 20 min to 4 h, and then DNA cleavage
activity was assayed. The half-life of PspGI at 95°C was
found to be approximately 2 h (Fig.
6). In DNA amplification reactions such
as PCR, the DNA denaturation step is usually set at 95°C for 30 to
60 s. For a 30-cycle PCR, the enzyme would be heated at 95°C for
15 to 30 min. To test the thermostability of PspGI in DNA
polymerase buffers, the enzyme was incubated in 1× Thermopol buffer
(NEB) for 30 cycles of thermocycling. PspGI retained 100%
activity after the thermocycling (data not shown).

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FIG. 6.
Half-life of recombinant PspGI at 95°C. One
unit of PspGI was heated at 95°C for 20 min to 4 h,
and then the enzyme was used to cleave 1 µg of T7 phage DNA at
75°C. DNA cleavage products were separated on an agarose gel,
transferred to a membrane, and detected with a Phototope-star
chemiluminescence detection kit. X-ray films were exposed for 10 s, 30 s, 50 s, 1 min, and 2 min to obtain a linear response
range and were scanned.
|
|
PspGI exhibits star activity when large numbers of units are
used in DNA digestion. PspGI star activity was detected when >128 U of PspGI was used to digest 1 µg of T7 phage DNA.
Minimal PspGI star activity was detected when <64 U of
PspGI was used to cleave 1 µg of T7 phage DNA (data not
shown).
To test PspGI activity in low-melting-temperature agarose, a
T7 DNA band was excised from low-melting-temperature agarose and melted
at 65°C. The DNA in the melted agarose was completely digested by
PspGI at 75°C (data not shown).
 |
DISCUSSION |
Thermostable restriction enzymes such as TaqI
isoschizomers have been characterized from Thermus sp.
strain SM32 and Thermus filiformis Tok6A1 (1, 2).
Native Tsp32II (from Tsp32 activity fraction II
containing TaqI isoschizomers) and recombinant
Tsp32I display partial activity at 85 to 90°C
(2). Recombinant Tsp32I can be added during
thermocycling (1a).
PspGI is the most thermostable restriction enzyme discovered
so far. To our knowledge, this is the first report of R-M genes cloned
and expressed from the extreme thermophile Pyrococcus. Recombinant PspGI has a half-life of approximately 2 h
at 95°C. This high degree of thermostability makes this enzyme useful
for DNA cleavage during DNA amplification reactions.
In the amino acid sequence analysis of four restriction enzymes that
recognize 5' CCWGG 3' and 5' CCNGG 3', we found a conserved segment of
87 amino acid residues. We propose that this segment is part of a
common DNA recognition domain for 5' CC_GG 3' If this prediction is
true, this motif should also be found in the amino acid sequences of
the BstNI, MvaI (5' CC^WGG 3'), and
ScrFI (5' CC^NGG 3') restriction endonucleases.
Multiple amino acid substitutions were introduced to change a
thermolysin-like protease from B. stearothermophilus to a
boiling-resistant extremozyme (28). The amino acid
substitutions were mainly located in the surface loop at the N
terminus. The substitutions made to the protease (T56 to A, G58 to A,
S65 to P, and A69 to P) were considered to stabilize the protein by a
reduction of the entropy of the unfolded state. The introduction of a
salt bridge or disulfide bond can also increase the thermostability of
the protease (28).
M.PspGI shows 53% similarity (44% identity) to
M.MvaI. M.PspGI is
isolated from Pyrococcus, whereas M.MvaI is
derived from a plasmid of the mesophile Micrococcus
variabilis. The homologous amino acid sequences between
M.PspGI and M.MvaI may reflect
functional or structural constraints on the proteins. Conserved
aminomethylase motifs have also been found among the type II methylases
in the genome of Methanococcus jannaschii (20a).
Four small segment deletions may have occurred in
M.PspGI to make it more compact or rigid and
thermostable (Fig. 3, Del1 through Del4). A comparison of the
M.PspGI and M.MvaI amino acid sequences
showed that there are 24 Ala residues in M.PspGI and 12 Ala residues in M.MvaI. Both
M.PspGI and M.MvaI have 20 Pro
residues. The increased number of Ala residues in
M.PspGI may contribute to its thermostability. The
local tertiary structures resulting from the nonsimilar residues are
likely to contribute to the thermostability of M.PspGI.
In the published sequence of Pyrococcus horikoshii OT3
(10), there are four putative type II methylases (PH0338,
PH0584, PH0905, and PH1032) that contain conserved motifs of
aminomethyltransferases. The putative methylase PH1032 is very similar
to M.DpnII (58% similarity and 47% identity);
therefore, it may be an M.DpnII isoschizomer. Open
reading frames adjacent to the putative methylases may encode the
cognate endonucleases. Another putative methylase (PH0039) contains 10 conserved motifs of cytosine-5 methylase (when a TTG codon is used as
the start codon for this open reading frame, the translated protein
will include cytosine-5 methylase motifs I to X). Two open reading
frames upstream of the PH0039 genes may encode the cognate
endonuclease. The P. horikoshii OT3 genome does not appear
to encode homologs of PspGI and M.PspGI.
The extreme thermostability of PspGI should allow the
simultaneous amplification of mutant DNA and cleavage of amplified
wild-type DNA. The loss of the PspGI site can be used as an
indicator of mutation in the coding or noncoding sequences. A two-step
amplification method has been developed to detect ras
oncogene mutations in a small fraction of cells (3). This
method introduces a restriction site at the codon of interest by use of
mismatched primers (e.g., introducing a BstNI site for the
detection of a codon 12 mutation in the ras oncogene). The
mutation is then detected by the loss of the restriction site (6,
8). With the two-step procedure, the amplified PCR product
containing the wild-type sequence was cleaved by BstNI. The
amplified mutant DNA was resistant to BstNI digestion and
was gel purified and then reamplified with a mutation-specific primer.
PspGI and BstNI are neoschizomers (enzymes with
the same recognition sequence but cleaving at different bases).
Presumably, one should allow adequate time for the completion of
restriction digestion before proceeding to the next cycle. Otherwise,
the wild-type sequence can also serve as a template for the next round of amplification. For DNA amplification in gene chips, PspGI
activity can be minimized at room temperature and can be activated by
heating the reaction mixture to 65 to 85°C.
 |
ACKNOWLEDGMENTS |
We thank Jack Benner II for N-terminal amino acid sequencing of
PspGI endonuclease; Laurie Moran, Jennifer Ware, Mehul
Ganatra, and Barton Slatko for DNA sequencing; Zhi-yu Chang and Michael Dalton for technical assistance in protein purification; H. W. Jannasch for providing Pyrococcus sp. strain GI-H; Roger
Knott for providing primers; Pei-Chung Hsieh for discussion; Ira
Schildkraut and Richard Roberts for critical comments; and Don Comb for
support.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: New England
Biolabs, Inc., 32 Tozer Rd., Beverly, MA 01915. Phone: (978) 927-5054. Fax: (978) 921-1350. E-mail: xus{at}neb.com.
 |
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Applied and Environmental Microbiology, October 1998, p. 3669-3673, Vol. 64, No. 10
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