Professional Documents
Culture Documents
Digestion of DNA With Restriction Endonucleases
Digestion of DNA With Restriction Endonucleases
LABELING OF DNA
Materials
DNA sample: 0.1 to 4 µg DNA in H2O or TE buffer
10× restriction endonuclease buffer
Restriction endonuclease
Loading buffer (UNIT 10.4)
0.5 M EDTA (optional)
1. Pipet the following into a clean microcentrifuge tube:
x µl DNA sample
2 µl 10× restriction buffer (see commentary)
18 − x µl H2O.
A 20-µl reaction is convenient for analysis by electrophoresis in polyacrylamide or agarose
gels. The amount of DNA to be cleaved and/or the reaction volume can be increased or
decreased provided the proportions of the components remain constant.
Most manufacturers provide 5× or 10× buffers optimized for the particular enzyme
purchased. It is best to use these, although the standard recipes provided in the reagents
and solutions section of this unit may be substituted.
2. Add restriction endonuclease (1 to 5 U/µg DNA) and incubate the reaction mixture
1 hr at the recommended temperature (in general, 37°C).
In principle, 1 U restriction endonuclease completely digests 1 µg of purified DNA in 60
min using the recommended assay conditions. However, crude DNA preparations, such as
those made by rapid procedures (UNIT 10.3), often require more enzyme and/or more time
for complete digestion (see critical parameters). The volume of restriction endonuclease
added should be < 1 ⁄1⁄⁄⁄0 the volume of the final reaction mixture, because glycerol in the
enzyme storage buffer may interfere with the reaction.
3. Stop the reaction and prepare it for agarose or acrylamide gel electrophoresis by
adding 5 µl (20% of reaction vol) loading buffer.
The reaction can also be stopped by chelating Mg++ with 0.5 µl of 0.5 M EDTA (final
concentration 12.5 mM). If the digested DNA is to be used in subsequent enzymatic
Digestion of DNA reactions (e.g., ligation or “filling-in” reactions), addition of EDTA should be avoided.
with Restriction DNA may be purified from the reaction mixture by extraction with phenol and precipitation
Endonucleases in ethanol (UNIT 10.1) or with GeneClean (Bio101).
10.8.1
Supplement 2 CPI Copyright © 1991 by Current Protocols
CLEAVAGE WITH MULTIPLE RESTRICTION ENDONUCLEASES ALTERNATE
PROTOCOL
It is often desired to cleave a DNA sample with more than one endonuclease. Two or more
enzymes may be added to the same reaction mixture if all are relatively active in the same
buffer and at the same temperature. Many enzymes are active over a wide range of salt
concentrations, so it is frequently possible to choose a buffer in which two or more
enzymes will retain activity (see Table 10.8.1 and commentary). However, if the reaction
conditions are too dissimilar, follow the procedure below. Alternatively, most restriction
endonucleases and some DNA-modifying enzymes are active to some extent in potassium
glutamate– and potassium acetate–based buffers (see reagents and solutions). Hence,
these buffers may be useful for digesting DNA with multiple enzymes.
1. Determine the composition of the manufacturer’s reaction buffer for the two enzymes
to be used. Digest the DNA with the enzyme(s) that is active at the lower NaCl
concentration.
If optimal digestion conditions differ only in incubation temperature, cleave the DNA with
one enzyme, then shift the temperature and add the second enzyme (the order of cleavage
does not matter). However, many enzymes with optimal activity at high temperatures are
also active at 37°C. In these cases, the enzymes can be added simultaneously and the
reaction mixture incubated at 37°C (it may be necessary to add more of the “high-tem-
perature” enzyme than usual).
2. For enzymes active at higher salt concentrations, add 1 M NaCl (1 to 3 µl for a 20-µl
reaction) so that the final concentration is appropriate for digestion by the next
enzyme(s).
Purification of the DNA fragments between digestions is the most reliable method to ensure
complete, multiple digestions. However, it is much more laborious and is rarely necessary.
1. For each sample to be tested, add a constant volume of DNA to a separate microcen-
trifuge tube.
It is critical to use a different pipet tip for each DNA sample in order to prevent
cross-contamination.
2. Prepare a “premix solution” containing sufficient 10× restriction endonuclease buffer
and water for digesting all the samples. Place solution on ice.
For example, if ten 3-µl samples of DNA are each to be digested in a 20-µl reaction mixture,
the premix will contain 20 µl of 10× restriction buffer and 150 µl water. It is prudent to
make up a solution for at least one more sample than is to be tested.
3. Add sufficient restriction endonuclease(s) for digesting all the samples. Mix quickly
by flicking the tube and replace on ice.
The solution to which the enzyme is added should not be more concentrated than 3×
buffer.
4. Add the appropriate amount of solution containing the restriction endonuclease (17
µl for above example) to each tube of DNA and incubate the reactions at the
appropriate temperature.
Molecular Biology
10.8.2
Current Protocols in Immunology Supplement 8
Table 10.8.1 Effect of NaCl Concentration on Restriction Endonuclease Activitya
100 150 100 150
0 mM 50 mM 0 mM 50 mM
Enzyme mM mM Enzyme mM mM
NaCl NaCl NaCl NaCl
NaCl NaCl NaCl NaCl
AatII + ++ ++ + BstXI ++ +++ +++ +++
AccI +++ +++ + + BstYI +++ +++ ++ ++
AciI + +++ +++ +++ Bsu36I + ++ +++ ++
AflII + +++ ++ ++ ClaI +++ +++ +++ ++
AhaII + ++ +++ +++ DdeI ++ +++ +++ +++
AluI + +++ +++ ++ DpnI + ++ +++ +++
AlwI +++ +++ ++ + DraI ++ +++ + +
AlwNI ++ +++ +++ + DraIII ++ +++ +++ ++
ApaI +++ +++ ++ + EaeI ++ +++ ++ +
ApaLI +++ +++ ++ + EagI ++ +++ +++ +++
AscI + ++ ++ + Eam1105I + ++ + +
AseI + +++ +++ +++ EcoNI +++ +++ +++ +++
AvaI +++ +++ +++ +++ EcoO109 +++ +++ +++ +++
AvaII +++ +++ ++ + Eco57I +++ +++ +++ ++
AvrII +++ +++ +++ ++ EcoRI b +++ +++ +++
BalI +++ ++ ++ + EcoRV + + + +++
BamHI + ++ +++ +++ Fnu4HI +++ +++ ++ +
BanI +++ +++ ++ ++ FokI +++ +++ +++ +++
BanII +++ +++ +++ +++ FspI + +++ ++ ++
BbvI +++ +++ +++ +++ HaeII +++ +++ +++ ++
BcgI +++ +++ +++ +++ HaeIII +++ +++ +++ +++
BclI + +++ +++ + HgaI +++ +++ + +
BglI + +++ +++ +++ HgiAI + + ++ +++
BglII ++ +++ +++ +++ HhaI + + + ++
BsaHI ++ +++ +++ + HincII ++ +++ +++ +++
BsmI +++ +++ +++ +++ HindIII ++ +++ +++ ++
Bsp1286 +++ +++ ++ + HinfI ++ +++ +++ +++
BspHI ++ +++ +++ +++ HinPI +++ +++ +++ +++
BspMI ++ ++ +++ +++ HpaI + +++ +++ +
BspMII ++ ++ +++ +++ HpaII +++ +++ ++ +
BssHII +++ +++ +++ +++ HphI +++ +++ +++ +
BstBI +++ +++ ++ + KasI + +++ + +
BstEII + ++ +++ +++ KpnI +++ + + +
BstNI ++ ++ +++ +++ MboI ++ +++ +++ +++
BstUI +++ +++ ++ + MboII +++ +++ +++ +++
continued
For most analytical purposes, the same pipet tip can be used to dispense the restriction
endonuclease solution provided that care is taken to avoid direct contact with the DNA at
the bottom of the tubes. For preparative purposes, it is advisable to use a different pipet tip
for each sample.
10.8.3
NaCl concentrations to its activity in recommended assay bufffer. Recommended assay buffers in some cases
differ widely in terms of pH and specific ion requirements. The conditions here varied only the NaCl
concentration. All buffers contained 10 mM Tris⋅Cl (pH 7.5) and 100 µg/ml bovine serum albumin. All
incubations were done for 60 min at the optimum temperature for each enzyme. Scoring is as follows:
+ <10% of the activity can be obtained using these conditions compared to the recommended conditions.
++ between 100% and 20% of the activity can be obtained using these conditions compared to the recommended
conditions.
+++ between 30% and 100% of the activity can be obtained using these conditions compared to the recommended
conditions.
bNot recommended because of star activity, which refers to cleavage at sites other than the usual recognition
sequence. Star activity occurs under nonoptimal reaction conditions, such as low ionic strength, high
endonuclease concentrations, high glycerol concentrations, high pH, and when Mn++ is used in place of Mg++.
10.8.4
Current Protocols in Immunology Supplement 8
COMMENTARY
Background Information identical or different sequences may generate
Restriction endonucleases are enzymes that identical DNA fragment termini. These en-
cleave DNA in a sequence-dependent manner. donucleases are said to produce compatible
Such cleavage is used for a wide number of ends. DNA fragments with compatible termini
applications in molecular biology, including (a) may be ligated with DNA ligases to produce
establishment of an endonuclease map of a hybrid DNA molecules.
plasmid or bacteriophage clone; (b) fragmen- For example, BglII recognizes a different
tation of genomic DNA prior to electrophoretic six-nucleotide sequence from BamHI, but gen-
separation and Southern blotting; (c) genera- erates cohesive termini compatible with those
tion of fragments that can be subcloned in of BamHI. BglII cleaves:
appropriate vectors; and (d) generation of frag- 5′ A↓G-A-T-C-T 3′
ments to be used as labeled probes in both 3′ T-C-T-A-G↑A 5′
Southern (UNIT 10.6) and northern (UNIT 10.12)
The hybrid sites generated by joining
blotting, and in nuclease protection analysis
BamHI and BglII cohesive ends cannot be
(UNIT 10.13).
cleaved by either enzyme.
Members of a large subgroup of these en-
Restriction endonucleases, generally found
zymes (type II restriction endonucleases) rec-
in prokaryotic organisms, are probably impor-
ognize short nucleotide sequences and cleave
tant for degrading foreign DNA (particularly
double-stranded DNA at specific sites within
bacteriophage DNA). Organisms that produce
or adjacent to the sequences. The recognition
restriction endonucleases protect their own
sequences are generally, but not always, 4 to 6
genomes by methylating nucleotides within the
nucleotides in length and are usually charac-
endonuclease recognition sequences. A spe-
terized by dyad symmetry (the 5′ to 3′ nucleo-
cific methylase covalently links methyl groups
tide sequence of one DNA strand is identical to
to adenine or cytosine nucleotides within target
that of the complementary strand). Two en-
sequences, thus rendering them resistant to
zymes, NotI and SfiI, recognize an 8-bp se-
cleavage by the restriction enzyme.
quence found infrequently in genomic DNA
Several sources provide comprehensive and
and hence are extremely useful for cleaving
up-to-date listings of restriction endonucleases,
DNA into large fragments. More than 600 type
including their restriction sites and reaction
II restriction endonucleases have been isolated.
conditions. One source is the catalogs of com-
Some type II restriction endonucleases
mercial suppliers of enzymes. Another
cleave at the axis of symmetry, yielding “flush”
source—updated annually and additionally
or “blunt” ends. Others make staggered cleav-
listing commercial suppliers of each enzyme—
ages, yielding overhanging single-stranded 3′
is a special supplement to Nucleic Acids Re-
or 5′ ends known as cohesive termini.
search (Roberts, 1991). The database repre-
BamHI cleavage generates cohesive 5′ over-
sented in this table is also available online
hanging ends:
through the GenBank computer resource. Fi-
5′ G↓G-A-T-C-C 3′ nally, an annually updated list of restriction
3′ C-C-T-A-G↑G 5′ enzymes and their suppliers is provided free of
KpnI cleavage generates cohesive 3′ over- charge in Biotech Buyers’ Guide (American
hanging ends: Chemical Society, 1991).
5′ G-G-T-A-C↓C 3′
3′ C↑C-A-T-G-G 5′ Critical Parameters
Purity of DNA. The efficiency of the
DraI cleavage generates blunt ends:
restriction endonuclease reaction is very de-
5′ T-T-T↓A-A-A 3′ pendent upon the purity of DNA. Contami-
3′ A-A-A↑T-T-T 5′ nants found in some preparations of DNA
Endonucleases with the same recognition (e.g., protein, phenol, chloroform, ethanol,
sequences are called isoschizomers. Isoschizo- EDTA, SDS, high salt concentration) may
mers may or may not cleave DNA identically inhibit restriction endonuclease activity. Such
to produce the same ends. Conversely, two or impurities are often present in DNA samples
more restriction endonucleases recognizing prepared by miniprep procedures (UNIT 10.3).
Digestion of DNA
with Restriction
Endonucleases
10.8.5
10.8.6
Current Protocols in Immunology Supplement 2
they differ by the amount of NaCl. Restriction Some restriction enzymes are expensive,
enzyme buffers may be stored at −20°C, as 10× others relatively inexpensive. Their use is dic-
concentrates, for more than a year. tated in part by their cost. Ironically, expensive
As an alternative to the four buffer system enzymes are often of lower quality.
described above, many laboratories use potas-
sium glutamate–based (McClelland et al., Anticipated Results
1988) and potassium acetate–based (O’Farrell Complete cleavage of the DNA by a restric-
et al., 1980) buffers (known as “universal” tion endonuclease should generate a set of dis-
buffers) for digestion of DNA with restriction crete DNA fragments that are bounded by the
endonucleases. The key features of these buff- restriction sites. Upon analysis by gel electro-
ers is that they include potassium glutamate or phoresis (UNIT 10.5), the cleavage products
potassium acetate instead of sodium chloride should be visualized as sharp bands.
and Tris⋅acetate instead of Tris⋅Cl. Most restric-
tion endonucleases are active in these buffers, Time Considerations
although some enzymes are less active (some- In principle, if 1 U of restriction endonu-
times only 20%) than under optimal conditions clease digests 1 µg of DNA in 1 hr, then incu-
specified by the manufacturer. Several DNA- bations for longer durations might be expected
modifying enzymes are also active in these to permit conservation of expensive enzymes.
buffers, including T4 DNA polymerase and T4 In practice, however, some restriction endonu-
DNA ligase. “Universal” buffers are useful for cleases have only limited stability in the reac-
digestion of DNA with multiple restriction en- tion mixture. Thus, enzyme reactions are usu-
donucleases, particularly when the endonu- ally carried out for 30 min to 2 hr unless very
cleases are incompatible in any one of the large amounts of DNA or expensive enzymes
standard buffers. are involved. In addition, beware that extended
Some restriction endonucleases “relax” incubations often reveal low levels of contami-
their recognition sequence specificity in nating nuclease activities, which may confound
“nonoptimal” reaction conditions (including experimental results.
high endonuclease concentrations, high glyc-
erol concentrations, low ionic strength, Mn++ Literature Cited
instead of Mg++, and high pH). This “star” American Chemical Society. 1991. Biotech Buyers’
activity cleaves DNA at other sites besides Guide 1991. ACS, Washington, D.C.
those containing the “correct” sequence. For Fuchs, R., and Blakesley, R. 1983. Guide to the use
example, EcoRI star activity cleaves some, but of type II restriction endonucleases. Methods
Enzymol. 100:3-38.
not all sequences of the form AATT (usually
sites with a 5 out of 6 match to GAATTC are McClelland, M., Hanish, J., Nelson, M., and Patel,
Y. 1988. KGB: A single buffer for all restriction
cleaved better than sites with a 4 out of 6 match).
endonucleases. Nucl. Acids Res. 16:364.
The cleavage products all contain the identical
O’Farrell, P.H., Kutter, E., Nakanishe, M. 1980.
cohesive ends as products generated by the true
Mol. & Gen. Genet. 179:411-435.
EcoRI activity.
Roberts, R.J. and Macelis, D. 1991. Restriction en-
Additional comments. Enzymes should be
zymes and their isoschizomers. Nucl. Acids Res.
stored at −20°C. While in use, enzymes should 19 (Supp.#1):2077-2109.
be carefully maintained on ice.
Be extremely careful to avoid contaminating
enzyme solutions, particularly with plasmid Contributed by Kenneth D. Bloch
DNA, other restriction endonucleases, or Massachusetts General Hospital
DNase I. Boston, Massachusetts
Digestion of DNA
with Restriction
Endonucleases
10.8.7