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680 Chapter 20 NEL

Restriction Endonucleases

Restriction endonucleases, otherwise known as restriction enzymes, are like molec-

ular scissors that can cut double-stranded DNA at a specific base-pair sequence. Each

type of restriction enzyme recognizes a particular sequence of nucleotides that is known

as its recognition site. Molecular biologists use these enzymes to cut DNA in a pre-

dictable and precise way. Most recognition sites are four to eight base pairs long and

are usually characterized by a complementary palindromic sequence (Table 2). For

example, look at the restriction enzyme EcoRI. This sequence is palindromic because

both strands have the same base sequence when read in the 5
to 3
direction.

restriction endonucleasean
enzyme that cuts double-stranded
DNA into fragments at a specific
sequence; also known as a
restriction enzyme

recognition sitea specific
sequence within double-stranded
DNA that a restriction
endonuclease recognizes and cuts

palindromicreading the same
backwards and forwards

sticky endsfragment ends of a
DNA molecule with short single-
stranded overhangs, resulting from
cleavage by a restriction enzyme

5 
 AT T AGAGA TGAATTCAGATTCAGATAGCAT 3


3 
 TAATCTCTACTTAAGTCTAAGTCTATCGTA 5

5 
 AT T AGAGA TGAATTCAGATTCAGATAGCAT 3


3 
 TAATCTCTACTTAAGTCTAAGTCTATCGTA 5

5 
 AT T AGAGA TG AATTCAGATTCAGA

TAATCTCTACTTAA GTCTAAGTCT

TAGCAT

ATCGTA

3 


3 
 5 

(c)

(b)

(a) EcoRI

EcoRI

EcoRI

Figure 4
Cleavage of DNA sequence using
restriction enzyme EcoRI.
(a)EcoRI scans the DNA molecule.
(b)EcoRI binds to the recognition
site.
(c)EcoRI cuts between the guanine
and adenine nucleotides,
producing two fragments with
complementary ends.

5 
-TC-3GAA T 


3 
-AG-5CTTA 

5 
--3GCAAT T 


3 
-G-5CTTAA 

3 
-CC-5GGGC 

5 
-GG-3CCCG 

3 
-TG-5CAGC 

5 
-AC-3GTCG 

3 
-AA-5TTCG 

5 
-TT-3AAGC 

3 
-A-5TCG 

5 
-T-3AGC 

3 
-GG-5CCC G 

5 
-CC-3GGG C 

3 
-T G-5CAGC 

5 
-AC-3GTCG

3 
-A A-5TTCG 

5 
-TT-3AAGC

3 
-A-5TC G 

5 
-T-3AG C 

Table 2 Restriction Enzymes and Their Recognition Sites

Microorganism Enzyme Recognition After restriction

of origin site enzyme digestion

Escherichia coli EcoRI

Serratia marcescens SmaI

Arthrobacter luteus AluI

Streptomyces albus SalI

Haemophilus HindIII

parainfluenzae

Figure 4shows the action of the restriction enzyme EcoRI.EcoRI scans a DNA mole-

cule and stops when it is able to bind to its recognition site. Once bound to the site, it

cuts the bond between the guanine and adenine nucleotides on each strand. At the end

of each cleavage site, one strand is longer than the other and has exposed nucleotides

that lack complementary bases. The overhangs produced by the exposed DNA nucleotides

are called sticky ends.EcoRI always cuts between the guanine and the adenine nucleotide

on each strand. Since A and G are at opposite ends of the recognition site on each of the

complementary strands, the result is the overhang, or sticky end, at each cleavage site.

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Maps and Libraries
Restriction endonucleases are also
used to create genetic maps and
libraries. Go to the Nelson Web site
for information on these
applications.