Properties of Exonucleases and Endonucleases

Enzyme	polarity	DNA substrate		Activity without 5' phosphate	Initiate at ds DNA with¹				Partial Digestion Generates Extension²	Products Produced^³
Enzyme	polarity	ss	ds	Activity without 5' phosphate	5'ext	3'ext	blunt	nick	Partial Digestion Generates Extension²	Products Produced^³
Lambda Exo	5'->3'	+/-	+	+/-⁴	+/-	+	+	-	3'	ss DNA, dNMP
T7 Exo	5'->3'	-	+	+	+/-	+	+	+	3'	ss DNA, dNMP, dinucleotide
Exo III	3'->5'	-	+	+	+	+/-	+	+	5'	ss DNA, dNMP
RecJ_f	5'->3'	+	-	+	+/-⁵	-	+/-⁶	-	NA	dNMP
Exo I	3'->5'	+	-	+	-	+/-⁵	+/-⁶	NR	NA	dNMP, dinucleotide
Exo T	3'->5'	+	-	+	-	+⁷	+/-⁶	NR	NA	dNMP
BAL-31 Nucl	3'->5',endo⁸	+	+	+	+	+	+	+	NA	ss DNA, dNMP
Mung Bean Nucl	endo⁹	+	-	+	+	+	-	-	NA	ss DNA, ds DNA
T7 Endo I	endo¹⁰	-	+	NA	NA	NA	NA	+/-	NA	ds DNA

This table is intended to be used as a guideline. Not all reported activities and properties for each exonuclease or endonuclease are listed. The amount of enzyme, substrate and time of incubation can have a dramatic effect upon the desired outcome of the experiment.

Table Legend:

+ :	Preferred substrate
- :	No significant activity
+/- :	Has detectable activity, but greatly reduced relative to preferred substrate.
NR :	Not reported
NA :	Not applicable
ss :	Single-stranded
ds :	Double-stranded
nt :	nucleotide
ext :	extension
dNMP :	deoxyribonucleoside monophosphate

Footnotes:

1	The ability to act on short extensions and blunt ends operationally distinguishes these enzymes; such ends are conveniently generated by restriction digestion.
2	Partial digestion of ds DNA by Lambda Exonuclease, T7 Exonuclease and Exonuclease III will produce ds DNA products with ss extensions. If digestion goes to completion, ss DNA will be produced.
3	Complete hydrolysis of the preferred substrate will generate the listed products. It has been reported that the initial product hydrolyzed from ds DNA by T7 Exonuclease is a dinucleotide. Subsequent hydrolytic cleavage by T7 Exonuclease releases dNMP. Exonuclease I releases dNMP from ss DNA, except at the last hydrolytic step where a dinucleotide is produced.
4	Lambda exonuclease initiates degradation very poorly without a 5' phosphate. Thus, if linear ds DNA has a 5' phosphate at one end and lacks a 5' phosphate on the other end, then lambda exonuclease will preferentially degrade the DNA from the phosphorylated end.
5	RecJ_f is not suitable for making 5' extensions blunt and Exonuclease I is not suitable for making 3' extensions blunt. Both RecJ_f and Exonuclease I appear to require long extensions to initiate.
6	Depending upon the DNA sequence and amount of exonuclease, RecJ_f, Exonuclease I and Exonuclease T may remove a few nucleotides from blunt termini.
7	Exonuclease T can be used to make 3' extensions blunt, but it was 2-4 fold less efficient than Klenow polymerase plus dNTP on a test substrate.
8	BAL31 has been reported as having ss endonuclease activity as well as 3'->5' ds exonuclease activity. Thus, any linear DNA is a substrate for BAL-31.
9	Mung Bean Nuclease is an endonuclease specific for ss DNA.
10	T7 Endonuclease I is an endonuclease that recognizes and cleaves non-perfectly matched DNA, cruciform DNA structures, Holliday structures or junctions. It will act more slowly on nicked ds DNA.