Product Name:

Alkaline Phosphatase(PAP)(from Shewanella sp. SIB1)*

Code No:

DE110

Size:

1,000 unit

Concentration:

5unit/μl

Supplied reagent

・10×Alkaline Phosphatase Reaction Buffer
・Dilution Buffer

Storage:

Store at -20℃

Source:E.coli harboring the plasmid encoding the gene of alkaline phosphatase froma psychrotrophic bacterium Shewanella sp. SIB1 (PAP).

Unit Definition:

One unit is defined as the amount required to hydrolyzed 1.0 μmole p-nitrophenyl
phosphate per 1 minute in glycine-NaOH buffer at pH10.5 and 37℃.

Assay conditions: The reaction mixture (100μl) contains 50mM glycine-NaOH buffer,
pH 10.5, 5mM MgCl2, 0.5mM ZnCl2, 100mM KCl,
5mM p-nitrophanyl phosphate.

Storage Buffer:

10mM
0.025mM
0.25mM50%

Tris-HCl
ZnCl2
MgCl2
glycerolpH7.5

Contaminants:
Dnase: When 0.5μg of λ/Hind III digest was incubated with 10units of this enzyme in a 40μl reaction
mixture for 18 hours at 37℃, no degradation of the DNA fragment is observed on agarose gelelectrophoresis.
Rnase: No RNase activity is observed by the use of RnaseAlert assay (Ambion). In this assay the reaction
mixture containing the fluorescent-labeled RNA substrate was incubated with 10units of this enzyme for
1 hours at 37℃.

* Licensed Under Japan Patent NO. 2001-172653

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Composition of Supplied Reagent:
10×Alkaline Phosphatase Reaction Buffer ( Store at –20℃)
1. 5M
125mM
0. 5%
0.25mM
2.5mM
60mM

Tris-HCl, pH7.3
glycine
TritonX-100
ZnCl2
MgCl2
NiCl2

Dilution Buffer ( 1×Reaction Buffer, Store at –20℃)
150mM
Tris-HCl, pH7.3
12.5mM
glycine0.05%
TritonX-100
0.025mM
ZnCl20.25mM
MgCl26mM
NiCl22
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Kit Manual
Dephosphorylation of 5’ end by PAP:
Linearized plasmid DNA * 1 88μl (5’ termini 10pmol)*2
10×Reaction buffer

10μl
32μl*4

Diluted PAP solution*

Incubate for 30 min at 60℃ (blunt end and 3’-protruding end)
or at 37℃ (5’-protruding end)
Inactivation by incubation for 5min at 95℃*5
Dephosphorylated Plasmid DNA

Ligation Reaction and Transformation:
Dephosphorylated Plasmid DNA

1μl (0.05pmol)*6Insert DNA (foreign)

1μl (0.05～0.3pmol)*7

10×Ligation buffer* 81μl

T4 DNA ligase

0.5 Weiss unit

10mM ATP1μl

H2Oup to10μl

Incubate for 1 houre at 12℃ (blunt end)
or at 16℃ (5’-protruding end and 3’-protruding end)
2μl (0.01pmol)* 9
Add 100μl of competent cellStore on ice for 30min
Heat shock for 30sec at 42℃
Store on ice 1min
Add 0.9ml of SOC medium
Incubate for 1hr at 37℃
Spread on a selective plate

Incubate overnight at 37℃*1 Before the dephosphorylation, the complete digestion of the plasmid DNA should be confirmed by
the agarose gel electrophoresis. Actually, it is difficult to completely digest vector DNA less than 4 kb in

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size. We recommend to purify the linearized vector DNA from agarose gel after electrophoresis by using
Gel Indicator (Code No. DM510).
Restriction enzyme buffer (such as low buffer, medium buffer and high buffer) and 1×TE buffer ispermissible as a buffer solution of the linearized plasmid DNA.
*2

Amount and length of the linearized plasmid DNATable 1
1kb linear DNA

10pmol of 5’-tremini=3.3μg

2kb linear DNA

10pmol of 5’-tremini

=

6.6μg

3kb linear DNA

10pmol of 5’-tremini=9.9μg

4kb linear DNA

10pmol of 5’-tremini=

13.2μgFor example, 10pmole of 5’-termini of the linearized pUC18 (2.69kb) is 8.8μg.
*3Amount of PAP
Amount of PAP should be modified depending on the kind of termini and the amount of 5’-terminiof linearized plasmid DNA. The following amounts are recommended:
Table 2Terminus

Units of PAP5’-Protruding(10pmol)

1.0 units (37℃ 30min)

Blunt(10pmol)

2.5 units (60℃ 30min)

3’-Protruding(10pmol)

5. 0 units (60℃ 30min)

PAP should be diluted with dilution buffer (1×reaction buffer) according to the table above. As theamount of PAP described in the table above are about ten times as much as that of the minimum effective
amount, the condition is sufficient for complete dephosphorylation. If you use over ten times amount ofPAP shown in the table 2, we recommend phenol extraction to inactivate PAP completely instead of heat
inactivation (see *4 and *5).
*4 Non-diluted PAP solution should be added not to exceed 10% in a volume of the final reaction buffer.
Glycerol in non-diluted PAP solution and high concentration of PAP protein hamper heat inactivation ofPAP. If the reaction mixture contains non-diluted PAP solution up to 20% of its volume, the activity of
about 1/7,000～1/50,000 still remains. When you use non-diluted PAP solution over 10% volume ofreaction mixture, we recommend phenol extraction for complete inactivation of PAP (see *5).
*5Heat inactivation
At least 10 μl of reaction mixture is required in 0.5ml tube for heat inactivation. Before heatinactivation, you should spin down solution in the tube. After heat inactivation, the white precipitate ofinactivated PAP protein is observed. It is not necessary to be removed, because the precipitate does not

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affect the next ligation reaction.
Nearly all of PAP are inactivated by incubation at 95℃ for 5min after dephosphorylation and trace
amount activity, 1/100,000～1/400,000, remains. It is negligible level in the next ligation reaction,
because the residual PAP activity can only dephosphorylate insert DNA (foreign) less than 1/10,000 of theinitial vector plasmid DNA in the molar amount, if you follow the above protocol.
If you use over ten times amount of enzyme the condition described in table 2 or use over 10%
volume of final reaction mixture, we recommend phenol extraction to inactivate PAP completely insteadof heat inactivation as follows;
Phenol Extraction:
Alkaline phosphatase reacton productPhenol/chloroform (1:1) extraction (2 times)
Chloroform extraction (3 times)
Add 10ul 3M Na Acetate pH5.2 or 10ul 1M NaCl
Add 70μl isopropanol
Centrifuge at 14,500 rpm for 10min
Wash with 70% ethanol
Dry under vacuum
Dephosphorylated Plasmid DNA

PAP is easily and completely inactivated even by one time phenol extraction. On the other hand, BAP is
known to be much more resistant to phenol extraction as well as heat inactivation. For example, about
2.5% of BAP remain active after one time phenol extraction and following ethanol precipitation(http://www.biodynamics.co.jp/).
*6 It is possible that alkaline phosphatase reaction mixture is directly added to ligation reaction
mixture up to 30% for cohesive end ligation, up to 10% for blunt end ligation of the final reaction volume
without interference.
The commercially available ligation kit such as DynaExpressDNA Ligation Kit ver.2 (BioDynamics
Laboratory.Inc, DS110), DNA Ligation Kit ver.2 (TaKaRa), Ligation High (TOYOBO CO., LTD), Quick
LigationTM Kit (New England Biolabs. Inc) and LigaFastTM Rapid DNA Ligation Kit (Promega) can beeffectively used in instead of this ligation protocol. During you use these kits, the orange precipitate
derived from reducted Ni is observed. It is not necessary to remove the precipitate because it does notaffect the ligation and the next transformation process.
*7

Chill the reaction mixture of insert DNA and vector DNA to 0℃ before ligation procedure.
The molar ratio of vector DNA to insert DNA should be between 1:1 and 1:6. The final DNA
concentration of vector DNA and insert DNA should be between 1ng/μl and 10ng/μl for an effectiveligation.

LigaFastTM and Quick LigationTM are trademarks of Promega Corporation and New England Biolabs, Inc.,
respectively.

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*8

10×Ligation buffer
660mM Tris-HCl (pH7.6), 66mM MgCl2, 100mM DTT*9Amount of ligation mixture should be added in a volume not to exceed 10% of that of competentcells. If you carry out transformation of E.coli by electroporation, we recommend spin column
purification of ligation mixture.

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