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Percent Agarose in a Gel and the Separation of Linear DNA Molecules

Description

DNA strands can be separated into bands by electrophoresis in agarose gel. Efficient separation depends on the size of the DNA strands and the percent agarose in the gel.


 

Efficient Range of Separation of Linear DNA Molecules

percent agarose in gel as weight per volume

lower end of range

upper end of range

0.3%

5,000 base pairs

60,000 base pairs

0.6%

1,000 base pairs

20,000 base pairs

0.7%

800 base pairs

10,000 base pairs

0.9%

500 base pairs

7,000 base pairs

1.2%

400 base pairs

6,000 base pairs

1.5%

200 base pairs

3,000 base pairs

2.0%

100 base pairs

2,000 base pairs

 

This data was analyzed in JMP. Since Figure 6.1 shows separation based on LOG10 of the DNA base pairs, the line approximations were done using percent vs LOG10 of the base pairs.

 

LOG10(lower end of DNA range) =

= (-0.6096 * ((percent agarose)^3)) + (2.485 * ((percent agarose)^2)) - (3.8473 * (percent agarose)) + 4.61554

 

where:

• The percent agarose is in the range of 0 to 100.

 

LOG10(upper end of DNA range) =

= (-0.4268 * ((percent agarose)^3)) + (1.9328 * ((percent agarose)^2)) - (3.32 * (percent agarose)) + 5.6148

 

percent agarose =

= (0.47975 * ((LOG10(lower end of DNA range))^2)) - (3.758 * LOG10(lower end of DNA range)) + 7.618

 

percent agarose =

= (0.72297 * ((LOG10(upper end of DNA range))^2)) - (6.93875 * LOG10(upper end of DNA range)) + 16.97386


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