Polyacrylamide Gels

Recommended Polyacrylamide % for Separation in Denaturing Gels

% Acrylamide Effective Range of Separation (nucleotides)
3.5 >500
5 151-500
10 61-150
15 30-60
20 <30


Dye Migration in Denaturing Polyacrylamide Gels

% Acrylamide Xylene Cyanol (nucleotides) Bromophenol Blue (nucleotides)
5 130 35
6 106 26
8 75 19
10 55 12
12 28 8


Adapted from Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) in: Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory.

Dye Migration in Nondenaturing Polyacrylamide Gels

% Acrylamide Effective Range of Separation (bp) Xylene Cyanol (nucleotides) Bromophenol Blue (nucleotides)
3.5 100-1000 460 100
5 100-500 260 65
8 60-400 160 45
12 50-200 70 20
15 25-150 60 15
20 5-100 45 12


Adapted from Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) in: Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory.

Agarose Gels

Recommended Agarose Percentage for Size Separation

% Agarose Size Fragments Separated (bp)
0.5 1,000 to 30,000
0.7 800 to 12,000
1.0 500 to 10,000
1.2 400 to 7,000
1.5 200 to 3,000
3-4 (sieving agarose) 10 to 1,000


Adapted from Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., Struhl, K. (1995) in "Current Protocols in Molecular Biology."