Useful Calculations

Nucleic Acid Data:
1 pmole of 1,000 b RNA = 0.33 µg
1 pmole of 1,000 bp DNA = 0.66 µg (3.03 pmoles of ends)
1 pmole of pUC18/19 DNA (2,686 bp) = 1.77 µg
1 pmole of lambda DNA (48,502 bp) = 32.01 µg

Molecular Weight Conversions:
MW of a double-stranded DNA molecule = (# of base-pairs) x (650 daltons/base-pair)

MW of a single-stranded DNA molecule = (# of bases) x (330 daltons/base)

MW of a single-stranded RNA molecule = (# of bases) x (340 daltons/base)

Estimating Tm of an Oligonucleotide:
Tm = [4°C x # of Cs and Gs in the oligo] + [2°C x # of As and Ts in the oligo]

Estimating Molar Amounts of Primer:
To estimate the weight of 1 picomole of oligodeoxynucleotide, multiply the number of nucleotides by 0.33 ng. For example, one picomole of a 24-mer is 7.92 ng (24 x 0.33 ng = 7.92 ng).

Estimating Molar Amounts of Template:
To estimate the weight of 100 fmoles of double-stranded DNA template, multiply the number of kilobases by 66 ng. For example, 100 fmoles of a 2.7 Kb plasmid is 178 ng (2.7 x 66 ng = 178 ng).

Approximate Amount of Template (in nanograms) Required for DNA Sequencing Reactions
Template Size (insert + vector) in Kilobases
Template Required (fmoles) 1 Kb 3 Kb 5 Kb 7 Kb 9 Kb
25 17 ng 50 83 120 150
50 33 100 165 230 300
75 50 150 250 350 450
100 66 200 330 460 600
150 100 300 500 700 900
200 135 400 660 930 1200
250 165 500 830 1200 1550
300 200 600 1000 1400 1800


Protein Yield Information

Bacterial Cells: Escherichia coli or Salmonella typhimurium

Cell Data

per cell

per liter at 109 cells per ml

Wet Weight 9.5 x 10-13 g 0.95 g
Dry Weight 2.8 x 10-13 g 0.28 g
Total Protein 1.55 x 10-13 g 0.15 g
Volume 1.15 µm3 = 1 femtoliter  
Protein concentration in the cell: 135 mg/ml

Theoretical maximum yield for a protein of interest from 1 liter of culture (109 cells/ml)

0.1% of total protein

150 µg/liter

2.0% of total protein

3 mg/liter

50.0% of total protein

75 mg/liter


Buffer and Gel Tables

Effective Range of Separation of DNAs in Polyacrylamide Gels
Acrylamide (% [w/v])a Effective range of separation (bp) Xylene cyanol FFb Bromophenol blueb
3.5 1,000 - 2,000 460 100
5.0 80 - 500 260 65
8.0 60 - 400 160 45
12.0 40 - 200 70 20
15.0 25 - 150 60 15
20.0 6 - 100 45 12
aN,N'-methylenebisacrylamide is included at 1/30th the concentration of acrylamide.
bThe numbers given are the approximate sizes (in nucleotide pairs) of fragments of double-stranded DNA with which the dye comigrates.

Separation of DNA in Denaturing Polyacrylamide (7 M Urea) Gels
% Polyacrylamide/
urea gel
Size of band (nucleotides) Xylene cyanol FF(nucleotides) Bromophenol blue(nucleotides)
4 >250 155 30

6

60 - 250

110

25

8

40 - 120

75

20

10

20 - 60

55

10

aThe numbers given are the approximate sizes (in nucleotide pairs) of fragments of double-stranded DNA with which the dye comigrates.

Agarose Gel Resolution Optimum Resolution for Linear DNA

% Gel

Size of Fragments in Nucleotides (bp)

0.6

1,000 - 20,000

0.7

800 - 10,000

0.9

500 - 7,000

1/2

400 - 6,000

1.5

200 - 3,000

2.0

100 - 2,000


Acrylamide Gel Resolution of Proteins

Recommended % Acrylamide

Protein Size Range

8%

40 - 200 kDa

10%

21 - 100 kDa

12%

10 - 70 kDa