Nucleic Acids and Protein Calculation Conversions

1. Nucleic Acids

ds DNA 10 kb = 6.60×106 Dalton 1 OD260 nm = 50 μg
ss DNA 10 kb =3.30×106 Dalton
(dNMP average molecular weight（Mw）=330 Dalton) 		1 OD260 nm = 33 μg
RNA 10 kb =3.45×106 Dalton
(NMP average molecular weight（Mw）=345 Dalton) 		1 OD260 nm = 40 μg

2. Protein

BSA : 1 OD280 nm= 1.67 mg (1 mg/ml =0.6 OD280 nm)
Average molecular weight of amino acids=110 Dalton

3. Nucleic Acids ←→ Protein

1 kb RNA= 37k Dalton
10k Dalton =273 Base RNA

4. Extinction coefficient of deoxyribonucleoside triphosphate (dNTP) (pH7.0)

dNTP ε 260 (×10-3)
dATP
dCTP
dGTP
dTTP
 15.2
7.4
11.5
8.3

5. Extinction coefficient of ribonucleoside triphosphate (NTP) (pH7.0)

NTPε 260 (×10-3)
ATP
CTP
GTP
UTP
15.2
7.2
11.5
9.9

6. Formulas for DNA Molar Conversions

Base number Average molecular weight Median weight (μg) Average mole number (nmol)
5
10
15
20
25
30
 1650
3300
4950
6600
8250
9900
 33
33
33
33
33
33		 20.0
10.0
6.7
5.0
4.0
3.3

To calculate the specific values of oligonucleotides, use the extinction coefficients of the various bases and calculate according to the following formulas.

weight (μg) =
330 (average MW of a nucleotide) × Base number
(15.2× number of A nucleotides)＋(7.4×number of C nucleotides)
＋(11.5×number of G nucleotides)＋(8.3×number of T nucleotides)
Molar (μ mol) =
1
(15.2× number of A nucleotides)＋(7.4×number of C nucleotides)
＋(11.5×number of G nucleotides)＋(8.3×number of T nucleotides)

7. Spectrophotometric Conversions

1 A260 unit dsDNA=50 μg/ml
1 A260 unit ssDNA=33 μg/ml
1 A260 unit ssRNA=40 μg/ml

8. Protein Molar Conversions

100 pmol of 100 kDa protein molecule = 10 μg
100 pmol of 50 kDa protein molecule = 5 μg
100 pmol of 10 kDa protein molecule = 1 μg
100 pmol of 1 kDa protein molecule = 100 ng

9. DNA Molar Conversions

1 μg of 1000 bp DNA = 1.52 pmol (3.03 pmol of ends)
1 μg of pBR322 DNA = 0.36 pmol DNA
1 pmol of 1000 bp DNA = 0.66 μg
1 pmol of pBR322 DNA = 2.8 μg

10. Protein/DNA Conversions

1 kb DNA can encode 333 amino acids = 37 kDa protein molecule
270 bp DNA = 10 kDa protein
9 amino acids = 1 kDa protein molecule
810 bp DNA = 30 kDa protein molecule
2.7 kb DNA = 100 kDa protein molecule

11. Formulas for DNA Molar Conversions

For dsDNA Average molecular weight
To convert pmol to µg:
pmol × N × 660 pg/pmol × 1 µg/106 pg = µg

To convert µg to pmol:
µg × 106 pg/1 µg × pmol/660 pg × 1/N = pmol

where N is the number of nucleic acid base pairs and
660 pg/pmol is the average MW of a nucleotide		 To convert pmol to µg:
pmol × N × 330 pg/pmol × 1µg/106 pg = µg

To convert µg to pmol:
µg × 106 pg/1 µg × pmol/330 pg × 1/N = pmol

where N is the number of nucleotides and
330 pg/pmol is the average MW of a nucleotide
The average molecular weight of an amino acid = 100 Daltons (Daltons)
Daltons (Da) kilo is another name for the atomic mass unit, kilodalton
Therefore, a protein with a mass of 46 kD is 46,000 grams of molecules per mole.

12. lsotope Data,Acids & Bases, Protein Data

Isotope

Isotope Released particles Half-life
14C b 5,730 years
3H b 12.3 years
125I g 60 days
32P b 14.3 days
33P b 25 days
35S b 87.4 days
1 Ci = 1,000 mCi
1 mCi = 1,000 μci
1 μCi = 2.2X 106 disintegrations/minute
1 Becquerel = disintegration/second
1 μCii = 3.7 X 104 Becquerels
1 Becquerel = 2.7 X 10-5 μCi

13. Acids and bases

Name Formula Molecular weight Density Mass percent C molar concentration
Glacial acetic acid-CH3COOH CH3COOH 60 1.05 99.5 17.4
Formic acid-HCOOH HCOOH 46 1.2 90 23.4
Hydrochloric Acid – HCl HCl 36.5 1.18 36 11.6
Nitric Acid – HNO3 HNO3 63 1.42 71 16
Perchloric Acid – HClO4 HCIO4 100.5 1.67 70 11.6
Phosphoric Acid – H3PO4 H3PO4 98 1.7 85 18.1
Sulfuric Acid – H2SO4 H2SO4 98.1 1.84 96 18
Ammonium Hydroxide – NH4OH NH4OH 35 0.9 28 14.8
Potassium Hydroxide – KOH KOH 56.1 1.52 50 13.5
Sodium Hydroxide – NaOH NaOH 40 1.53 50 19.1
β-hydrophobic ethanol-HSCH2CH2OH HSCH2CH2OH 78.1 1.11 100 14.3

14. Protein

Strain: E. coli or Salmonella typhimurium

Cell Single cell Culture system/L (109 cells /ml)
Wet weight 9.5 x10-13 g 0.95 g
Dry weight 2.8 x10-13 g 0.28 g
Total protein 1.55 x10-13 g 0.15 g
Volume 1.15 um3 = 1 femtoliter
Protein concentration in each cell :135 mg/ml
Theoretical value of the target protein produced in 1L culture system (109 cells/ml):
0.1% of total protein: 150 μg/L
2.0% of total protein: 3 mg/L
50.0% of total protein: 75 mg/L

15. Nucleotide Physical properties

Nucleotide Molecular weight Absorption wavelength λ max (pH7.0) Absorbance at λ max
ATP 507.2 259 15400
CTP 483.2 271 9000
GTP 523.2 253 13700
UTP 484.2 262 10000
dATP 491.2 259 15200
dCTP 467.2 271 9300
dGTP 507.2 253 13700
dTTP 482.2 267 9600

16. Nucleic acid data

The average DNA molecular weight of a base pair (sodium salt) =650 Dalton
1.0 A260 unit dsDNA= 50 μg/ml = 0.15mM (in nucleotides)
1.0 A260 unit ssDNA= 33μg /ml= 0.10mM (in nucleotides)
1.0 A260 unit ssRNA= 40μg /ml= 0.11mM (in nucleotides)
dsDNA molecular weight (Dalton)= the number of base pairs ×650
Number of dsDNA molecule terminal moles=2×DNA mass(g) /DNA molecular weight (Dalton)
Number of DNA terminal moles after restriction endonuclease digestion:
a) Circular DNA molecule :2× number of DNA moles × number of bits
b) Linear DNA molecules :2× number of DNA moles × number of bits +2×number of DNA moles
1 μg 1000 bp DNA= 1.52 pmol = 9.1 × 1011 molecules
1 μg pUC18/19 DNA (2686 bp) = 0.57 pmol= 3.4× 1011 molecules
1 μg pBR322 DNA (4361 bp) = 0.35 pmol = 2.1 ×1011 molecules
1 μg M13mp18/19 DNA (7249 bp) = 0.21 pmol = 1.3× 1011 Molecules
1 μg λDNA (48502 bp) = 0.03 pmol = 1.8×1010 molecules
1 pmol 1000 bp DNA = 0.66μg
1 pmol pUC18/19 DNA (2686 bp) = 1.77μg
1 pmol pBR322 DNA (4361 bp) = 2.88μg
1 pmol M13mp18/19 DNA (7249 bp) = 4.78μg
1 pmol λDNA (48502 bp) = 32.01μg
1.0 kb DNA= the coding amount of 333 amino acids ≈37,000 Dalton protein
10,000 Dalton protein ≈270 bp DNA
50,000 Dalton protein ≈1.35 kb DNA