Nucleic Acids and Protein Calculation Conversions

1. Nucleic Acids

ds DNA	10 kb = 6.60×10⁶ Dalton	1 OD_{260 nm} = 50 μg
ss DNA	10 kb =3.30×10⁶ Dalton (dNMP average molecular weight（Mw）=330 Dalton)	1 OD_{260 nm} = 33 μg
RNA	10 kb =3.45×10⁶ Dalton (NMP average molecular weight（Mw）=345 Dalton)	1 OD_{260 nm} = 40 μg

2. Protein

BSA : 1 OD_{280 nm}= 1.67 mg (1 mg/ml =0.6 OD_{280 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)

NTP	ε 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

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