Frequently Asked Questions About Our Products And Services

For your convenience, please use our Oligo Analysis Tool or apply the formula below:

The extinction coefficient at 260 nm (e₂₆₀) is a unique physical property of each oligonucleotide. It is defined as the absorbance at 260 nm of a 1 M aqueous solution measured at 20 °C in an optical cell with 1 cm pathway (Lambert-Beer's law).
Purinic bases show a higher absorption (OD₂₆₀) than pyrimidinic bases. Interactions between neighbouring bases, as well as modifications that absorb at 260nm, also influence optical absorbance. As a consequence, the extinction coefficient strongly depends on oligonucleotide sequence and composition.

The most accurate method to calculate the extinction coefficient of an oligonucleotide is based on the nearest-neighbor model. The average error of calculated extinction coefficients was shown to be around 4 % using following formular:

For your convenience, please use our Oligo Analysis Tool or apply the formula below:

N [nmol] = OD x 100 / 1.54 x n_A + 0.75 x n_C + 1.17 x n_G + 0.92 x n_T

n = number of nucleosides of the type X


Example:
Sequence: GAA ATG AGT GCT CAT CAC TAC TTC CGC (27mer)

n_A=7; n_C=8; n_G=5; n_T=7
OD=12 (measured)

N [nmol] = 12 x 100 / 1.54 x 7 + 0.75 x 8 + 1.17 x 5 + 0.92 x 7
= 41.3

For your convenience, please use our Oligo Analysis Tool or apply the formula below:

M[µg] = N x MW / 1000
MW = Molecular weight


Example:
Sequence: GAA ATG AGT GCT CAT CAC TAC TTC CGC (27mer)

n_A=7; n_C=8; n_G=5; n_T=7
MW (calculated) = 8219 g/mol
N= 41.3 nmol

M[µg] = 41.3 x 8219 / 1000 = 339

For your convenience, please use our Oligo Analysis Tool or apply the formula below:

MW [g/mol]= 249.23 x n_A + 240.21 x n_T + 265.23 x n_G + 225.20 x n_C + 63.98 x (s-1) + 2.02

n = number of nucleosides of the type X
s = number of all nucleosides per sequence


Example:
Sequence: GAA ATG AGT GCT CAT CAC TAC TTC CGC (27mer)

n_A=7; n_C=8; n_G=5; n_T=7

MW [g/mol]= 249.23 x 7 + 240.21 x 7 + 265.23 x 5 + 225.20 x 8+ 63.98 x (s-1) + 2.02 = 8219.33

The melting temperature T_M, characterises the stability of the DNA hybrid formed between an oligonucleotide and its complementary strand.

For your convenience, please use our Oligo Analysis Tool or apply the formula below:

Sequences with 15 or less bases 
T_M [°C] = 2(n_A + n_T) + 4(n_G + n_C)

Sequences with more than 15 bases
T_M [°C] = 69.3 + [41(n_G + n_C) / s - (650 / s)]

n = number of nucleosides of type X 
s = number of all nucleosides per sequence 


Example:
Sequence: GAA ATG AGT GCT CAT CAC TAC TTC CGC (27mer)

nA=7; nC=8; nG=5; nT=7 s= 27

Sequences with 15 or less bases
T_M [°C] = 2(7 + 7) + 4(5 + 8) = 80.0

Sequences with more than 15 bases
T_M [°C] = 69.3 + [41(5 + 8) / 27] - (650 / 27) = 69.3 + 19.7 - 24.0 = 65.0

PCR                  T_A [°C] = [(T_M1 + T_M2) / 2] - 3

Sequencing        T_A [°C] = T_M + 3