Calculate extinction coefficient of an oligo by either summing up the extinction coefficients of the individual bases times their number of occurrences. Or use a formula that takes into account nearest neighbor effects. An algorithm for this calculation can be found on the web. Just type in the sequence and the program will calculate the concentration of a l A260/ml solution.
To calculate the MW of the aminomodified oligo just add 179.16 to the calculated MW of the unmodified oligo.
10-1001
7-deaza-dA
270
11.3
9.4
10-1003
N6-Me-dA
266
16.9
15.2
10-1006
Etheno-dA
295
3.4
274
5.9
4.7
10-1007
8-Br-dA
16.4
14.8
10-1008
8-Oxo-dA
268
12.2
11.1
10-1014
pdC
7.7
234
14.7
5.1
10-1017
Pyrrolo-dC
339
2.36
229
17.5
2.41
10-1021
7-deaza-dG
259
12.6
10-1027
8-Br-dG
253
12.1
10-1028
8-oxo-dG
294
5.2
250
6.7
10-1031
5'-OMe-dT
9
8.3
10-1035
Carboxy-dT
297
16.1
261
10-1036
2-thio-dT
278
220
10
10-1040
dI (Inosine)
249
12.5
7.5
10-1041
dNebularine
262
7.1
7.0
10-1043
3-Nitropyrrole
283
8.8
10-1044
5-Nitroindole
328
8.5
265
17.0
16.0
10-1045
4-Methylindole
7.9
7.2
10-1046
2-Aminopurine
303
6.8
243
5.7
1.0
10-1047
dP
231
7.4
2.9
10-1048
dK
279
10.7
10-1050
dU
10.0
10-1052
4-thio-dU
330
30.4
3.6
10-1053
5-OH-dU
280
7.8
4.9
10-1054
pdU
291
11.4
3.5
10-1055
d-pseudoU
7.6
10-1060
5-Me-dC
277
9.0
10-1061
5-Me-dZ
314
4.8
218
8.6
1.8
10-1063
5-OH-dC
292
6.3
13.3
10-1065
5-Me-isodC
260
10-1067
10-1076
7-deaza-dX
284
6.5
252
10.4
10-1077
iso-dG
11.0
4.6
10-1078
10-1080
5-Br-dC
287
6.0
3.1
10-1081
5-I-dC
293
3.3
10-1085
2,6-diaminoPurine
10.2
255
9.3
10-1090
5-Br-dU
9.7
10-1091
5-I-dU
3.7
10-1094
Furano-dT
10-1095
2,4-difluoro-toluene
2.3
10-1097*
AP-dC
362
10.5
10.9
10-1530
dihydro-dT
210
<0.1
10-1550
dihydro-dU
Note: Biotin and Cholesterol have no absorbance at 260nm.
*With an extinction coefficient of approximately 10,500 M-1 and a quantum yield of fluorescence of 0.2, AP-dC is 2-3 times as bright as our popular Pyrrolo-dC analog. In addition, AP-dC exhibits a Stokes’ shift greater than 100 nm. As with most fluorescent base analogs, it is substantially quenched upon forming a duplex. The quantum yield drops to 0.1 while gaining significant structure in the emission spectrum (Figure 4), making it an ideal probe of DNA structure.
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