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EXTINCTION COEFFICIENTS AND FLUORESCENCE DATA

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.

CAT. NO.

Nucleoside

l max-1

Emax-1

l max-2

Emax-2

E260

(nm)

(ml/µmole)

(nm)

(ml/µmole)

(ml/µmole)

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

266

16.4

14.8

10-1008

8-Oxo-dA

268

12.2

11.1

10-1014

pdC

295

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

12.6

10-1027

8-Br-dG

253

12.1

11.3

10-1028

8-oxo-dG

294

5.2

250

6.7

5.9

10-1031

5'-OMe-dT

266

9

8.3

10-1035

Carboxy-dT

297

16.1

261

14.7

14.7

10-1036

2-thio-dT

278

17.5

220

14.8

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

 

 

7.7

10-1044

5-Nitroindole

328

8.5

265

17.0

16.0

10-1045

4-Methylindole

265

7.9

 

 

7.2

10-1046

2-Aminopurine

303

6.8

243

5.7

1.0

10-1047

dP

294

6.7

231

7.4

2.9

10-1048

dK

279

10.7

 

 

7.7

10-1050

dU

262

10.0

 

 

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

11.3

231

11.4

3.5

10-1055

d-pseudoU

262

7.7

 

 

7.6

10-1060

5-Me-dC

277

9.0

 

 

5.7

10-1061

5-Me-dZ

314

4.8

218

8.6

1.8

10-1063

5-OH-dC

292

6.3

220

13.3

3.4

10-1065

5-Me-isodC

260

6.3

 

 

6.3

10-1067

5-Me-isodC

260

6.3

 

 

6.3

10-1076

7-deaza-dX

284

6.5

252

10.4

8.8

10-1077

iso-dG

292

11.0

 

 

4.6

10-1078

iso-dG

292

11.0

 

 

4.6

10-1080

5-Br-dC

287

6.0

 

 

3.1

10-1081

5-I-dC

293

5.7

 

 

3.3

10-1085

2,6-diaminoPurine

278

10.2

255

9.3

8.5

10-1090

5-Br-dU

278

9.7

 

 

5.1

10-1091

5-I-dU

287

7.7

 

 

3.7

10-1094

Furano-dT

See plot

10-1095

2,4-difluoro-toluene

266

2.3

 

 

1.8

10-1097*

AP-dC

362

10.5

 

 

10.9

10-1530

dihydro-dT

210

6.3

 

 

<0.1

10-1550

dihydro-dU

210

6.3

 

 

<0.1

10-1550

dihydro-dU

210

6.3

 

 

<0.1

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.

FLUORESCENCE DATA

Dye E 260 nm E lambda max Excitation max Emission max QY Notes
(L/mol cm) (L/mol cm) (nm) (nm)
Acridine 39,500 9,120 421 497
2-aminopurine 1,000 3,600 303 371
Cy3 4,930 136,000 547 563 0.15
Cy3.5 24,000 116,000 591 604 0.15
Cy5 10,000 250,000 646 662 0.3
Cy5.5 21,500 209,000 688 707 0.3
Dabcyl-dT 29,100 32,000 476
5'-Dabcyl 11,100 32,000 468
Eclipse Quencher 6,600 33,300 530 N/A 0
Etheno-dA 4,800 5,800 276 405 0.035
6-FAM 20,900 75,000 495 521 0.9
3'-(6-Fluorescein) 13,700 494 522
Fluorescein-dT 38,800 75,000 494 522 0.9
HEX 31,580 96,000 537 556 0.7
NBD 3,700 19,500 485 535 0.1
Psoralen 16,500 11,000 301      
Pyrrolo-dC 4,000 3,700 345 470 0.07/0.02 QY 0.07 single-stranded; 0.02 ds, deprotected in ammonia 55°C ON
Pyrene-dU 18,500 42,200 402
Redmond Red 12,100 74,000 (pH 9.1)
52,300 (pH 7.1)
579 595 0.84
TAMRA 32,300 89,000 556 580 0.7
TET 16,255 86,000 519 539 0.9
Yakima Yellow 23,700 83,800 530.5 549 0.96

 

PHYSICAL PROPERTIES OF BLACK HOLE QUENCHERS

Quencher lmax (nm) E260 (L/mol.cm) Emax (L/mol.cm)
BHQ-0 493 7,700 34,000
BHQ-1 534 8,000 34,000
BHQ-2 579 8,000 38,000
BHQ-3 672 13,000 42,700