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 λ A260/ml solution.

CAT. NO. Nucleoside λmax-1 Emax-1 lmax-2 Emax-2 E260 E260 Notes
(nm) (ml/µmole) (nm) (ml/µmole) (ml/µmole) (L/mol.cm)
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
10-1043 3-Nitropyrrole 283 8.8 7.7
10-1044 5-Nitroindole 328 8.5 265 17 16
10-1045 4-Methylindole 265 7.9 7.2
10-1046 2-Aminopurine 303 6.8 243 5.7 1
10-1047 dP 294 6.7 231 7.4 2.9
10-1048 dK 279 10.7 7.7
10-1050 dU 262 10 10
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 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 4.6
10-1078 iso-dG 292 11 4.6
10-1080 5-Br-dC 287 6 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
10-1554 5-Ethynyl-dU 287 10.3 3.8
10-3055 PseudoUridine 8,100 Ref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851715/

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 λ 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
Ferrocene-dT 14,200        
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 λmax (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

 

VIEW PRiNTABLE VERSION


http://www.glenres.com/Technical/Extinctions.html