Alexa Dyes, Cy Dyes and other Fluors: succinimidyl esters (from Pharmacia-Amersham and Molecular Probes)   Approx. Color ¶ Dye Abs/Em * Catalog No. Molecular weight e CF280 ý CF260 § Blue AF 350 346/442 A-10168 410 19,000 0.19 0.25 Blue-green AF 430 433/539 A-10169 701 16,000 0.28 ND Green AF 488 495/519 A-20000 643 71,000 0.11 0.30 Yellow AF 532 532/554 A-20001 724 81,000 0.09 0.24 Orange AF 546 556/573 A-20002 1080 104,000 0.12 0.21 Red-orange AF 568 578/603 A-20003 792 91,300 0.46 0.45 Red AF 594 590/617 A-20004 820 73,000 0.56 0.43 Fuchsia AF 633 ¶ 632/647 A-20005 1200 100,000 0.55 ND Purple AF 647 ¶ 650/668 A-20006 1300 239,000 0.03 0.00 Indigo AF 660 ¶ 663/690 A-20007 1100 132,000 0.10 0.00 Deep Purple AF 680 ¶ 679/702 A-20008 1150 184,000 0.05 0.00 Dintrophenyl 349/NA D-2248 400 18,000 0.18 AMCA 346/442 A-6118 450 19,000 0.19 Cascade Blue 400/420 C-2284 600 28,000 0.65 0.18 Marina Blue 365/460 20,000 0.30 Fluorescein/FITC 494/518 F-6130 600 68,000 0.20 0.32 Oregon Green 488 496/524 O-6147 510 70,000 0.12 0.31 Rhodamine Green 505/527 620 68,000 0.19 0.24 BODIPY FL 504/513 68,000 0.04 0   BODIPY TMR 535/574 50,000 0.05 0.15   BODIPY TR 588/617 45,000 0.22 0.11   Oregon Green 514 511/530 70,000 0.19   Rhodamine Red 570/590 120,000 0.17   Tetramethylrhodamine 555/580 65,000 0.30 0.27   Texas Red 595/615 T-6134 800 80,000 0.18 0.23   BODIPY 630/650 ¶ 632/640 D-10001 100,000 0.10 0.09   BODIPY 650/665 ¶ 651/660 100,000 0.13 0.07   QSY 7 560/NA 90,000 0.22   FluorX 494/520 587 68,000 0.29 0.29   Cy2 bis 489/506 900 150,000 0.15 0.08   Cy3 mono 550/570 765 150,000 0.08 0.08   Cy3.5 mono 581/596 1100 150,000 0.24 0.08   Cy5 mono ¶ 649/670 800 250,000 0.05 0.05   Cy5.5 mono ¶ 675/694 1130 250,000 0.18 0.05   Cy7 mono ¶ 743/767 1000 250,000 0.05 0.05   DEAC 432/472 D-1412 350 56,000 0.12 0.14   R6G 524/552 C-6157 550 92,000 0.29 0.24   TAMRA 547/573 T-6105 640 91,000 0.19 0.32   Nucleic acid A260 factor MW e_base   ds DNA 50 330 6600   ss DNA 33 330 8919   oligonucleotide 33? 330 10000   RNA 40 340 8250 * = Approximate absorption (Abs) and fluorescence emission (Em) maxima for conjugates, in nm. ¶ = Human vision is insensitive to light beyond ~650 nm, and therefore it is not possible to view the far-red&endash;fluorescent dyes by looking through the eyepiece of a conventional fluorescence microscope. e = Extinction coefficient at l max in cm -1 M -1 . ý = Correction factor for absorbance readings (Abs280) at 280 nm; e.g. Abs280,actual = Abs280,observed - (CF280 • Absmax). § = Correction factor for absorbance readings (Abs260) at 260 nm; e.g. Abs260,actual = Abs260,observed - (CF260 • Absmax). AF = Alexa Fluor ND = not determined. NA = not applicable.   Calculations: DNA A = e (extinction) * l (path cm) * c (M concentration) {Beer-Lambert law} A_base = A_260 - (A_dye*CF) base:dye = (A_base*e_dye)/(A_dye*e_base) conc (mg/ml) = [(A_base*MW)/(e_base*path length in cm)]*dil Proteins A_protein = A_280 - (A_dye*CF) prot conc (M) = (A_prot*dilution)/(e_280*path cm) mole dye/mole prot = (A_dye*dilution)/(e_280*M prot conc) conc (mg/ml) = [(A_prot*MWprot)/(e_280*path cm)]*dil