NanoPhotometer
®
NP80/N60/N50/C40
User Guide Version 3.1
51
Table 2. Dye Types, Absorbance Max, Extinction coefficient, and dye-dependent
correction factors
NanoPhotometer
®
Model
Dye Type
Absorbance
maximum of
Dye (nm)
Dye-dependent
ext. coeff.
ε
dye
in M
-1
*cm
-1
Dye-dependent
correction factor
at 260 nm cf
dye
NP80/N60/N50/C40
Alexa Fluor 350
345
18,400
0.25
NP80/N60/N50/C40
Alexa Fluor 488
492
62,000
0.30
NP80/N60/N50/C40
Alexa Fluor 532
525
82,300
0.24
NP80/N60/N50/C40
Alexa Fluor 546
555
104,000
0.21
NP80/N60/N50/C40
Alexa Fluor 555
555
150,000
0.04
NP80/N60/N50/C40
Alexa Fluor 568
576
93,000
0.45
NP80/N60/N50/C40
Alexa Fluor 594
588
80,400
0.43
NP80/N60/C40
Alexa Fluor 647
650
239,000
0.00
NP80/N60/C40
Alexa Fluor 660
660
107,000
0.00
NP80/N60/C40
Alexa Fluor 680
680
164,000
0.00
NP80/N60/N50/C40
Cy3
550
150,000
0.08
NP80/N60/N50/C40
Cy3.5
581
150,000
0.08
NP80/N60/C40
Cy5
649
250,000
0.05
NP80/N60/C40
Cy5.5
675
250,000
0.05
NP80/N60/N50/C40
Oyster-500
503
78,000
0.29
NP80/N60/N50/C40
Oyster-550
553
150,000
0.05
NP80/N60/N50/C40
Oyster-556
560
155,000
0.03
NP80/N60/C40
Oyster-645
649
220,000
0.05
NP80/N60/C40
Oyster-650
653
200,000
0.04
NP80/N60/C40
Oyster-656
660
200,000
0.04
NP80/N60/N50/C40
Texas Red
593
85,000
0.23
Ratios
Reactions utilizing nucleic acids often require minimum purity standards. Common contaminants
of nucleic acid samples include: proteins, organic compounds, and other. Based on the common
contaminants of nucleic acid samples, the 260/280 and 260/230 ratios are calculated for nucleic
acids to give an indication of the purity of the samples. Pure DNA and RNA preparations have
expected 260/280 ratios of
≥
1.8 and
≥
2.0 respectively. An elevated absorbance at 230 nm can
indicate the presence of impurities as well; 230 nm is near the absorbance maximum of peptide
bonds and also indicates buffer contamination since TRIS, EDTA and other buffer salts absorb
at 230nm. When measuring RNA samples, the 260/230 ratio should be > 2.0; a ratio lower than
