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Protein and DNA Microarrays

A microarray (multiplex lab-on-a-chip) is a collection of microscopic protein or DNA spots (2D array) on a solid surface (a glass slide or silicon thin-film cell) that assays large amounts of biological material by high-throughput screening.

Our highly bright and photostable SeTau dyes (squaraine rotaxanes) also exhibit high chemical stability in particular against oxidative reagents such as peroxides or ozone (see here) and therefore are excellent detection reagents for use in microarrays where the fluorescence signals of cyanine dyes such as Cy5 and  Alexa 647 are strongly dependent on the concentration of ozone during post-hybridization array washing. Controlled exposures of microarrays to ozone confirmed the susceptibility of cyanine dyes (Cy5 or Alexa 647) to ozone levels as low as 5-10 ppb for periods as short as 10-30 s.

Below is the confirming data by one of our Cancer Center customers:

Fluorescent squaraine rotaxanes are available in reactive form with carboxy, NHS ester and maleimide functionalities but also as hydrophobic probes for imaging.

Excitation Light Sources Characteristics
Product Number
(Specs Sheet)
Product Name
(Product Info)
Target Group 380 405 436 488 532 594 635 650 680 700 750 780 Medium λ abs
[nm]
ε
[M –1
cm–1]
λ em
[nm]
QY
[%]
FLT
[ns]
Buy
                   
K8-3335
K8-3335
Seta-555-NHS
Seta-555-NHS
NH2 PB 7.4 555 155000 570 7
K9-4119
K9-4119 new
SeTau-665-NHS
SeTau-665-NHS
NH2 PB 7.4 664 160000 712 53 3.1
K9-4148
K9-4148
SeTau-647-Maleimide
SeTau-647-Maleimide
SH PB 7.4 648 200000 692 45 3.2
K9-4149
K9-4149
SeTau-647-NHS
SeTau-647-NHS
NH2 PB 7.4 649 200000 695 61 3.2
K9-4169
K9-4169 new
SeTau-670-NHS
SeTau-670-NHS
NH2 PB 7.4 673 275000 694 36 1.6
K8-3402
K8-3402
Zy3-NHS
Zy3-NHS
NH2 PB 7.4 549 150000 564 4 0.3
K9-4179
K9-4179 new
SeTau-680-NHS
SeTau-680-NHS
NH2 PB 7.4 683 215000 705 58 2.9


Seta-555-NHS (K8-3335) and SeTau-647-NHS (K9-4149) are amine-reactive dyes specifically developed for a wide range of DNA and protein microarray applications for the Cy3 and Cy5 channel. These reactive dyes are ideal for labeling of oligonucleotides, amino-modified cDNA, antibodies, peptides, and other types of biomolecules for microarray imaging applications. Aminoallyl groups can be introduced into DNA and RNA by incorporation of modified nucleotides containing an aminoallyl group.

 

 

Above is a comparison of the Seta-555 and SeTau-647 dyes with other dyes commonly used in these microarrays. The dyes were diluted starting from 100ug/ml, 4x dilution, 10 spots. The data shows much higher fluorescence for the Seta-555 and SeTau-647 dyes and there was also no detectable channel-to-channel crosstalk (data not shown).  These dyes are ideal for both one- and two-color microarray measurements, have extremely high ozone stability and are more affordable compared to the dyes of our competitors. Try and experience the difference yourself!

 

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