FAQ: CodeLink® Activated Slides

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General Questions

Are CodeLink Activated Slides compatible with all systems?

CodeLink Activated Slides are compatible with any system that can accept a slide with the following dimensions: (width x length x thickness) 25 mm x 75 mm x 1 mm. Fluorescently labeled targets are most commonly applied, and can be monitored by scanning; radioactively labeled DNA can be quantified by phosphorimaging.

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Can proteins be immobilized on CodeLink Activated Slides?

Yes. Researchers generate good results in ELISA-based formats. Protocols have not been optimized for this application and will have to be developed by the researchers.

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Coating

What are the dimensions of the coated surface?

The CodeLink coating covers the entire topside of the 25 mm x 75 mm slide.

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Is the coating based on silane?

The CodeLink coating is comprised of a silane base layer and a hydrophilic, amine reactive, polymeric topcoat.

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What is the chemical nature of CodeLink Activated Slides?

CodeLink Activated Slides are prepared using a hydrophilic polymer containing N-hydroxysuccinimide ester groups. This polymeric coating is attached covalently to the silane basecoat.

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Stability

How stable are CodeLink Activated Slides?

CodeLink Activated Slides are stable for 10 months in their original heat-sealed, desiccated packaging. Once the original packaging has been opened, any unused slides must be resealed and stored desiccated in the original packaging or any sealable bag.

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Are CodeLink Activated Slides stable after opening the package?

CodeLink Activated Slides are stable until the expiration date (printed on the package) if they are stored desiccated in a sealed bag.

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How long can the CodeLink Activated Slides be exposed to higher humidity without affecting the reactive groups?

CodeLink Activated Slides should be printed below 50% relative humidity. The recommended range is 30-45% relative humidity. At 50% relative humidity, an 8 hour printing run is possible. Use lower humidity levels for longer print times.

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Are CodeLink Activated Slides stable after printing?

If CodeLink Activated Slides are stored desiccated (which also inhibits microbial contamination) the slides will be stable for an extended period. Ten-month stability has been demonstrated.

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Are CodeLink Activated Slides stable at high hybridization temperatures?

Perform long (>24 h) hybridization experiments at or below 55°C.

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Are CodeLink Activated Slides stable at high pH?

Due to the silane base coating, do not expose CodeLink Activated Slides to environments greater than pH 9.

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Printing and Coupling

Is it necessary to use the recommended CodeLink print buffer (50 mM sodium phosphate pH 8.5)?

The print buffer is designed specifically for use with CodeLink Activated Slides. This pH (8.5) allows maximum binding of the amine to the surface. Acceptable sodium phosphate concentrations are 50-150 mM at pH 8-9.

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Is there any advantage to using highly purified oligonucleotides?

We have seen no significant advantage to further purification. The oligonucleotide must be desalted to remove competing amines (i.e., Tris).

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What size spots are expected with CodeLink Activated Slides?

Due to the hydrophilic nature of the coating, the spot size may be slightly larger than that achieved with coatings that are more hydrophobic. Adding 2-8% sodium sulfate to the print buffer will decrease the spot size slightly. This addition decreases slightly the amount of DNA immobilized.

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Can additives such as DMSO, betaine, or glycerol be used to prevent drying out of printed spots to facilitate the reaction?

These additives decrease binding and/or destroy spot morphology. The nature of the CodeLink Activated Slides does not require that the printed DNA spots remain solubilized for effective immobilization.

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How should PCR products be purified prior to printing?

The amine primers will compete with the PCR products for binding sites on the slide surface. These primers must be removed as directed in the protocol. Do not use Tris buffers in the final elution.

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Are any additional chemicals needed for coupling to occur?

No.

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Why is incubation in a saturated NaCl chamber required when this step is not required for other types of slides?

Binding of amine-labeled DNA to the slide surface occurs through a thermochemical reaction. The saturated NaCl solution creates a 75% relative humidity environment that provides sufficient moisture for this reaction to proceed. If the printed slides are exposed to 100% relative humidity, the spots may enlarge or distort.

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Amine Modification

How is the amine moiety added to PCR products or oligonucleotides?

Oligonucleotides must be synthesized with an amine attached at either the 5'- or 3'-end. PCR products are prepared by including a 5'-amine-modified primer in the amplification reaction. Primers labeled at the 3'-end will also function in PCR, but they are more expensive to synthesize and less commonly applied. If 3'-OH is blocked, no amplification will take place through Taq polymerase.

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What is the recommended spacer length?

C6 is most common and cost effective; other lengths will also work.

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Is it necessary to use amine-modified DNA samples?

The best results are obtained using aminated DNA. Non-aminated DNA will provide lower levels of immobilization and hybridization signal. Non-aminated DNA binding decreases with decreasing length.

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Hybridization

What is the standard sample amount applied per slide?

Target prepared from 0.5-2 mg of polyA RNA or 10-40 mg of total RNA is standard.

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Can CodeLink Activated Slides be stripped and rehybridized?

CodeLink Activated Slides are not intended for rehybridization. Alkali treatment will remove the silane base coating. If desired, slides can be boiled to strop off the hybridized target.

 

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