Which dyes are available and are there specific dyes that are most compatible with active translation? Is there one specific nucleotide that can accommodate the dye better than others with respect to translation?

Bulky dyes may block the ribosome during translation and we have seen lower translational efficiencies with more substitutions. We recommend not to fully substitute, but only substitute 10-50%. For our catalog products, we use a 25% substitution of the dye-labeled nucleotide. Please contact us for any additional information.

Are there protocols for polymorphic microsatellite analysis using IRDye labeled nucleotides instead of primers? There must be some issue because I cannot find any. -Janine

Dear Janine,

Thank you for your question. Labeled primers are typically used versus labeled dNTPs to allow for control over the number of fluorophores that are associated with each fragment. I am unaware of a protocol that uses labeled dNTPs.

If you decide to use labeled primers, TriLink offers a range of IRDyes for oligonucleotide labeling through OligoBuilder®. I’m sorry I could be of more help and good luck with your research.

Best regards,
Natasha Paul, PhD

I’d like to order dye-modified DNA. [TTTTT/{Texas-Red-X}/TTTTT] In terms of internal dye molecules, could you please let me know how the dye can bind between the sequences? And, I wonder if there is agap between front-bases and back-bases, because I want to hybridize this with other complementary DNA(A10). -Taeseok Oh

Dear Taeseok,

Thank you for your question. You can order your dye-modified oligo through OligoBuilder®, our online ordering system.

Texas Red can be incorporated into your oligo by using a selective amino linker, like Thymidine-5-C2 Amino Linker or the C6 version. This modification can replace one of your bases and hybridize with your target.

Please let me know if there is anything else I can help you with.

Best regards,

How do I insert a dye or conjugate on an internal linker?

Several modifications are available in the amidite form and can be added to your sequence simply by clicking on them. These modifications are marked “Amidite.” For all other internal dyes and conjugates you will need to choose the appropriate selective placement linker. To add an internal dye or conjugate click the linker of choice, followed by the dye or conjugate of choice from the internal modifications menu. The modification will appear at the end of your current sequence. Continue adding bases as needed. To view all available selective placement linkers, dyes and other non-fluorescent conjugates, see our Custom Oligonucleotide Components menu.