Hi, can Trilink synthesize a RNA di-nucleotide containing at least one intrisically fluorescent ribo-nucleotide analogue? Thank you-Egor

Dear Egor,

We are able to synthesize an RNA dinucleotide containing an intrinsically fluorescent ribo-nucleotide analog.

I have included a link to the product page for a few options we can offer:

Isomorphic-Intrinsically Fluorescent

For a formal quotation, please contact us through sales@trilinkbiotech.com

Best Regards,

Tiffany Teng

Product Specialist I

Is there an advantage in using a c12 linker over c6 linker in coupling probes to magplex magnetic beads from Luminex. The objective is to develop a 34 target multiplex assay for detection of various viruses and bacteria using the MagPix instrument from Luminex. -Rachel

Dear Rachel,

Thank you for your question. We suggest using the C12-amino linker as recommended in the Luminex probe/primer design manual. It is likely that the protocol was optimized for this linker.

Please let us know if you have any additional questions.


I am interested in an aptamer that would be able to detect a Salmonella typhimurium cell at one end and able to specifically hybridize to a ssDNA at the other end. Is it possible for you, and how difficult would that be for such an aptamer to achieve and maintain its 3D conformation in vitro? – Aristea

Dear Aristea,

Thank you for your interest in TriLink BioTechnologies, Inc. Unfortunately, we do not offer aptamer design or selection services. We recommend Base Pair Bio who should be able to help you with your research needs.

We can synthesize the aptamer once the sequence is determined. Please let us know once you have a sequence identified and we will gladly provide a quotation.


I would like to block ligation at the 3′ end of an oligo. The traditional way to block described in the literature is C3 spacer. I was wondering if I label the 3′ end of an oligo with the Cy5 dye, would the dye molecule effectively block ligation? -Chun-Nan

Dear Chun-Nan,

The blocking groups most often described in the literature are 3′ dideoxy-C, 3′ C3 Spacer (C3-OH) or 3′ Amino Linker (C6-NH2). All the mentioned modifications permanently block the 3′ hydroxyl group of the 3′ base. We can use the 3′ Amino Linker and label it with the Cyanine 5 dye which would continue to block the 3′ hydroxyl group.

Please contact us if you have any other questions.

Best regards,
Sabrina Shore, MS
Scientist, Research & Development

I obtained a oligo from Trilink 47 bp in length with the presence of a random fragment that was 10bp. Scale ordered: 0.2umole Extinction coefficient: 457.1 units/umol Od= 63.5 MW= 14334.9 g/mole I calculated the molarity as umol= OD/extinction coefficieint = 63.5/457.1= 0.138umol To make 1mM of the oligo I added 138ul of water to the mixture. Now total MW= 0.138 * 14334.9 = 1978.2ug But as there are 138 ul each ul should have a concentration of 14.339 ug but each ul of my sample had 1 ug concentration. Is there an error to my calculations? -Anjali

Dear Anjali,

Thank you for your inquiry. A final concentration of 1 uM means you have 1 μmole or 14.34 ug per L. Concentrations should be confirmed with OD readings of the final solution. Please remember, the extinction coefficient and molecular weight reported is calculated average and the final values of a randomer oligonucleotide may vary.

We’re happy to discuss how to measure the concentration of you solution. Please email us to discuss measuring the absorbance.

Best regards,

I’m working with magnetic nanoparticles (10 nm) for hyperthermia approaches and I want to functionalize (coat) it with DNA (aptamer). what is the best conjugation method that could be used? – Mahmoud

Dear Mahmoud,

Thank you for your inquiry. TriLink is able to offer different attachment chemistries. Based upon your application, we would match up the functional group on the oligo based upon the reactive group of the magnetic nanoparticles. Some possible chemistries include Thiol/Maleimide or NHS-ester/primary amine of a linker.

TriLink’s DADE (decanoic acid diester) linker offers a novel way of preparing conjugates more economically and with much more flexibility. We can readily prepare 5′ carboxyl linkers. This linker can be used to conjugate to amines using conventional carbodiimide chemistry. Though less convenient than the solid phase method described in DADE: A Pre-activated Carboxyl Linker, Applications and Methods, solution phase methods may be necessary at times. The DADE linker is also useful for conjugation to amine bearing molecules.

We can also employ other attachment chemistries if you can provide the reactive group on the nanoparticles. Please contact our Product Management group to continue the discussion.

Best Regards,

I have ordered 5’end-modified RNA oligonucleotides and would now like to 3’end label them. Unfortunately, I cannot find any info on the nature of the 3’end of your RNA oligos. Is it a standard -OH group? -Eva

Dear Eva,

Thank you for your interested in our RNA oligonucleotides. You are correct, the 3′ end of an unmodified oligonucleotide would be the terminal base in your sequence with hydroxyl groups (-OH) on the 2′ and 3′ sugars.

We also offer a variety of linkers that can be used to have different chemistries on the 5′ and 3′ end of an oligonucleotide. You can use an amino linker for reactions with and activated carbonyl and a thiol linker for reactions with maleimides. The order of the chemistry performed is important as a maleimide will react with the free amine.

Please let us know if you’d like to discuss your project or quote a new oligonucleotide.

Best regards,

In order to obtain accurate concentration measurements using extinction coefficients provided by Trilink Biotech, what variables need to be held constant? I am assuming that extinction coefficients are determined experimentally by Beer’s law, when volume and path length are held constant. Can you provide details? Thank you, Jacob

Dear Jacob,

Thank you for your question. TriLink calculates the extinction coefficient of an oligonucleotide by using the nearest neighbor method and reports it on the Certificate of Analysis. You can learn more about extinction coefficients in our Technical Article, An Introduction to Extinction Coefficients and Molecular Weights of Oligonucleotides. After diluting an oligonucleotide, the concentration can be determined by measuring absorbance with a spectrophotometer with UV lamp and quartz cuvette. Beer’s law can be used to calculate the concentration. If your oligonucleotide was supplied lyophilized, I recommend diluting to your preferred concentration using the method described.

Please let us know if you have any further questions.

Best regards,

I would like to synthesize an mRNA that contains a modified nucleotide that I have prepared. I would like to place this nucleotide as a specific site of incorporation and have prepared a phosphoramidite version. Can you custom synthesize something like this? -Christopher

Dear Christopher,

Thank you for your interest in TriLink. We have the ability to use custom phosphoramidites for oligonucleotide synthesis and routinely do so. Depending on the final length of your construct, we also offer chemical addition of a 5′ N7-Methyl-G cap to mimic natural mRNA.

We will need to discuss your project to understand the full request and discuss the options to incorporation a site specific mRNA modification. Our Product Management will be in contact with you shortly.

Best regards,