Frequently Asked Questions - Oligonucleotide Synthesis

Product & Services

Do you also offer the synthesis of MGB-probes?

Yes, we do offer MGB probes with FAM and Yakima Yellow as dyes.

The modification (5’ FAM 3’ MGB-Q500) can be ordered directly through our webshop.

I work with degenerated oligos and need an unequal base distribution. Can you synthesize such oligos?

We can offer degenerated oligos with an unequal base distribution. This service is included, when ordering high fidelity wobbles. When ordering this service you can send us the base distribution, and we will prepare a premixture of the synthesis compounds prior synthesis. The fee for the high fidelity wobble is charged once per type of degenerated base per order. ons.

Do you design primers? If yes what is the price?

Yes, we perform primer design for customers (standard PCR primers, qPCR assays as well as siRNAs). The price is depending on the request. Up to 5 primer designs per day and customer are free of charge. If the design is special or significantly more primer designs are needed, we will give you an offer about the pricing. We prefer NCBI-Accession numbers for primer designs, but also accept sequences in plain text / fasta format.

Are your primers and probes compatible with commercially available supermixes for use in digital droplet PCR?

Yes.

Microsynth primers can be further used in EvaGreen or probe based assays (e.g. drop-off assays for mutation screening).

Order Related Questions

I want to order control siRNA. How should I proceed?

Order by email the control siRNAs indicating which and how many aliquots of control siRNA you need (oligo.support@microsynth.ch).

It is also possible to add presynthesized control siRNA to your order of custom siRNAs. During the ordering of your siRNAs you can specify the name(s) and number of aliquots of the required control siRNAs in the field "special comment".

I want to order oligos in 384 well plates. Is this possible?

Yes, we can deliver oligos in 384 well plates. Please download our excel order sheet under Upload entry in the webshop. Paste your sequences in the file and send the excel file by email to oligo.support@microsynth.ch. Do not submit the excel sheet directly in the webshop. We will come back to you with an offer and more details about your order.

How can I order hybrid oligos (DNA/RNA/2’-O-Methyl-RNA)?

Replace the different DNA/RNA or 2’-O-Methyl-RNA Bases in your sequence by the internal modifications 5, 6, 7 and 8 (e.g. TTAGCrAArGTTrUrC -> TTAGC5A6TT78). Login our webshop and enter your sequence into the sequence field. Define the modification in the drop down menu for 5, 6, 7, 8 (either RNA/DNA or 2’-O-Methyl-RNA bases).

How can high fidelity wobbles be ordered?

Please enter your sequence in the webshop as you are used to, including the IUB-Code for mixed bases (K = G, T; M = A, C; R = G, A; S = G, C; W = A, T; Y = T, C; B = G, T, C; D = G, A, T; H = A, T, C; V = G, A, C; N = G, A, T, C). Choose the 3’ modification “others” and submit your order. Answer to the conformation email with your needed nucleotide distribution.

I want to order oligonucleotides in an 96 well-plate, but I need a special layout. How can this be done?

You can shift the position of oligonucleotides in the 96 well plate by placing empty position. To accomplish that enter an oligo dataset with the following properties:

i. Oligoname: Leerposition
ii. Scale: Genomics
iii. Purification: Desalted
iv. Sequence: TT

Is there a minimal amount of oligonucleotides, that I have to order, to receive the oligo order in an 96 well plate?

The minimum amount of oligos to receive an 96 well plate is 40 oligonucleotides.

I want to order oligos longer than 150 DNA bases. How should I proceed?

We would like to discuss the proposed experiment/application with you beforehand to guarantee the best possible outcome. Such long oligos are not recommended for direct cloning experiments but can be applied for PCR amplification and subsequent cloning or as templates (positive control) for qPCR assays.

Oligos longer than 150 DNA bases can be ordered in the 0.2 µmol synthesis scale as well as in desalted quality only. When ordering such long oligos through our webshop, please proceed as follows:

Shorten your sequence to 100nt
Choose “others” for 3’ modification
Follow the further instructions and submit your order (due to the 3’ modification “others” the production will be halted until we got the entire sequence from you)
When receiving the order confirmation email from Microsynth, reply to this email by including the entire sequence information (others = entire DNA sequence). Do not forget to indicate the 5’ and 3’ end of the sequence in the email.

I want to order an oligo with an internal dye modification. How should I proceed?

Usually, internal fluorescence modifications are incorporated as dT-compounds (e.g. FAM-dT). The ordering procedure for this type of modifications is very simple:

Select a “T” DNA nucleotide within your sequence and replace the “T“ by “5”
Select your preferred dye (e.g. FAM-dT) in the drop-down menu under “Inner Modification (5=...)”
Follow the further instructions and submit your order

Should you need the internal dye modification on a different nucleotide please get in contact with us. You will need to add the modification using “others” and inform us on the actual modification.

How best to order oligos with different production times?

Partial delivery of oligos from one single order is not possible. If your order comprises several oligos with different delivery periods, you will receive all items as a single consignment as soon as all products are ready for shipment. Please use distinct orders, if delivery speed is critical.

General Technical Questions

I would like to know the 5‘ and 3’ moiety of the standard DNA oligos you provide. Are they 5’OH?

By standard, there is a OH-group at the 5’ and 3’ of an oligo.

What is the stability of DNA/RNA oligos and how should they be stored?

More information on DNA oligo handling, storage and stability can be found here.

More information on RNA oligo handling, storage and stability can be found here.

How does Microsynth calculate the molar extinction coefficient of oligonucleotides?

Molar extinction coefficients of oligonucleotides are calculated according to the „base composition model“. [1-3] It includes the absorption of the individual nucleobases and potential base modifications and/or dyes. More accurate values for unmodified oligonucleotides are obtained from the „nearest-neighbor model“, which considers stacking effects of adjacent nucleobases. According to our calculations this model reduces the extinction coefficient approximately to 90 % compared to the base composition model. Therefore the extinction coefficients of oligonucleotides are estimated according to the below equation.

Tataurov A.V., You Y., and Owczarzy R. (2008) Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids, Biophys. Chem. 133, 66-70.
Fasman, G.D. (Ed.) (1975) Handbook of Biochemistry and Molecular Biology, Volume 1: Nucleic Acids, pp 589, 3rd edition, CRC Press.
Cavaluzzi M.J., and Borer P.N. (2004) Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA, Nucleic Acids Res. 32, e13.