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Frequently Asked Questions - Oligonucleotide Synthesis
Product & Services
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.
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.
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.
Yes.
Microsynth primers can be further used in EvaGreen or probe based assays (e.g. drop-off assays for mutation screening).
Order Related Questions
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".
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.
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).
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.
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
The minimum amount of oligos to receive an 96 well plate is 40 oligonucleotides.
- 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.
- 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
Initial screening using different siRNAs: for such an application our customers usually use desalted siRNA which has undergone cartridge purification. Herewith purity levels of ~80 % are achieved which is fairly enough for initial screening purposes.
Advanced screening or for use in cell cultures: if your experiment becomes more sophisticated and hence more expensive, we usually recommend to select HPLC (~85%) or even PAGE purification (~95%).
Yes, Microsynth does offer custom siRNA for use in animal experiments. The processing options include various HPLC purification methods, counter ion (Na+) exchange and sterile filtration.
By standard, there is a OH-group at the 5’ and 3’ of an oligo.
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.
