Below are some frequently asked questions about our Oligo Synthesis services. Should you have any questions other than listed below, feel free to contact us at firstname.lastname@example.org and we will be happy to clear your thoughts.
HAP stands for "High Affinity Purification"; it is a patented, novel purification method for custom oligos developed by Bio Basic. After synthesis the DMT-ON-oligo in the crude oligo mixture is selectively absorbed on a high affinity resin within a HAP column, this allows incomplete oligo fragments pass through while keeping majority of the full length oligos. The full length oligo is retrieved by removing the DMT protection group under mild acid conditions. The HAP process provides two major advantages, higher purity and a low cost comparable to PAGE or HPLC methods.
O.D. stands for Optical Density units; it is based on absorbance readings at 260nm. For synthesis facilities that use phosphoramidite synthesis, O.D. measurements are a means to quantify the amount of available oligo after purification i.e. the FINAL YIELD of the oligo. As a rough estimate 1 O.D. ~ 33 ug. When comparing oligo synthesis services, the O.D. should be compared (the final yield) and not the initial synthesis scale (in "nmol") which is the quantity of the starting material required before synthesis of the oligo. From this, the final "nmol" yield will vary on the length, sequence and molecular weight of the individual oligo.
We can synthesis oligos up to 130 bases in length. Due to manufacturing restrictions we only offer synthesis under PAGE or HPLC purification. Note, there is a size restriction for our desalted and HAP oligos between 11-59 bases.
You can order by "nmol" reference but note that "nmol" is assumed to be the initial amount of material used to synthesize an oligo unless otherwise noted. This is not accurate means to compare oligos between facilities as our manufacturing procedures are likely different and therefore the corresponding final yield and price rates will differ. If you’re switching providers and aren’t quite sure what to pick, don’t hesitate to ask and we will be happy to match an equivalent or better oligo service.
The "nmol" references refers to the initial amount of material used for each base in the oligo sequence. Like with all chemical reactions 100% completion is not possible. The average yield cycle is ~98%. The longer an oligo is, the increased likelihood of an error being introduced in the sequence. For example a 60-bases long oligo the yield of full length oligos is 0.98^(60-1) or 30.36% of full length material available. There are additional reductions in yield due to purification and minor loses due to material transfers and quality control analysis.
Fill out one of our order forms and submit it to email@example.com. Note these orders are NOT confirmed. You will receive a quotation within 24 hours which is non-obligatory (commitment free). Order will only be confirmed upon your review and approval of the quotation. Likewise you can estimate the cost of your oligos using our pricing list. If you wish to proceed with the order as outline in the quotation sent to you, have your billing details ready (PO, Credit Card or Wire) along with confirmation to proceed.
On average it takes about:
2 business days for standard oligos (Desalt and HAP).
+2-3 days for PAGE or HPLC purification.
+1-2 days for longer oligos (longer than 60 bases). Turnaround times will vary on current throughput, volumes and complexity of the order.
Yes you can! May we recommend down-packing your oligo? Oligos are most stable left in their lyophilized state. If you’re not using all your oligo at once we can offer down packing for your oligos at no extra cost to you; Please let us know when placing your order (we recommend a max. of 20-40OD down-packed in a single tube if you plan to work within that given tube). Otherwise, the max. quantity of oligo we can down-pack in each tube are: Standard Tube (2ml) : 200 OD Special Tube (5ml) : 1000 OD
We have a large variety of common modifications. You can find our full list on our oligo modifications page. If you cannot find the modification you’re interested in, don’t hesitate to contact us. Note that some of our modifications may have alternate names as some modification names are propitiatory, therefore we are not allowed to list them on our website. You can always contact us at firstname.lastname@example.org to request an equivalent.
Oligos are lyophilized in microcentrifuge tubes or lyophilized in 96-well plates for automated operations.
A minimum of 48 oligos must be ordered for the 96-well Plate format.
Accurate MW: MW=(A bases x 313.2)+(C bases x 289.2)+(G bases x 329.2)+(T bases x 304.2)-61.
Average MW: Average MW per base = 324.5.
To reconstitute: Centrifuge the tube for a few seconds to collect the DNA in the bottom of the tube. Carefully open, add an appropriate volume of buffer of choice, close, re-hydrate for two minutes and vortex for 15 seconds (common buffers are Tris or TE, TE typically used for stability / long term storage).
It is recommended that oligos be reconstituted at concentrations > 10u molar and stored at -20°C.
Storage at -20°C:
the stability of the lyophilized (dry) and reconstituted material (including TE and and nuclease-free water) is approximately 2 years.
Storage at at 4°C:
The stability of the lyophilized (dry) and reconstituted material (including TE and and nuclease-free water) is approximately 1 year.
Storage at Room Temperature:
The lyophilized (dry) and TE reconstituted oligos are stable for approx. 6 months, while oligos reconstituted in nuclease-free water would be stable for less than 1 month.
- Oligos are more stable when re-suspended TE buffer rather than in their lyophilized (dry) form. This is because of the stabilization effect caused by the Tris (maintains pH) and EDTA (inhibits nucleases).
- Stability varies with modified oligos as the different attachments, linkers, etc. alter the stability of the oligos.
- Avoid exposure of oligos to UV light to minimize photodegradation.
For non-modified oligos:
Denatured polyacrylamide gel (PAGE) in the presence of 7M urea is recommended for oligo DNA electrophoresis analysis. Agarose gel is not recommended.
For modified oligos:
Please note that components such as urea in PAGE can cause modified oligos to degrade or may cause modifications to detach. Smearing / short bands may be visible because of this.
EB staining is suitable for measuring DNA concentration, but not suitable for measuring OD value of oligos, as A, C, G and T have different binding capacities with EB.
The ideal range of OD reading in UV spectrometer at 260 nm is from 0.3 to 0.8 OD. If the solution is too diluted or too concentrated the measured total OD units may not be correct.
No, they are not phosphorylated. Both ends of the oligo have a free hydroxyl group.
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