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OligoMix® Oligonucleotide Mixture - FAQs |
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GeneralManufacture
Cost
Applications
OrderingDeliveryStorageAdditional QuestionsAnswers - GeneralOligoMix® is a product that contains thousands of customer-specified oligonucleotide (oligo) sequences synthesized simultaneously in parallel, cleaved into solution, and delivered as a mix in a single microtube ready for many multiplex applications (Zhou et al., 2004 [abstract]; Tian et al., 2004 [abstract]). ManufactureHow is OligoMix® manufactured? OligoMix® synthesis is based on a patented synthesis technology developed by our partner, Atactic Technologies (reviewed in Gao et al., 2004 [abstract] . This technology allows parallel synthesis of a large number of different oligo sequences using conventional DMT-chemistry (Caruthers 1991) at high yield. The synthesized sequences are removed from the surface and processed using our proprietary protocols to provide the final product. [References] What is the makeup of OligoMix® ? OligoMix® is a completely custom product of DNA or RNA oligonucleotides. The customer has the flexibility to specify: sequence, length, 5’- or 3’-labeling, modification, amount, and the product delivery format (e.g. single stranded or duplex). Is there a limit to how many sequences can be ordered? There is no limit to the number of sequences that you can order. We currently fit up to 3,918 sequences per synthesis. For larger numbers of sequences, multiple syntheses will be preformed. Our method of synthesis is very flexible, and thus we can tailor the product to suit your needs. Is there a minimum order of sequences? No. The product is typically used for experiments and applications which need multiple sequences. How long can the sequences be? Can the sequence lengths vary? We routinely synthesize oligo sequences up to 100-mers and the sequence lengths in the OligoMix® can vary from sequence to sequence. The base price is for 25-mers and a charge of $5 per additional base for longer sequences. What synthesis chemistries are available for the product? You can order sequences that normally can be obtained from an oligo synthesis house, such as DNA, RNA, nucleotide analogs, and hybrid sequences. How much product will I receive? There will be sub-fmols per sequence and total of pmols per OligoMix® tube. We deliver a minimum of 2.4 x 10-3 OD/260. What if I need more quantity of the product? We provide services for special requests like this. What is the synthesis (coupling) efficiency? High throughput synthesis versus single sequence synthesis is judged differently. Since the sequences are synthesized in parallel in miniaturized quantities, it is difficult to measure the efficiency of the reactions. In general the synthesis efficiency is comparable to conventional oligo synthesis. However, OligoMix® as a raw product also contains impurity sequences from failed synthesis on solid surfaces. What is the quality control for the synthesis? OligoMix® is synthesized using chemical reagents of the highest quality. Every synthesis has to pass a rigorous QC process, which involves the detection of hybridization on multiple reaction sites using a standard detection oligo solution and the match (PM) and mismatch (MM) hybridization signal ratios. We use standardized parameters, such as signal intensity, signal covariance (CV), and PM/MM ratio as criteria. Can I use electrophoresis to check OligoMix® ? OligoMix® is a mixture of sequences and it usually shows as a smearing band on gel, especially for single stranded sequences. The results are not particular revealing. The gel should be run after the amplification reaction. Yes, we currently provide service for purification of the sequences up to 45-mer length. Since we use hybridization of the OligoMix® sequences to their complementary sequences, the purification would be less efficient for longer sequences. We highly recommend for the applications which are more demanding on purity, such as gene synthesis, one should consider ordering purified sequences. Although the cost is higher, the purified product can be used more efficiently. What level of purity can be attained through purification? A nine-fold improvement in sequence fidelity was reported in our published work (Tian et al., 2004 [abstract]). Can OligoMix® be modified? What types of modifications can be incorporated? Yes. There are many options for synthesis modifications including backbone modifications, modified nucleotides, and 5’ or 3’ end modifications. What 5’-end modifications are available? Amino or thiol linkers, phosphate modification, labeling with biotin, FAM or other fluorescent dye, and others. What 3’-end groups are available? 3’-OH, 3’-phosphate, and others. CostThe basic price for the synthesis of OligoMix® is $700. This includes up to 3,918 sequences synthesized up to a length of 25 bases. If any of the sequences (it doesn’t matter how many) are longer than 25 bases (longest length=N), we add $5 x (N-25) to the basic price. If the number of sequences is greater than 3,918, we can synthesize additional chips at a charge of $700 per chip. That depends on how many sequences are ordered and the length of the sequences. Example 1: A full plate (3,918) of 30-mers
$735 + $5.25(30-25) =
$761.25 = 0.6˘ per base Example 2: A full plate (3,918) of 60-mers
$735 + $5.25(60-25) =
$918.75 = 0.4˘ per base What is the cost for modifications or purification? We have competitive price for modifications and please see the LC Sciences OligoMix® Pricing Page. ApplicationsWhat applications can OligoMix® be used for? Library construction Applications
Multiplexing Applications
Microarray Applications
Other Applications
Yes, the oligo sequences will be designed to contain primers at both ends. We suggest the use of 1% of the total product volume as the template strands; use of thermal DNA polymerases of strong displacement capability, such as Vent; primers which are longer than the length of the variable region/2; use of multiple PCR conditions (annealing and extension times) and less reaction cycles; and combine the PCR samples to minimize the sequence bias of the PCR reactions. Can LC Sciences perform experiments for me? Yes, LC Sciences provides full service from helping you design the experiments, to synthesis of the sequences, to delivery of final data. OrderingYou can find and download the Online Order Form from our website, complete the form with your contact information and oligo sequences, and send it to us by email. We will send you an order confirmation within 24 hours. DeliveryHow long will it take to deliver OligoMix® ? Your OligoMix® will be delivered in 5-10 days once the sequences are confirmed. How will OligoMix® be delivered? OligoMix® will be shipped as a mix in ~ 20 µl buffer solution in a single microtube (unless otherwise specified). StorageHow should I store OligoMix® ? Single stranded OligoMix® , which tends to aggregate, is best to be at room temperature if it is to be used in a few days, but in the refrigerator at -20oC for long term storage. Double stranded OligoMix® is stored in the refrigerator at -20oC. Additional QuestionsWhere can I find more technical information? See our publications and technical bulletins pages.
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