OligoMix® 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]).
OligoMix® synthesis is based on a patented synthesis technology developed in house (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]
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).
There is no limit to the number of sequences that you can order. We have several sequence density designs and our method of synthesis is very flexible, thus we can tailor the product to suit your needs.
No. The product is typically used for experiments and applications which need multiple sequences.
We routinely synthesize oligo sequences up to 150-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.
You can order sequences that normally can be obtained from an oligo synthesis house, such as DNA, RNA, nucleotide analogs, and hybrid sequences.
We deliver a minimum of 2.4 x 10-3 OD/260. There will be sub-fmols per sequence and total of pmols per OligoMix® tube. One fmole per sequence is the calculated amount of starting material for oligo synthesis. As with all standard oligonucleotide synthesis, the resulting final material will be of less quantity depending on the sequence length, composition, and other factors.
The OligoMix® product can be amplified by incorporating a set of common primers in all sequences. See use of OligoMix® below for more details.
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.
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.
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. There are many options for synthesis modifications including backbone modifications, modified nucleotides, and 5’ or 3’ end modifications.
Amino or thiol linkers, phosphate modification, labeling with biotin, FAM or other fluorescent dye, and others.
3’-phosphate, and others.
The price will depend on the number of sequences ordered. We have several sequence density designs and our method of synthesis is very flexible, thus we can tailor the product to suit your needs.
For example – The price for the basic 4K sequence design OligoMix® is $735. 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.
That depends on how many sequences are ordered and the length of the sequences. We have several chip designs with various sequence densities. Below is an example of a 4K array design:
Example 1: A full array (3,918) of 30-mers
$735 + $5.25(30-25) = $761.25 = 0.6¢ per base
3918 * 30 117,540 (bases)
Example 2: A full array (3,918) of 60-mers
$735 + $5.25(60-25) = $918.75 = 0.4¢ per base
3918 * 60 235,080 (bases)
Use of OligoMix®
Users need be aware of that the amount of each individual sequence is very small and the product is not in a purified form. As result, the product may behave somewhat differently from a simple mixture of individually synthesized oligos.
In order to effectively utilize the product, the following experiment approaches should be considered.
- Incorporate one set of common primers in all sequences and use PCR to amplify the product before use. An added benefit of the amplification is a purification effort since some of the failure sequences would not be amplified.
- We suggest the use of 2% of the total product volume as the template strands.
- For PCR amplification, Pfu, Vent, and Platinum Taq have been known to work. Regular Taq is not recommended.
- Additional recommendations – 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.
- If multiple groups of sequences are going to be extracted from the product, use nested PCR to first amplify all sequences and then use inner primer regions to amplify the individual groups. Attempting to extract multiple groups in the first round PCR may not produce satisfactory result.
Library construction Applications
- Inserts for siRNA or shRNA expression vectors
- Templates for in vitro transcription or RNA sequences
- cDNA libraries for proteins, antibodies, and peptides
- Gene Synthesis by oligonucleotide assembly (Zhou et al., 2004 [abstract]; Tian et al., 2004 [abstract])
- Large scale mutagenesis (codon modifications of existing cDNA, antibodies, protein mutants, etc.)
- Primers for multiplexing and/or allele specific PCR
- Gene expression, SNP, and alternative splicing analysis by ligation of specific oligos
- Dye-labeled control/reference oligos for gene expression microarray experiments (replacing expensive and time-consuming control sample preparation)
- On chip probe optimization/validation (oligos as specific target sequences)
- Dye labeled gene-specific staining reagent
Yes, LC Sciences provides full service from helping you design the experiments, to synthesis of the sequences, to delivery of final data.
Your OligoMix® will be delivered in ~14 days once the sequences are confirmed.
OligoMix® will be shipped as a mix in ~ 20 µl buffer solution in a single microtube (unless otherwise specified).
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.