Product Information

pdfOligoMix® is a versatile, innovative, custom product for genomics discoveries. We synthesize thousands of oligonucleotide sequences in massive parallel on a microarray chip and then cleave the oligos, releasing them into solution in a single microtube. Synthesis occurs via standard DMT chemistry assuring efficient stepwise yield and a high quality final product. The product is delivered as a pool in a single microtube – ready for use in your experiment.

  1. Economical – At less than 0.8¢ per base, OligoMix is about 20 times more cost and time efficient than conventional oligos. Delivered in a single microtube, it enables inexpensive genome-scale experiments.
  2. Customizable – Customers can specify each oligonucleotide sequence (lengths up to 150-mers). We can synthesize oligonucleotides in OligoMix containing labels, such as terminus phosphate, amino and thiol with linkers, biotin, FAM or other dyes.
  3. Reliable – Innovative microfluidic array platform ensures high quality synthesis. Multiple QC steps are implemented at various stages of OligoMix manufacturing. OligoMix is subjected to both hybridization and qRT-PCR assays to assess final quality.
  4. Simple & Fast – Download our excel spreadsheet order form, paste in your sequences and email back to us. Product can be delivered in 1-2 weeks.

Microfluidic Array Platform—in situ Synthesis

OligoMix® achieves high synthesis purity because it is produced via an advanced microarray synthesis technology (µParaflo®) that integrates a photo-generated acid (PGA) chemistry, digital photolithography (DLP), and advanced microfluidics to enable high throughput parallel synthesis of custom DNA microarrays. The PGA chemistry enables the use of standard oligo building blocks, and eliminates the need for any specially modified nucleotides which may exhibit lower coupling efficiency. DLP technology enables programmable synthesis of custom sequences and the µParaflo® microfluidic device contains the synthesis reactions each within a picoliter-scale reaction chamber, producing more uniform synthesis than reactions performed on the open surface of a slide.

Biomarker

  • Conventional Chemicals
  • Established Synthesis Processes

  • Efficient Stepwise Yield
  • Quality Final Product

Synthesis Technology References

  • Gao X, Yu PY, LeProust E, Sonigo L, Pellois JP, Zhang H. (1998) Oligonucleotide synthesis using solution photogenerated acids. Journal of the American Chemical Society 120, 12698-12699 [abstract].
  • Srivannavit O, Gulari M, Gulari E, LeProust E, Pellois JP, Gao X, Zhou X. (2004) Design and fabrication of microwell array chips for a solution-based, photogenerated acid-catalyzed parallel oligonucleotide DNA synthesis. Sensors and Actuators A. 116, 150-160 [abstract].
  • Zhou X, Cai S, Hong A, Yu P, Sheng N, Srivannavit O, Yong Q, Muranjan S, Rouillard JM, Xia Y, Zhang X, Xiang Q, Ganesh R, Zhu Q, Makejko A, Gulari E, Gao X. (2004) Microfluidic picoarray synthesis of oligodeoxynucleotides and simultaneously assembling of multiple DNA sequences. Nucleic Acids Research 32, 5409-5417 [abstract].
  • Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G. (2004) Accurate multiplex gene synthesis from programmable DNA chips. Nature 432, 1050-1054 [abstract].

FISH Applications

Fluorescence in situ hybridization (FISH) utilizes fluorescent probes to bind portions of DNA that have a high degree of sequence complementarity. This allows researchers to detect and localize specific DNA sequences on chromosomes or RNA targets in various cell and tissue types to determine the spatial-temporal patterns of gene expression within. In medicine, FISH can be used to diagnose or evaluate the progression of a disease, such as cancer, to identify a particular species or to perform various types of karyotyping.

Developing a FISH assay requires the use of oligonucleotide probe sets, like oligopaint probes, which are fluorescently labeled, single-stranded DNA oligonucleotides that can be used to visualize genomic regions ranging in size from tens of kilobases to many megabases. LC Sciences’ OligoMix offers a unique solution for researchers looking to generate oligopaint probes, as users are able create fully designed libraries of tens of thousands of specific, single-stranded oligonucleotide sequences for binding particular genomic regions. Several researchers have demonstrated the effectiveness of OligoMix in their FISH-assays and have provided model strategies for generating oligopaint probes through their work. The strategies they present are important because they provide an experimental model other individuals can emulate and apply to new areas of fluorescence hybridization.

FISH

 

The basic protocol for generation of the oligopaint FISH probes begins with a complex ssDNA library of thousands to hundreds of thousands of unique oligos; like the OligoMix libraries which are quickly and inexpensively generated using LC Sciences’ microfluidic array.

In one strategy, oligos can be designed with a pair of primer sequences (a forward primer and a reverse compliment of the reverse primer) that flank a genomic sequence bound on either side by sites for nicking endonucleases2.

Incorporating two nicking endonuclease sites allows for the production of strand specific probes. Amplification with a labeled F primer and digestion yields a probe targeting the reverse complement of the genomic sequence.

FISH

 

In a second strategy, circle-to-circle amplification (c2ca) is used instead of PCR, to generate oligopaint probes. In circle-to-circle amplification, targeted template strands are cyclized via ligation into circular template strands, which are subsequently synthesized into chain-like repeated copies of the circular template by an enzyme with high processivity and strand displacement capacity3.

This amplification method is unique, because it overcomes some of the drawbacks of PCR like sequence-dependent amplification bias. In addition to this, c2ca is an isothermal process and therefore does not require quick temperature changes which impede the scalability of PCR reactions.

Because c2ca amplified oligos do not carry a direct label, a common binding site is used for a fluorophore-labelled ‘secondary’ oligonucleotide.

The strategies presented here provide a framework for generating oligopaint probes from OligoMix which can be subsequently be used in various FISH applications. By emulating the strategies detailed here, researchers can develop their own oligopaint libraries to apply to new areas of fluorescence hybridization.

Product Descriptionmix of DNA oligonucleotide sequences
Number of Oligosthousands of sequences or more per tube
Oligo Formsingle stranded (ss); desalted and ready for reaction
Lengthup to 150 mers (inquire for longer oligos)
5’ or 3’ Terminus Modificationsphosphate, fluorescent dyes, biotin, linkers, and others
Internal Modificationsmodified DNA or RNA bases
Yield*tens of attomoles per sequence and a total of sub-fmols per OligoMix® tube
Price(see www.lcsciences.com/oligomix)
Delivery14 days

 


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