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Oligonucleotides Technology Overview
The outcome of a successful experiment may depend on the quality of an oligonucleotide. The Synthesizing Department at Ocimum Biosolutions uses Polyplex, BioAutomation’s MerMade-192 to produce custom oligonucleotides. The MerMade-192 Oligonucleotide Synthesizer is designed to synthesize two chucks of oligonucleotides, containing either 96 well plates or columns, in a single run using standard or modified phosphoramidite chemistry. Our department synthesizes a combination of standard, degenerate, or modified oligos, in a plate or column format, with our reaction scale of 50nm, 200nm and 1000nmol. Additionally, the chucks may be synthesized in sequence or in parallel.
Typical applications for the oligos are for use in microarray experiments, dye terminator sequencing reactions, gene building, polymerase chain reactions (PCR), Ligase Chain Reaction (LCR), hybridization studies, site directed mutagenesis, cloning, RTPCR antisense studies, siRNA, dual labeled probes and other techniques. Oligos up to 150 bases in length have been made with a coupling efficiency in excess of 98%.
The current purification procedures preformed at Ocimum ensure the highest quality possible. Ocimum Biosolutions offers the following purification methods:
Standard Purification Method
Ocimum Biosolutions uses the Salt Free method as its standard method for purification. The desalting method purifies the oligonucleotides from any synthesis by-products, and any impurities resulting from post-synthesis processing.
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| Production details |
| Scales of synthesis |
0.01 µM, 0.05 µM, 0.2 µM, 1 µM, 2 µM, 5 µM, 10 µM and 15 µM |
| Purification methods |
Desalted (RP Cartridge), HPLC, Elchrom Submarine
Electrophoresis, PAGE |
| Quality Analysis |
Capillary Gel Electrophoresis, PAGE, Analytical HPLC, Pyrosequencing |
| Available Modifications |
| Standard modifications |
5’ |
3’ |
Internal |
| Aminolink-C6 (TFA), Aminolink-C6 (MMT), Disulfide |
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| Aminolink-C3, Aminolink-C7 |
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| Phosphorylation, Aminolink-C12 |
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| Digoxigenin, Thiol C6, Biotin |
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| Dye |
| Cy2, Cy3, Cy3.5, Cy5, Cy5.5, HEX, TET |
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| BH Quencher 1, BH Quencher 2, Dabcyl |
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| IR Dy681, IR Dy781, Dy547 (Cy3 alternative), Dy647 (Cy5
alternative), Dy554, Texas Red, Rhodamine, CAL Fluor Orange 650 |
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| JOE, ROX, Tamra, 6 FAM, Fluorescein |
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| Base Modification |
| Bromo-deoxyUridin |
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| Uridine, Uracyl, Deoxyinosine |
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| Antisense |
| PTO |
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| Molecular Beacons/ Dual labeled probes |
| FAM, HEX, TET, ROX, JOE, Cy Dyes, Texas Red, Others |
For large quantities, custom modifications, and special analysis please contact oligos@ocimumbio.com.
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| The Ocimum Advantage |
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A reliable production of oligonucleotides of high quality and excellent coupling efficiency (>99.3%). |
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Pure oligonucleotides cleaned from toxic compounds, chemicals, n-1 products and salts by purification with our optimized SPE technology. |
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Unique numbered (barcode) oligonucleotides. |
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Oligonucleotides that are produced according to certified quality management guidelines by our facility, which is ISO 9001-2000 certified. |
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OciChip™ array Concept
Oligonucleotides 
