CLICK
for your FeedBack
Begin your Search
NeuProCell
| Takara Bio | Genet Bio | Gene Bridges | USBiologicals | Prospec Tany |
| Isogen- Oligo | Isogen-Peptide | e-Bioscience | Alpha-DNA | IBA-GmBH |
CLICK
for your FeedBack
Begin your Search
| Custom DNA Synthesis (Custom Oligonucleotides) | ||||||||
| OD Scale | Guaranted yield 260 nm | Synthesis Scale nmol | Price / base (Rs.) | |||||
| 16 | 6 ( upto 35 mer ) | 100 nmol | 25.22 | |||||
| 20 | 10 (upto 35 mer | 200 nmol | 41.736 | |||||
| 60 | 50 ( 10 mer - 35 mer) | 1000 nmol | 130.425 | |||||
| Note # 1 | Standard Purity includes Free Desalting | |||||||
| # 2 | at 1000 nmol scale Oligos of <10 mer will be priced as 10mer | |||||||
| # 3 | Other purification eg, PAGE , HPLC prices on request. | |||||||
| Custom Oligo Modification | ||||||||
| Type of Modification | Charges per Insertion 100 /200 nmol | Charges per Insertion 1000nmol | ||||||
| Degenarated Base ( Equimolar Mix ) | 0.00 | 0.00 | ||||||
| Degenarated Base ( Non-Equimolar Mix also known as ' Doping' ) | 141.00 | 282.00 | ||||||
| 5' Acrydite | 2820.00 | 5640.00 | ||||||
| Inosine( Deoxyinosine, dI ) | 470.24 | 916.50 | ||||||
| Uridine ( Deoxyuridine ,dU ) | 470.24 | 916.50 | ||||||
| 3'- Phosphorylation | 1057.50 | 2115.00 | ||||||
| 5'-Phosphorylation | 1692.00 | 3384.00 | ||||||
| 3'-Amine | 1057.50 | 2115.00 | ||||||
| 5'-Amine - C6 | 1692.00 | 3384.00 | ||||||
| 3' Thiol | 1762.50 | 3525.00 | ||||||
| 5' Thiol | 2820.00 | 5640.00 | ||||||
| 3'-Biotin labeling | 1762.50 | 3525.00 | ||||||
| 5'-Biotin labeling | 2749.50 | 5499.00 | ||||||
| 3' Digoxigenin | 8460.00 | 16920.00 | ||||||
| 5' Digoxigenin | 8460.00 | 16920.00 | ||||||
| 3'end 6-FAM/HEX or TET | 3454.50 | 10504.50 | ||||||
| 5'end 6-FAM/HEX or TET | 2044.50 | 8460.00 | ||||||
| 3'-BHQ-1 ( Black hole quencher) | 3525.00 | 7050.00 | ||||||
| 3'-BHQ-2 ( Black hole quencher) | 3525.00 | 7050.00 | ||||||
| 3'-BHQ-3 ( Black hole quencher) | 3525.00 | 7050.00 | ||||||
| 3'-Dabcyl | 3454.50 | 6979.50 | ||||||
| 3'-TAMRA | 3454.50 | 10504.50 | ||||||
| 5'-TAMRA | 5640.00 | 12690.00 | ||||||
| 3'-Fluorescein (FITC) | 1762.50 | 3525.00 | ||||||
| 5'-Fluorescein (FITC) | 1762.50 | 3525.00 | ||||||
| 3'-Cy3 Dye | 5640.00 | 11280.00 | ||||||
| 5'-Cy3 Dye | 7050.00 | 14100.00 | ||||||
| 3'-Cy5 Dye | 5640.00 | 11280.00 | ||||||
| 5'-Cy5 Dye | 7050.00 | 14100.00 | ||||||
| 2--O-Me-RNA | 282.00 | 564.00 | ||||||
| Phosphorothioated oligonucleotides (PTO) | ||||||||
| Synthesis Scale | Basic Cost per Base | Additional charge per PTO Base | ||||||
| 200 nmol | 33.84 | 105.75 | ||||||
| 1000 nmol | 105.75 | 105.75 | ||||||
| Example : | ||||||||
| One oligo of 20 bases at the 200 nmole scale, of which 3 bases at each end are phosphorothioated: 20 x Rs.33.84 = Rs.676.80, plus (3+3) x Rs. 105.75= Rs. 634.50, for the total of Rs. 1311.30 only | ||||||||
Oligos with degenerated positions
We synthesize "degenerated" oligonucleotides with equimolar base mixes at no additional charge.For non-equimolar mixes or equimolar manual mixes ("doped" oligonucleotides, produced by installing additional reagent bottle with manually mixed bases) additional charges apply according to the
prices posted here. When the degenerated oligos are used as custom primers for DNA sequencing, the level of degeneracy should not be very high, to avoid mispriming.
Oligonucleotides with modified bases
There are numerous possibilities for modification of some or all of the bases in an oligonucleotide: bases could be coupled with a fluorescent dye (e.g. fluorescein), psoralin (for cross linking), cholesterol (for easy penetration into living cells), 5'-phosphate group (to facilitate cloning), the phosphate backbone of the
oligonucleotide could be partially or completely replaced by a phosphorothioate backbone (for the "antisense" technology), etc. We do synthesize all modified oligonucleotides, for which reagents are freely available on the market, and some prices are included here .
| Oligonucleotide Purification ----desalting , OPC , PAGE , HPLC | |||||||||
| Standard purity Oligos are desalted at no extra cost. | |||||||||
| OPC ( Oligonucleotide Purification Cartridge) : | |||||||||
| Purification per oligo at Rs. 1500 only for 100 & 200 nmole scale | |||||||||
| HPLC : | Purification per oligo at Rs. 2500 only for 100 nmole scale | ||||||||
| Purification per oligo at Rs. 3500 only for 200 nmole scale | |||||||||
| PAGE : | Purification per oligo at Rs. 3500 only for 100 nmole scale | ||||||||
| Purification per oligo at Rs. 5000 only for 200 nmole scale | |||||||||
NOTE : Extra 24- 48 hrs needed to complete these purification . Please note that even PAGE purification, although the best currently available method, does not guarantee 100% error-free oligonucleotide products. We strongly encourage you to order OPC, HPLC or PAGE purification for your long oligos. However, if you prefer that we supply you the basic product without purification. Generally, our replacement warranty does not cover these non-purified long oligos
Oligonucleotide for Cloning purpose :Points to ponder………
Regardless of the length of the oligos, if they are intended for cloning purposes (usually for PCR, followed by cloning), it would be a much better choice to order these oligos additionally purified, at least by OPC. However, even when the oligos are additionally purified, the customer may wish to consider the following dangers:
1) Internally deleted (n-1, n-2 etc.) products. Most common and upfront limitation of the chemical DNA synthesis, which cannot be completely overcome by additional purification. The chemical synthesis of DNA is not as exact as the DNA synthesis in the living cell, whereby numerous "proofreading" and reparation systems exist to reduce sequence infidelities down to one mutated base per million bases or even one in billion. Even the PCR reaction has a better fidelity, such as one in thousand or one in ten thousand, because the fidelity of the synthesis is additionally enhanced by its enzymatic nature. Unlike the DNA synthesis in living cells, or the DNA synthesis in enzyme-based PCR reactions, the currently used protocol for chemical synthesis of DNA has the upfront limitation of generating sequence infidelities at a rate of approximately one in one hundred for each cycle of the synthesis.
2) Sequence infidelity in in final product : Insertion of one nucleotide, for example G-duplication, is another frequent sequence infidelity in some molecules of the final product. When a G-duplication or another one-base insertion is combined with a (n-1) deletion in the same DNA molecule, the total length will be equal to that of the wild-type (desired) DNA molecules, and thus impossible to separate by OPC, HPLC or PAGE.
3) Low Yields : In addition, the OPC, HPLC and especially the PAGE are "lossy" methods, resulting in low yields (30% to 50% for OPC and HPLC, 10% to 30% for PAGE), because a large number of "good" DNA molecules (of full length and correct sequence) will be removed together with the undesired DNA molecules.
These drawbacks of the oligonucleotide synthesis are explained in the above-mentioned article of Hecker KH, and Rill R. (Error analysis of chemically synthesized polynucleotides. Biotechniques 1998 Feb;24:256-60). In that article, the authors synthesized and
PAGE purified long oligos, used them for cloning, and sequence verified 10 clones. They found 7 single base pair deletions, one 4-base deletion, and one G-C transversion. In addition to these infidelities, others have described G-duplications, branching and other n+x products.
There are some methods to fight infidelities: a) additional purification is recommended; in that case not only are the oligos purified, but the synthesis method is modified to enhance the purity; b) when used for cloning, the OPC-, PAGE- or HPLC-purified oligos (and the PCR products obtained with them) should be expected to give
some "mutant" clones (clones with sequence infidelities, originating in the oligonucleotides), therefore selection and sequence analysis of several independent clones is advised (not just one or two clones). Generally speaking, the chances of finding a clone with the wild-type sequence are very good, as long as truly independent
clones are selected. For this purpose, c) shorter pre-incubation times without antibiotic are suggested immediately after transformation (because very long incubation without antibiotic may lead to amplification of a single “mutant” clone, which will be later falsely taken for multiple “independent” clones on the Petri dish with
antibiotic); d) the bacterial colonies should be picked up when not very large, and preferably located away from each other on the dish; e) where possible, shorter oligos should be used instead of longer ones.
The customer should not feel intimidated by the above warnings, there are very good chances to find a clone with the desired sequence, especially if the oligonucleotides are ordered with additional purification. In addition, most oligos (all short ones, and the additionally purified long ones) are covered by unconditional
replacement warranty ("free replacement, no questions asked"). The above suggestions are posted on this page only to facilitate customer's understanding of the potential problems, and provide some help during ordering and use of custom DNA.
Want to look at the other other Custom Oligo Sources too.......... CLICK below links
Contact Information
Electronic mail Write to webmaster@neuprocell.com with questions or comments about this web site.
Copyright © 2006 NeuProCell
Last modified:
06/22/06