oligos and cloning

New Product for 1-18-10 to 1-24-10 High Throughput DNA Oligos!

Need a plate of high quality oligos fast and for a great price? Allele’s newest product can help…

Introducing High Throughput DNA Oligos!

Anywhere from 48 – 96 desalt oligos per plate

Oligos 20 – 50 bases long

Available in two synthesis scales:

25 nmol scale only 13 cents per base

50 nmol scale only 17 cents per base

Every oligo is strictly controlled for quality:

Oligo quality is verified using MALDI-TOF mass spectrometry or Electrospray Ionization Mass Spectrometry.

Shipped or hand delivered in 5 days!

Oligos can be provided normalized at a specific concentration with fixed or variable volumes. Concentration options depend on the oligo length, purification, and scale of synthesis being ordered.

No minimum number of plates per order required!

To order, simply email your oligo sequences and names, indicate 25 nmol or 50 nmol, concentration preference in excel or notepad format to oligo@allelebiotech.com A template will be posted online here soon, please check back.

Allele…Continuing to introduce cost efficiency to research!

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Tuesday, January 19th, 2010 oligos and cloning, Uncategorized No Comments

Allele Biotech is 10 Years Old and Celebrating with FREE Oligos!

Allele Biotech is 10 years old!!!!!!! December 1999 was when Dr. Jiwu Wang and colleagues started this great company as a DNA oligo and siRNA service provider to the San Diego area. Since then he has fearlessly lead Allele into the forefront of the biotechnology industry with multiple RNAi patents, numerous NIH grants, revolutionary iPSC and fluorescent protein technologies, the acquisition of Orbigen, a continuously growing catalog of over 1000 molecular biology products and signature Allele Biotech Reagents, and a business culture that is approachable, encouraging, and reverential of research advancement through global communication and collaboration.

What a difference a decade makes. Today Allele Biotech is a top oligo service provider all around the country with customers in all of America’s major academic institutions. Currently, we are the sole oligo provider on the University of California San Diego’s central purchasing site, Marketplace; a collaboration designed to provide top quality oligonucleotides to UCSD research departments while saving them thousands of dollars annually. We now produce many of our own oligo synthesis and modification reagents, further cutting the costs to our valuable customers which enabled us to continue operations this last year without raising prices due to the worldwide acetonitrile shortage which more than quadrupled in cost! Allele Biotech has stood out over the years not only to our loyal customers but other oligo providers as well. Less than 5 years into our operation we were approached by one of the well known, top three, oligo providers in an attempt to buy us out! We resisted and are still here to proudly serve the research community with the Allele brand!

It all started with oligos…Now ten years later we want to honor our accomplishment by giving away a FREE month of oligos to one lucky customer! To enter you must be an Allele Biotech Facebook fan or friend. A winner will be randomly selected from our friends/fan pool on Sunday, February 14th, 1210 at noon. That lucky winner will receive FREE oligos for the month of March 2010! Limitations apply. Click here for terms and conditions.

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Q&A About Choosing Modified Oligos

Allele’s New Products of the Week, Oct 19-26, 2009: DNA oligonucleotide synthesis reagents dA, dT, dC, dG controlled pore glass (CPG) beads for oligo synthesis. With previously launched CPG beads and phosphoramidites for modified oligos, this product line now provides the most essential materials for oligo synthesis by university core facilities, company internal oligo production groups, or commercial oligo providers at significantly reduced prices.

Allele’s Weekly Promotion Oct 19-26, 2009: In accordance with the launch of the above new products, all 3’ amino, thiol, Dabcyl, FAM, biotin modified oligos of 50 to 200 nmol scale are offered at unprecedented $10/modification.


What do you have available that can be added to the 3’ end of a primer/probe to stop PCR amplification?

There are a few commonly used modifications on the 3′ of an oligo to block polymerase extension, e.g. C3 spacer, amino-modified C6, inverted dT, phosphate. Although no 3′ blocking modifications are 100% effective, the amino-modified C6 offers the best result, leaving1% or less unblocked; phosphate is not as effective of a block, with up to 2% unblocked. We recommend 3’ amino group also because it is less expensive compared to other 3’ modifications if ordered from Allele Biotech.


Can you provide 5’ digoxigenin as a standard modification on your oligos?

5’ Dig is typically added by conjugating the digoxigenin group to a 5’ amino added during oligo synthesis. 5’ amino modification can be ordered from almost all oligo suppliers including Allele. You may need to add digoxigenin using a commercial kit by yourself. If you are interested in having Allele Oligo Service perform the chemical linking, email oligo@allelebiotech.com.


Is Dabsyl a misspelling of Dabcyl?

DABCYL acid is the abbreviation of 4-(dimethylaminoazo)benzene-4-carboxylic acid. Sometimes DABSYL (4-dimethylaminoazobenzene-4”-sulfonyl chloride) is mistaken for ‘DABCYL’. They do share similar properties as fluorescence quenching agents, with minor difference in maximum absorbance, but can in general be used interchangeably in pair with fluorescent dyes such as FAM. Allele uses Dabcyl as its standard 3’ modification and, by using its own oligo synthesis reagents for adding this group, offers a price less than half of most other oligo manufacturers (check back for pricing updates next week for even lower prices). DABCYL is one of the most popular acceptors for developing FRET-based nucleic acid probes and protease substrates.

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Wednesday, October 21st, 2009 oligos and cloning, Uncategorized No Comments

HPLC Purified siRNA with Known RNAi Effects at $149/12.5nmol

RNA oligo is significantly more difficult to synthesize than DNA oligos, mainly because the efficiency of coupling each new ribonucleotide during RNA synthesis is a few fold lower than deoxyribonucleotide during DNA synthesis. Typically, there is an ~10% chance a DNA oligo of 21 bases will have a mutation (most frequently a deletion mutation); for an RNA oligo of 21 bases, as in an siRNA pair, such chance is much higher. Furthermore, after combining the sense and antisense siRNA strands, some RNA molecules will remain as single-stranded thereby not fitting for the RNAi apparatus.

RNA interference is a dose-sensitive process — specificity of gene silencing is meaningful only relative to the active concentration of siRNA used. When the concentration is too low, even the most effective siRNAs would fail to cause gene expression knockdown; when too high, non-specific effects will be duly observed. Therefore, it is essential that the concentrations of siRNAs are measured correctly. When doing so, one must consider not only what the apparent concentrations are by OD260 reading, but also whether the RNA strands are of full-length and whether only dsRNA molecules are counted. This issue might not affect data interpretation if appropriate controls are included in one set of RNAi experiments, but it could have significant influence on conclusions if data from different experiment sets or labs are compared or combined.

HPLC purification currently provides the best means to remove RNA molecules with deletions or remain single-stranded, however, the price tag added by most reagent providers for such treatment has been prohibiting because manufacturers either need to start synthesis at a much bigger scale to obtain promised amount, or they do not promise the delivery quantity at all. The phosphoramidites (oligo building blocks) for RNA synthesis can be 10 times or more expensive than for DNA. Some companies offer alternative purification methods such as a cartridge type device, but they can only remove salt and small impurities, not RNA oligos of shorter lengths accumulated at each cycle of amide coupling. The AllHPLC siRNAs within Allele’s RNAi product line, pre-validated or custom made, are uniformly HPLC purified with 5 OD or 12.5 nmol of double-stranded, annealed siRNA delivered. Allele passes to customers the cost savings from manufacturing our own RNA amidites and other reagents for oligo synthesis. The pre-validated HPLC purified double-stranded siRNA is offered today at $149/12.5 nmol.

Before purchasing siRNAs, even at a low cost of $29 per pair of HPLC purified control siRNA from Allele, researchers still need to consider how well their cells can be transfected. For hard-to-transfect cells, lentiviral vectors carrying a shRNA expressing cassette is often a better choice. To establish stable cell lines, plasmid vectors should be considered. For low cost target screening, the PCR format linear siRNA expression cassettes have advantages.

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Thursday, September 17th, 2009 oligos and cloning, Uncategorized No Comments

Economy and Your Research: Carpets and Oligos

Do you believe in six-degrees of separation? If you really don’t care how close you are related to Roger Tsien or Bill Gates or the dean of your graduate school, maybe you are still curious about how the economy downturn, oil production, and floor carpet production got to do with you–not just in the sense how the job market is shaping up, but also how your lab research budget and how your DNA oligos are served.

To illustrate how events far and away can influence your daily activities, just use oligos as an example. Starting in 2008 when the oil price was still near its peak (remember paying $4+/gallon?), it became too expensive for carpet producers to continue using petroleum for manufacturing carpets. They switched to some other source or halted business altogether. Side effect was production and supply of Acetonitrile (ACN) dried up. Yes, one of the most commonly used organic solvent is a by-product from making carpets. That, combined with facility shutdowns in Northern China in preparation of the summer Olympics (for clean air) and in Florida by a major hurricane, the price of 4 liters of Acetonitrile changed from ~$40 to about $400 plus lots of begging. This event alone pushed individual customer based (as compared to large scale or prefabricated) oligo businesses like Allele’s to be at a loss.

Eventually the situation changed, price went back to about $90/4L, but not before a long period when Acetonitrile was completely unavailable and alternative solvent had to be used. Long story short, that was some storm to whether! If you didn’t feel it in price or service from Allele Oligo, good, that means we did a fair job shielding the wind and shouldering the pressure from the collapsing roof.

Everything really is connected, sometimes by a few degrees less than you would imagine.

Allele’s mottos: care about the environment, help everybody whenever we can, do the right thing even when nobody is looking, have fun, and contribute to the good of mankind through science and innovation.

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Friday, August 14th, 2009 oligos and cloning, State of Research No Comments