IDT Offers Advice for Improved Oligo Quantification

CORALVILLE, Iowa - March 20, 2013 - PRLog -- Integrated DNA Technologies (IDT) (http://eu.idtdna.com/site), the world leader in oligonucleotide synthesis, has released a series of tips for accurate oligo quantification. The advice is available in this quarter’s edition of the IDT newsletter, DECODED (http://eu.idtdna.com/Pages/docs/decoded-archive/decoded-vol-3-no-1.pdf?sfvrsn=6), and particularly highlights the importance of using the correct molar extinction coefficient (ε) for calculating oligonucleotide concentration. Inaccuracies or generalizations in the value of the molar extinction coefficient used can result in discrepancies in yield readings, leading to the use of incorrect oligo concentrations in experiments.

A material’s molar extinction coefficient (molar absorptivity) is influenced by numerous factors. This is especially true for oligonucleotides, where the ε of constituent bases differs depending on the number of conjugated double bonds within the structure. Consequently, subtleties in base composition and sequence order, as well as sequence length actually have a notable impact on molar absorptivity of the oligo.

Rather than using general conversion factors to estimate the impact of double/single-stranded DNA and single-stranded RNA on absorbance, IDT calculates the extinction coefficient for each oligo, via the ‘Nearest Neighbor Method’. By establishing this value more specifically, the resulting oligo quantification is more accurate and reliable, particularly for short oligos and those with repeating sequences. IDT offer a free program on their website, the OligoAnalyzer tool (http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/), for calculating the molar absorptivity of any sequence by this method.

The article provides readers with some additional recommendations for maximizing the reliability of oligo quantification. Access the complete article (http://eu.idtdna.com/pages/decoded/decoded-articles/pipet...) in the latest edition of the DECODED newsletter from IDT.

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