A material’s molar extinction coefficient (molar absorptivity) is influenced by numerous factors. This is especially true for oligonucleotides, where the e 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, 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 in the latest edition of the DECODED newsletter from IDT.
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About IDT
Integrated DNA Technologies (IDT) is the largest supplier of custom nucleic acids in the world, serving academic, government, and commercial researchers in biotechnology, clinical diagnostics, and pharmaceutical development. IDT's primary business is the manufacture of custom, synthetic DNA and RNA oligonucleotides. Today, IDT synthesizes and ships an average of 36,000 custom oligos per day to more than 86,000 customers worldwide. IDT manufacturing locations include facilities in Coralville, Iowa; San Diego, Calif.; Leuven, Belgium; and Singapore. For more information visit www.idtdna.com.
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