OligoSpec Calculator

The OligoSpec™ calculator provides the physical properties for your oligo design. Quickly calculate your oligo’s molecular weight and extinction coefficient.

5' Modification

Sequence Internal modification

3' Modification

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Illegal sequence!

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Protonated MW calc:{{ecmwCtrl.protonated}}

Counter ion MW calc:{{ecmwCtrl.ion }}

Important notes

The OligoSpec calculator outputs the physical properties for a particular oligo design. Extinction Coefficient Calculation - The extinction coefficient is calculated with the following method: ε260 = [(Sum of ε260 for all bases*) + (ε260 for all modifications*)] x 0.9, to adjust for hyperchromicity.

Where:

ε260 of bases = dA (ε260=15,200), dC(ε260=7,050), dG(ε260=12,010), and T(ε260=8400).
All ε260 values are reported in units of M^-1•cm^-1

*The extinction coefficient values for all other bases and modifications can be found on the oligo modifications pageunder the 'Technical Specs' tab available for each oligo modification, or bydownloading this PDF.

Molecular Weight Calculation -
Molecular weight backbone (g/mol) is calculated using the following formula: MW(backbone) = Σ(nbase * MWbase) + MW Modifications + (nPO2 * MWPO2) + MWHAdj

Where:

MWbase = molecular weight of the deprotonated nucleoside.
MWMod = molecular weight of the deprotonated form of each individual modification
nPO2 = total count of internal phosphates, i.e., nbases + nmods - 1.
MWPO2 = molecular weight of PO2, i.e., 62.97. This is the MW for that portion of a phosphate linkage not already included in MWbase or MWmod.
MWHAdj = 0, 1, or 2 protons (i.e., 0, 1.01, or 2.02), depending on the presence and structure of 3' and 5' modifications.

The addition of counter ions is simply the molecular weight backbone plus the total weight of counter ions. This added weight is typically equal to the number of phosphates in the oligo multiplied by the weight of the counter ion. The weight of each counter ion is generally assumed to 102.2 for Triethylammonium (TEA). Note that some modifications add additional phosphate groups to the molecular weight calculation, such as a 3’ phosphate modification or 3’ thymidine linked modifications.

The protonated molecular weight is also typically equal to the backbone weight plus the total number of phosphates multiplied by 1.01 for each proton (H+). This is the molecular weight that is typically observed by electrospray mass spectrometry run in negative ion mode.