Oligo Calculator
Molecular weight, extinction coefficient and the water volume that gives a 100 µM stock.
Sequences containing U are treated as RNA.
Learn more
What it does
Every oligo that arrives from a synthesis company comes with an amount in OD260 and no instruction on how much water to add. Getting that volume wrong means either a stock that is too dilute to use or one you have to re-order. This calculator turns the sequence itself into the answer.
How it works
The molecular weight comes from summing the residue mass of each base, subtracting the water removed to form each phosphodiester bond, and adding the terminal water. The extinction coefficient uses published per-base absorbance values at 260 nm, which are dominated by G and C. Beers' law then gives the yield: 1 OD260 corresponds to 10⁶/ε nanomoles of oligo, and dividing that by your target concentration gives the resuspension volume. Because ε depends on the actual bases, two primers of the same length can need noticeably different volumes — a 20-mer of all G and C carries roughly twice the extinction coefficient of an all-A/T 20-mer.
Worked example
Load the sample, 5'-CACGCACCTAACAGTCTAAG-3'. The calculator reports 20 nt, 50% GC, a single-strand molecular weight of 4,957.74 g/mol and an extinction coefficient of 220,200 L·mol⁻¹·cm⁻¹. That works out to 4.54 nmol per OD260, so a 1 OD tube needs 45.4 µL of water to reach 100 µM — the standard storage concentration for a working primer stock.
When to use it
Use it when a tube arrives and you need to know what to dissolve it in, when converting an older primer that is recorded only in µg, or when preparing a duplex for a ligation reaction where you need the double-stranded mass. It is also the quickest way to check that a primer ordered as 5 OD really contains enough material for the number of reactions you are planning.
FAQ
- How is the molecular weight calculated?
- By summing the residue mass of every base, then subtracting the water lost to each phosphodiester bond and adding the terminal water. Sequences containing U are treated as RNA and use the ribonucleotide masses.
- What is 1 OD260 and why does it matter?
- It is the amount of oligo that gives an absorbance of 1 in a 1 cm cuvette. Synthesis is billed and shipped by OD, so the OD-to-nanomole conversion tells you how much material is actually in the tube.
- Why does the resuspension volume differ between primers?
- Because the extinction coefficient depends on the sequence. A G-rich oligo absorbs more per mole than a T-rich one of the same length, so the same 1 OD contains fewer nanomoles and needs less water to reach 100 µM.
- Should I use the single-stranded or double-stranded values?
- Use single-stranded for the primers you order — they arrive as single strands. The double-stranded figures matter when the oligo is already annealed into a duplex, such as a hairpin or a double-stranded adaptor.