Tools

Oligo properties

Nucleotide sequence


Temperature (Celcius)
Salt concentration (M)
Primer concentration (M)

Result

Paste the oligo sequence in the field on the left and press Calculate.


Information

Oligos, or primers, are primarily used for polymerase chain reaction (PCR) to amplify specific DNA fragments; however, to be of any use and also to be efficient, primers have to fulfill a number of criteria. The "Oligo Properties" function presented here is able to calculate the sequence properties of a DNA oligonucleotide to optimize your primer design. This tool will calculates GC percentage, molecular weight, melting temperature (Tm), thermodynamics, and all possible primer dimers and hairpins of a single oligo. In-Silico Online also allows for the usage of ambiguous nucleotides "N" and will consequently calculate the uncertainty of each property expressed as delta, considering any potential nucleotide (A, T, G, or C).


References

  1. Marmur J, JMB 5:109-118 (1962)
  2. Howley PM, Journal of Biological Chemistry, 254(11):4876-4883 (1979)
  3. Breslauer KJ, PNAS 83:3746-3750 (1986)
  4. SantaLucia J, Biochemistry 35:3555-3562 (1996)
  5. SantaLucia J, PNAS 95:1460-1465 (1998)
  6. Sugimoto N, Nucleic Acids Research 24(22):4501-4505 (1996)