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| The oligo length. For unmodified oligos, this is equal to the number of bases in the sequence. For modifications, including 3’- and 5’-modifications, the software assumes these are bases, and are represented as such in the oligo size. This will be correct if the modifications are actually modified bases (for example, inosine, dU, etc.), and incorrect if the modification is not a modified base (for example, phosphate, amino linker, etc.). |
| The percentage of G+C in the oligo. The calculation is the total number of G and C divided by the total number of bases in the oligo. |
| The molecular weight of the oligonucleotide is equal to the sum of the molecular weights of the individual ribo/deoxyribonucleotides, plus any modifications, it is composed of. Please see our Physical Parameters Technical Sheet here for the table of molecular weights used by the software. |
| The Gene Link algorithm to calculate Tm is based on the salt-corrected nearest neighbor method (please see our Physical Parameters Technical Sheet here for the specific equations, details, and references). |
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The EC260, or e260, is called the
extinction coefficient (260 nm), and is defined as
the fraction of light of a given wavelength (l) lost to both
scattering and absorption per unit distance traveled in a specific medium (here,
a dilute aqueous solution of A260 = e260 x b x coligo where b = path length (the distance the light travels through the solution—typically 1 cm), coligo = concentration of the oligo in aqueous solution, and A260 = the absorbance of the DNA solution at a light wavelength of 260 nm. At Gene Link, e260 is in units of mM-1cm-1. For a path length of 1 cm, the concentration of oligo (in mM) in a solution can be determined by dividing A260 by e260. Please see our Physical Parameters Technical Sheet here for details of how Gene Link calculates EC260. |
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The concentration of the oligo in micrograms per A260 (OD) unit at 260 nm. The formula is |
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The concentration of the oligo in number of nanomoles
(10-9 mol) per A260 (OD) unit at
260 nmol. The formula is |