Oligo Extinction Coefficient Calculator

Taken from: http://www.scripps.edu/mb/gottesfeld/ExtCoeff.html (website no longer active)

This form can be used in two different ways. You can either enter your sequence (lower/upper case, spaces OK) or enter the number of each nucleotide (in addition to the absorbance, pathlength*, sample volume of stock measured, total volume in cuvette*, and total volume of your stock). If you choose to enter the number of each nucleotide, be sure that the sequence textbox is empty (the 'Clear Form' button will ensure this). Also, make sure to choose whether your oligo is DNA (the default) or RNA. Finally, the date does not appear upon loading, however it will show up once you click the 'Calculate' button.

*Defaults have been set for these values, but they can be changed.

DNA RNA Date:
Name of Oligo:
Sequence:
Absorbance at 260 nm: Pathlength* (cm):
Volume of stock measured (uL): Total volume in cuvette* (uL):
Total stock volume (uL):
Number of As: Number of Cs: Number of Gs: Number of Ts:
Number of Us:   
Total oligo length:
Total oligo mass (Da):
Millimolar extinction coefficient§ (mM-1 cm-1):
Stock Concentration (uM or pmol uL-1):
Total pmols in stock:
Total mass in stock (ug):
Tm of DNA oligo (°C):


§Extinction coefficients for individual NMPs are based on:
A = 15.4 mM-1 cm-1
C = 7.4 mM-1 cm-1
G = 11.8 mM-1 cm-1
T = 9.6 mM-1 cm-1
U = 9.9 mM-1 cm-1

Tm calculation for DNA oligo is based on the following equation: Tm = 81.5° + 0.41°(%GC) - 675°/length of oligo

 

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