User manual

Section 3- Applications
To use the Oligo Calc:
1. Use one of the following options to enter in a base sequence:
- The buttons below the Base Sequence display.
- The keyboard. (Only the A, C, G, T, and U keys will work to enter bases.)
- Copy and paste a base sequence into the display from another application. (Only the letters A, C, G, T,
and U can be pasted into the Base Sequence display.)
- To clear the Base Sequence display, click Clear to the right of the display. Individual bases can only be
manually deleted.
2. Select degree of phosphorylation, if applicable: Mono-phosphate for DNA, mono or tri-phosphate for RNA.
3. Select Double-Stranded if applicable. The complementary base sequence will be included in the analysis.
4. From the drop down list, select the type of nucleic acid to be analyzed. The default is DNA.
5. For additions to the base sequence select Modification and enter the molecular weight associated with the
addition.
Oligo Calc analysis result fields include:
• Molecular Weight- displays calculated base sequence molecular weight.
• Extinction Coefficient- displays the 260 nm wavelength-dependent extinction coefficient in ng-cm/µL.
• Concentration Factor- the constant, based on the extinction coefficient that is used to calculate the
concentration of the base sequence.
• Number of bases- displays how many bases have been entered.
• % GC- shows the percentage of the total number of bases made up by guanine and cytosine.
To calculate the melting point of a DNA sequence:
1. Enter the base sequence as described above.
Note: If a base sequence has already been entered in the Oligo Calc Tab, then the base sequence box
in the Melting Points Tab will be auto-populated with that sequence.
2. Enter the appropriate values in the each of the boxes as described below:
- Oligo Molarity- enters the oligo molarity of the sample. A default value of 10 uM is displayed, but may be
changed to a value more appropriate for the sample.
- Cation Molarity- enters the concentration of cations in the sample. A default value of 50 mM is displayed,
but may be changed to a value more appropriate for the sample.
- % Formamide - enters the percentage concentration of formamide in the sample. A default value of 0.00
% is displayed, but may be changed to a value more appropriate for the sample.
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