User manual

Section 3- Applications
To calculate the melting point of a DNA sequence:
1. Enter the base sequence as described above. 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 can 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 can 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 can be changed to a value more appropriate for the sample.
Melting Point analysis result fields include:
• Salt-Adjusted - calculates the melting point of the base sequence without accounting for the effect of
interaction between neighboring bases.
• Nearest-Neighbor - displays the melting point of the base sequence when the effect of interaction between
neighboring bases is taken into account.
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