User manual

Section 3- Applications
After the measurement:
- Simply wipe the upper and lower pedestals using a dry laboratory wipe and the instrument is ready to
measure the next sample.
- When using the cuvette option, remove the cuvette, rinse thoroughly and dry between samples.
Oligo Calc
Oligo Calc is used to calculate molecular weights, extinction coefficients, concentration factors and melting points
for specific nucleic acid sequences. Selecting this Task bar will bring up two tabs:
• Oligo Calc - used to enter sequences of interest and select appropriate sample type variables.
• Melting Points - displays the calculated melting points of a DNA strand. This tab is available only for DNA
sequences.
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.
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