Section 6- MicroArray
Baseline Calculation & Normalization
The software normalizes the visual spectrum display for all readings at 750nm and will automatically calculate a baseline
between 400 and 750 nm for dye concentration calculations. The green vertical line on the screen represents the peak
wavelength position for Dye 1, and the red vertical line represents the peak wavelength position for Dye 2.
Unique Screen Features
Max Absorbance: used to rescale the upper limit of the vertical axis.
Sample Type: used to select the (color-keyed) type of nucleic acid being measured. The user can select ‘DNA-50’ for
dsDNA, ‘RNA-40’ for RNA, ssDNA-33’ for single-stranded DNA, or ‘Other’ for other nucleic acids. The default is ssDNA-
33’. If ‘other’ is selected, the user can select an analysis constant between 15-150. When navigating amongst the three
(3) general sample types within the Micro Array module, the last value of the constant entered within the ‘Constant’
Sample Type will be retained. See “Concentration Calculation (Beer’s Law)” in the appendix for more details on this
calculation.
λ and Abs Norm: the user selected wavelength (black cursor) and corresponding absorbance at the 1mm pathlength.
The wavelength can be selected by dragging the black cursor or using the up/down arrows in the wavelength box. Note:
The user-selected wavelength and absorbance at the 1 mm pathlength are not utilized in any calculations.
Dye 1 (or 2): user selected dye
Abs. Norm: normalized absorbance of selected Dye at the 1 mm pathlength.
pmol/ul: concentration based upon selected Dye’s extinction coefficient. See “Concentration Calculation (Beer’s
Law)” in the appendix for more details on this calculation.
ng/ul: concentration of nucleic acids in the sample calculated using the absorbance at 260 nm minus the absorbance at
340 nm (i.e. normalized at 340 nm) and the nucleic acid analysis constant. See “Concentration Calculation (Beer’s Law)”
in the appendix for more details on this calculation.
260/280: ratio of sample absorbance at 260 and 280 nm. The ratio of absorbance at 260 and 280 nm is used to assess
the purity of DNA and RNA. A ratio of ~1.8 is generally accepted as “pure” for DNA; a ratio of ~2.0 is generally accepted
as “pure” for RNA. If the ratio is appreciably lower in either case, it may indicate the presence of protein, phenol or other
contaminants that absorb strongly at or near 280 nm. See “260/280 Ratio’” section of the Troubleshooting section for
more details on factors that can affect this ratio.
6-2
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