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Color Probe 1.0 --- Probe Fluorescent Labeling Calculator Beta           Click here for PCR primer design tools.
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Color Probe 1.0 --- Probe Fluorescent Labeling Calculator

How to use Color Probe 1.0 --- Probe Fluorescent Labeling Calculator (beta-testing)

Color Probe is designed for calculations of microarray direct-cDNA labeling, oligo fluorescent labeling, protein fluorescent labeling, and coupling of fluorescence dyes to antibodies.

Throughout the calculations, we assume the path length for all absorbance measurements is 1 cm.

  • Select your probe type (DNA, protein, or antibody) and fluorescent dye type (e.g., Cy3, FTIC).
  • Input your absorbance measurements at 260 nm for DNA or 280 nm for proteins. Input your absorbance measurements at the wavelength of your fluorescent dye's maximum absorption wavelength.
  • Input the total volume for your probes.
  • Input the amount of probe you would like to use in your experiments (Desired probe amount).


    There are two options:
    (1) Use the same amount of probe DNA/protein. For this option, simply enter the desired amount in pmol or mg in the probe type column (center).
    (2) Use the same number of fluorescent dyes. For this option, enter the desired amount for the fluresent dye (right column).

  • Click on "Calculate" to calculate. Results will be shown in the results window.

    For microarray experiments, it is suggested the following conditions being met:
    (1) Dye incorporation is greater than 15 pmol.
    (2) The number of labeled nucleotides per 1000 nucleotides is greater than 20.
    (3) 20 pmol of dye labels are used.

    For proteins, the extinction coefficient varies depending on a protein's amino acid compositions. For more information on how to calculate protein's extinction coefficient, please use BioToolKit.

    Extinction coefficients for the following dyes are included in Color Probe 1.0. For dyes that are not in the following list, please use the "Other" dye option and enter the extinction coefficient for your dye.

    fluorescent dyes and absorbance wavelengths (nm): 5-Fluorescein (FITC) A495, Alexa Fluor 350 A350, Alexa Fluor 405 A405, Alexa Fluor 430 A430, Alexa Fluor 488 A488, Alexa Fluor 532 A532, Alexa Fluor 546 A546, Alexa Fluor 555 A555, Alexa Fluor 568 A568, Alexa Fluor 594 A594, Alexa Fluor 633 A633, Alexa Fluor 647 A647, Alexa Fluor 660 A660, Alexa Fluor 680 A680, Alexa Fluor 700 A700, Alexa Fluor 750 A750, AMCA 353 A422, BODIPY 493 / 503 A493, BODIPY 507 / 545 A508, BODIPY 530 / 550 A535, BODIPY 558 / 568 A560, BODIPY 564 / 570 A563, BODIPY 576 / 589 A575, BODIPY 581 / 591 A581, BODIPY 630/650 A632, BODIPY 650/665 A651, BODIPY FL A504, BODIPY R6G A528, BODIPY TMR A535, BODIPY TR A588, Carboxyfluorescein (FAM) A495, Cascade Blue 400 A420, Cy3 A550, Cy3.5 A588, Cy5 A650, Cy5.5 A675, FAR Blue A660, FAR-Fuchsia A567, FAR-Green One A800, FAR-Green Two A772, HEX A535, IRD700 A685, IRD800 A787, JOE A527, Marina Blue 365 A460, Oregon Green 488 A496, Oregon Green 500 A499, Oregon Green 514 A511, Oyster 556 A556, Oyster 645 A645, Oyster 656 A656, Pacific Blue 416 A451, Rhodamine Green A505, Rhodamine Red A505, ROX A576, TAMRA A544, TET A521, Tetramethylrhodamine A550, Texas Red A583, X-Rhodamine A575.

    Thanks for using Color Probe 1.0! Please let us know your suggestions and comments.

  • THIS SOFTWARE IS PROVIDED BY CHANG BIOSCIENCE ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CHANG BIOSCIENCE OR ITS SPONSORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


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