Sauer:Nucleic acid quantitation

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(Making your own Extinction coefficients)
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ss RNA, Divide by 0.025.  There is no good way of calculating a value for folded RNA so see the next entry.
ss RNA, Divide by 0.025.  There is no good way of calculating a value for folded RNA so see the next entry.
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===Making your own Extinction coefficients===
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===Making your own RNA Extinction coefficients===
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I couldn't find extinction coefficient for individual ribosomal subunits, so I did the following.
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Use this reference for more info:  Cavaluzzi MJ, Borer PN. 2004.
 +
 
 +
I purified the subunits.  Then, I prepared several samples.  Each was diluted to the same extent in the final reaction.  One "Native" folded form that was in a translation buffer, one "dissociated" in Phosphate and EDTA, and one "hydrolysed" to get an accurate concentration measurement.
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The hydrolyzed sample was prepared by incubating 5 &mu;L of ribosome with 20 &mu;L of 1.0 N NaOH for 1 hour at 37 degrees.  Then I neutralized the sample with 20 &mu;L of 1.0 N HCl.  I Added 1 mL of 100 mM NaH<sub>X</sub>PO<sub>4</sub> at pH 7.0 with 1 mM EDTA.  (this is the same pH used by Cavaluzzi and Borer).
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Measure the absorbance of all three samples.  I did mine in triplicate and averaged the final values.
 +
 
 +
So, use the known extinction coefficients obtained by Cavaluzzi and Borer.  Use a word processor to determine the number of each nucleotide in your particular RNA and multiply by the extinction coefficient for that nucleotide.  Then sum the four values.  This will give a "formal" extinction coefficient for your RNA. 
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Ext. Coeffs at 260;
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pA = 15,020
 +
 
 +
pC = 7,070
 +
 
 +
pG = 12,808
 +
 
 +
pU = 9,660
 +
 
 +
 
 +
Using the observed A<sub>260</sub> for your fully hydrolyzed RNA sample, determine the concentration of your RNA.
 +
 
 +
Now, with that known concentration and the measured A<sub>260</sub> of the native and unfolded samples, generate extinction coefficients for these conditions.  In the future, you wont have to hydrolyze the samples, just dilute them in a buffer an measure.
 +
 
 +
I calculated the following:

Revision as of 18:07, 25 January 2007

SAUER LAB

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Extinction coefficient and Tm calculator

The originator actually mean "quantification" sorry.

Ambion has a good site that gives a variety of parameters for nucleotides and nucleic acids [1].

Contents

Intro

Lot's of ways. I like the spec.


Measuring nucleic acid concentration in a spectrophotometer

Pipette your nucleic acid sample into a cuvette and record an absorbance scan from 240-340 nm.

Most calculations are done from the Abs at 260 nm.

DNA

Divide the absorbance at 260 nm by 0.02 for dsDNA or 0.027 for ssDNA. This is the "concentration" in μg/mL. Actually, to get concentration, you have to know the length of your molecule and use the mass/volume to calculate a concentration.

RNA

ss RNA, Divide by 0.025. There is no good way of calculating a value for folded RNA so see the next entry.

Making your own RNA Extinction coefficients

I couldn't find extinction coefficient for individual ribosomal subunits, so I did the following.

Use this reference for more info: Cavaluzzi MJ, Borer PN. 2004.

I purified the subunits. Then, I prepared several samples. Each was diluted to the same extent in the final reaction. One "Native" folded form that was in a translation buffer, one "dissociated" in Phosphate and EDTA, and one "hydrolysed" to get an accurate concentration measurement.

The hydrolyzed sample was prepared by incubating 5 μL of ribosome with 20 μL of 1.0 N NaOH for 1 hour at 37 degrees. Then I neutralized the sample with 20 μL of 1.0 N HCl. I Added 1 mL of 100 mM NaHXPO4 at pH 7.0 with 1 mM EDTA. (this is the same pH used by Cavaluzzi and Borer).

Measure the absorbance of all three samples. I did mine in triplicate and averaged the final values.

So, use the known extinction coefficients obtained by Cavaluzzi and Borer. Use a word processor to determine the number of each nucleotide in your particular RNA and multiply by the extinction coefficient for that nucleotide. Then sum the four values. This will give a "formal" extinction coefficient for your RNA.

Ext. Coeffs at 260;

pA = 15,020

pC = 7,070

pG = 12,808

pU = 9,660


Using the observed A260 for your fully hydrolyzed RNA sample, determine the concentration of your RNA.

Now, with that known concentration and the measured A260 of the native and unfolded samples, generate extinction coefficients for these conditions. In the future, you wont have to hydrolyze the samples, just dilute them in a buffer an measure.

I calculated the following:

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