If you are reading this, you probably have already recorded a good CD spectrum and you may have a rough idea of the secondary structure of a protein or of a RNA; however, now you would like to obtain some more detailed information.
In the following paragraphs, you will find some help to do so (non-Jasco users must correct the protocol).
Simple data normalization.
As you will see, the process of CD spectra deconvolution involves the comparison of your actual CD spectrum with a reference set of spectra, either calculated or experimental.
This means that you should normalize your data to make them comparable to other data.
In particular, you want to get rid of effects from:
a) the buffer effects;
b) the sample concentration;
c) the cuvette path length;
d) the sequence length.
To correct for buffer effects, open the Standard Analysis component of the Jasco software (or its equivalent if you are working with a different instrument) and load the sample and the buffer spectra (measured in identical conditions). Go to the "Mathematics" menu and select the "Arithmetics w. Spectrum" option. Select the sample spectrum as Spectrum1 and the buffer spectrum as Spectrum2. Specify the subtraction sign and then press "OK". The corrected spectrum should appear.
As you can see in the What is Circular Dichroism ? section of this tutorial, to correct for sample concentration and cuvette path length you must transform your data either in molar ellipticity or molar CD.
Depending on the particular software you want to use for the deconvolution (see table III for details) you should choose one of the two measurement units. To do the transformation, go again to the "Mathematics" menu and choose the "Optical constant" option. Select the buffer-subtracted spectrum and then (if not already present in the box) specify the cuvette pat length and the sample concentration. Select the appropriate measurement unit and then press "OK".
The last thing to do is to normalize for the sequence length. To compare a protein of 50 A.A. with one of 300, or a DNA of 12bp with one of 30, you must divide your spectrum for the number of residues in your molecule. Go again to the "Mathematics" menu and select the "Arithmetic w. Constant" option. Select the spectrum normalized for concentration and then select the division sign. Specify in the constant box the number of residues in your molecule (the number of A.A. or the number of bases in an oligonucleotide or the number of the CD contributing chromophores in any other class of compounds) and then press "OK".
Save the residue mean molar ellipticity (or CD) spectrum you obtained and go on.