Circular dichroism spectroscopy (CD) actually measures the difference between the absorption of left and right circularly polarized light of any optically active chiral molecules. CD spectroscopy is very important for proteins to study about their secondary structure. But why CD spectroscopy is important for DNA?
Typical B-form signature is a positive band around 275nm, negative band around 240 and crossover somewhere around 258. This positive/negative band is reported to result from degenerate exciton interaction among the stacked bases at the standard absorption band.
While CD has made considerable contributions to protein structure, the CD spectra of DNA is considerably more complicated. A fundamental reason is that (unlike the situation for proteins) the spectrum is sequence- and composition-dependent. Still the technique is sensitive to structural changes of a given sequence.
While it may be a little old now and ridiculously expensive, the book "Circular Dichroism: principles and applications" (ISBN-13: 978-0471330035) has a number of good examples of applications of CD to understanding nucleic acid structure.
Hi Debasish,
Another useful text is
"Circular Dichroism and the Conformational Analysis of Biomolecules" edited by Gerald D. Fasman.
One Chapter you will find particularly useful is "Determination of Nucleic Acid Conformation by Electronic CD" by W. Curtis Johnson.
Best,
John
Thank you very much Mr. Berndt and Mr. Hansen. I don't have the book "Circular Dichroism and the Conformational Analysis of Biomolecules" by Gerald D. Fasman. But I have the another one, "Circular Dichroism: principles and applications" (2nd edition) by Berova, Nakanishi & Woody. This is very nice book also.
As per I understand with the help of your reference and some other excellent paper:
The CD spectroscopy actually determines the asymmetry in a system. The CD spectrum for a solution of DNA molecules is sensitively dependent upon both the sequence and the conformation of the DNA. The CD of a DNA is highly diagnostic of its secondary structure. The purine and pyrimidine bases of DNA are largely responsible for the CD spectra of nucleic acids. The sugar and phosphate groups do not absorb significantly in this region. The types of spectra clearly demonstrate the different ion binding modes on DNA. There are three bands exist in CD spectra located at 220 nm (positive), 245 nm (negative) and 275 nm (positive). The B-DNA conformation, the most frequent conformation found in aqueous solution has a positive CD band near 275 nm due to base stacking and a negative band of similar magnitude near 245 nm due to the polynucleotide helicity. Typical this positive band around 275nm, and negative band around 245 and crossover somewhere around 258 is the signature of the B-form DNA. This positive/negative band are the result from degenerate exciton interaction (Although this is not clear to me) among the stacked bases at the standard absorption band. From the standpoint of CD, their main function is maintaining the relative geometries of the bases.
I am confused about that the peak of DNA UV-absorption band is at 260 nm, but in CD the peak shifted to 275 nm. Why? If this is due to cotton effect then what is actually mean by cotton effect (any reference )?
The description of the source of the CD bands I gave above is purely qualitative. It is not intuitive (at least not to me). The books that @John and I mentioned describe quantum mechanical calculations using magnetic and electronic transition dipoles.
Why the difference in maximuma/mininuma in CD versus isotropic absorbance? Recall that CD is caused by the difference in extinction coefficients of a chromophore for left and right polarized light (el - er). Therefore CD effects can only occur where there is (regular) isotropic absorbance. However the magnitude of the CD effect can be very different compared to isotropic absorbance (el + er) and hence the maxima and minima will likely be different.
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