UV spectroscopy of the DNA bases

The UV absorbance of nucleic acids from 200-300 nm is due exclusively to transitions of the planar purine and pyrimidine bases. The backbone begins to contribute at about 190 nm. The accessible region of the spectrum is therefore 

Rgure 18 Probable transition polarizations for UV transitions of guanine and cytosine. (Source Circular dichroism and linear dichroism, A. Rodger and B. Nord6n, 1997, by permission of Oxford University Press.) 

1 Empirical structural analysis of DNA CD The simplest application of CD to DNA structure analysis is to identify the polymorph in a sample (4). Since the DNA CD from 200-300 nm is due to the skewed orientation of the bases, if the DNA is untwisted or the bases are tilted, a change from what is observed for B-DNA would be expected in the CD spectrum. Somewhat surprisingly, observed CD spectra often vary more with changes in base orientation (DNA polymorph) than as a function of the base composition of the DNA, though they are of course a sensitive function of DNA sequence as well. 

Rgure 19 CD spectra of duplex DNAs (pH = 6.8, 5 mw NaCI, 1 mw cacodylate) of varying G-C base pair content Clostridium perfringens (26% GC), calf thymus (42% GC), Micrococcus lysodeikticus (72% GC), poly[d(G-C)]2 (100% GC). Also shown is Z-form poly[d(G-C)]2 (100% G-C, pH = 6.8, 5 mw NaCI, 1 mM cacodylate, 50 jjim [Co(NH3)e] ). The 195 nm negative signal of Z-DNA Is obscured by the CD induced into the transitions of [Co(NH3)f when this molecule Is used to induce Z-form DNA. (Source Circular dichroism and linear dichroism, A. Rodger and B. Nord6n, 1997, by permission of Oxford University Press.) 

Hgure 20 (a) Poly[d(A-T)]2 (44 p.M 1 mM phosphate) in B-form (20 mu NaCI) and condensed (1 M NaCI and 45% v/v ethanol), (b) Poly[d(G-C)]2 as a function of increasing spermine, [NH3(CH2)3NH2(CH2)4NH2(CH2)3NH3], concentration showing the B Z transition. Spermine concentrations are indicated in the figure. (Source Circular dichroism and linear dichroism, 

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