Circular Dichroism Study of Stacking Properties of Oligodeoxyadenylates and Polydeoxyadenylate

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Abstract
The temperature dependence of the circular dichroism (CD) spectra of a series of deoxyadenylates (dA)n, n= 2, 3, 6, 9, 12, ∞, in aqueous solution was studied. The data were interpreted on the basis of a new conformational model for the stacked state suggested by our previous proton NMR studies on (dA)2 and (dA)3 [C. S. M. Olsthoorn, L. J. Bostelaar, J. H. van Boom & C. Altona (1980) Eur. J. Biochem. 112, 95–110]. In this model the stacked regions of the single-stranded oligomers consist of residues taking up a geometry resembling that of the B-DNA genus of structures (all sugars S or C2′-endo) except those residues at the 3′ end that do not ‘feel’ a following stacking interaction. The deoxyribose rings in the latter residues retain (or regain when melting out removes a stacking interaction somewhere along the chain) the conformational freedom (S ⇄ N, N = C3′-endo) that these rings possess in the monomers 2′-deoxvadenosine 5′-methylphosphate or in 2′-deoxyadenosine 3′,5′-bis(methylphosphate). as the case may be. It is shown that this model allows (a) construction of the CD spectra of (dA)n, n= 3. 6. 9, 12. from those of the dimer and the polymer; (b) the separation of the weak CD displayed by the regular S-S stacking mode and the far stronger CD exhibited by the 3′-end S-N stacking (the latter CD resembles that of the A-DNA genus of structures); (c) delineation of the thermodynamics of stacking. The melting temperature remains constant and independent of chain length (about 50° C whereas ΔH0 and ΔS0 show a slight increase in absolute values on increasing n from 2 to ∞ owing to small cooperativity effects. Near 0° C the dimer occurs for about 90% in the stacked form, the oligomers attain even higher conformational purities. It is suggested that premelting phenomena observed in the CD spectra of double-helical DNAs may also involve local transitions from the normal B-like—-S-S-S—-stacking mode to an A-like—-S-S-N—-stacking geometry.