Circular Dichroism Study of Stacking Properties of Oligodeoxyadenylates and Polydeoxyadenylate

Abstract

The temperature dependence of the circular dichroism (CD) spectra of a series of deoxyadenylates (dA),,, n = 2, 3, 6, 9, 12, cxi, 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 N M R studies on (dA)2 and (dA)3 Biochmz. 112, 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'-enrb) 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'-deoxyadenosine 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 C D spectra of (dA),, n = 3, 6, 9, 12, from those of the dimer and the polymer; (b) the separation of the weak C D displayed by the regular S-S stacking mode and the far stronger C D exhibited by the 3'-end S-N stacking (the latter C D 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) whercas AH" and AS" show a slight increase in absolute values on increasing n from 2 to x 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 C D 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.The correlation between the mode of pucker of the ribose (or deoxyribose) ring, the phosphate diester backbone conformation and vertical base-base stacking in oligonucleotides to form a specific type of single helix has been the subject of several studies conducted in our laboratory [l-91. We now present a conformational study of a series of oligodeoxyadenosine nucleotides (dA),, n = 2, 3, 6, 9, 12, a, (cf. Fig. 1) carried out by means of temperature-dependent circular dichroism. The reasons for this study are manifold; however, three main objectives may be discerned: (a) the need for a quantitative insight into the thermodynamics of stacking of single helices; (b) to find an explanation for the curious C D spectral properties displayed by poly(dA) at neutral pH, which in no way resembles that of the dimer (dA)2; (c) to explore a possible correlation between the C D properties and the unexpected conformational behaviour of (dA)z and (dAh recently discovered by means of NMR spectroscopy [7]. It was discovered that these three objectives This paper is part XVII in the series on Nucleic Acid Constituents from this laboratory; part XVI appeared earlier in this j...

Single-stranded nucleic acid-induced helical self-assembly of alkynylplatinum(II) terpyridyl complexes

“…We also observe that concomitant with the remarkable UVvis absorption changes, for poly(dT) 25 , poly(dC) 25 , and poly(dG) 25 , upon mixing of the platinum(II) complexes and the oligonucleotides together, new emission bands at Ϸ800 nm appear. Fig.…”

“…Depending on the sequence of the oligonucleotide, the intensity changes vary quite significantly. For poly(dT) 25 , new intense emission bands are observed at Ϸ760 nm and 782 nm for the mixtures with complexes 1 and 2, respectively. In contrast, very broad emission bands with no clear band maximum are observed for mixtures of complexes 1 and 2 with poly(dA) 25 ; the emission intensity is moderate for complex 1 and particularly weak for complex 2.…”

“…For poly(dT) 25 , new intense emission bands are observed at Ϸ760 nm and 782 nm for the mixtures with complexes 1 and 2, respectively. In contrast, very broad emission bands with no clear band maximum are observed for mixtures of complexes 1 and 2 with poly(dA) 25 ; the emission intensity is moderate for complex 1 and particularly weak for complex 2. For the mixtures of complexes 1 and 2 with poly(dC) 25 and poly(dG) 25 , new emission bands with band maximum at Ϸ800 nm and of moderate intensity are observed for both complexes.…”

“…Depending on the sequence of the oligonucleotide, the absorption changes vary quite significantly. Whereas, for poly(dT) 25 , new bands form at Ϸ544 nm and 581 nm for complexes 1 and 2, respectively, no new band formation occurs and only weak absorbance changes are observed for poly(dA) 25 . For poly(dC) 25 and poly(dG) 25 , new band formations for complexes 1 and 2 with moderate intensity are observed.…”

“…Fig. 2 Upper shows the UV-vis absorption spectra of complexes 1 and 2, and the corresponding spectral changes when mixed with various oligonucleotides, namely poly(dT) 25 , poly(dC) 25 , poly(dG) 25 , and poly(dA) 25 , respectively. In an aqueous solution with constant pH and ionic strength (5 mM Tris⅐HCl/10 mM NaCl, pH 7.5) at ambient temperature, remarkable absorption changes are observed.…”