Conformational Characteristics of the Trinucleoside Diphosphate dApdApdA and Its Constituents from Nuclear Magnetic Resonance and Circular Dichroism Studies

Abstract

Proton NMR studies at 360 MHz were carried out on the trinucleoside diphosphate dApdApdA, the dinucleoside monophosphate dApdA and the methylphosphate esters of the monomers pdA, pdAp and dAp. The compounds were also investigated by means of circular dichroism at varying temperatures. Complete NM R spectral assignments are given. The thermodynamics of stacking derived from the circular dichroic spectra was used to extrapolate the observed coupling constants, measured at a range of temperatures, to values appropriate to the pure stacked states of the dimer and the trimer.The data were interpreted in terms of the N and S deoxyribose pseudorotational ranges [Altona, C. and Sundaralingam, M. (1972) J . Am. Clzem. Soc. 94,8205 -82121 and it is shown that the right-handed single helix of the trimer occurs in two distinct forms : the major one corresponds to a B-DNA-like structure, S-S-S ; the minor one (30 '%;) has the sugar rings in a hitherto unsuspected S-S-N conformational sequence. The dimer behaves quite similarly, a mixture of 70% S-S and 30% S-N stacks being indicated. The detailed geometry of the S-type sugar rings is not invariable but appears to undergo a slight shift when another base stacks on top of a given nucleotide unit. The backbone angles of the fully stacked B-DNA-like single helix in solution are (starting the notation at P) /3 = 187", y = 50°, 6 = 138", E = 186".

Circular Dichroism Study of Stacking Properties of Oligodeoxyadenylates and Polydeoxyadenylate

“…Furthermore, the detailed geometry of the S-type sugar rings appears to undergo a shift when another A residue stacks on top of a given nucleotide unit [7]. The NMR results are summarized in Table 1.…”

“…Indeed, without the aid of this vital piece of information the present analysis would not have been feasible. In short, our NMR study [7] showed conclusively that all residues in the fully stacked right-handed (dA),, single helix adopt a B-DNA-like geometry, except the final pdA unit, which still possesses two conformational degrees of freedom. It is well known [29] that the €3-DNA genus of geometries (B, C, D-DNA) displays a single outstanding common feature, i.e.…”

“…As it turns out, our parallel NMR investigation of the conformational characteristics of stacked (dA)1, (dA)3 and higher oligomers [7] brought to light an unexpected conformational property common to all members of the (dA)n series. Indeed, without the aid of this vital piece of information the present analysis would not have been feasible.…”

“…Evidently, the dimer consists of a mixture of S-S and S-N stacked conformers; in the trimer the dA(1) -pdA(2) part is completely S-S stacked whereas the 3'-OH terminal sugar ring retains conformational freedom (about 70% S, 30% N); the population distribution of S and N conformers of the terminal residue appears to be unaffected with respect to the monomer (Me)pdA (69% S at 25 "C). In addition, from a preliminary investigation of the H-1' ribose region of the 360-MHz NMR spectrum of (dA)s it was concluded that the nonamer is appropriately described as a 70:30 mixture of stacked (S)s-S and (S)s-N forins [7]. Extending these results to intermediate and longer sequences, it is obvious that on increasing the (dA),, chain length the relative amount of S-S stacking will increase at the expense of the terminal S-N stack and therefore the percentage of S-S stacked states averaged over the number of stacking interactions ( n -1) present in an oligomer ( n residues) increases with increasing chain length.…”

“…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 journal [7].Ahb~ti~iutions. CD, circular dichroism; ORD, optical rotatory dispersion; NMR, nuclear magnetic resonance; abbreviations for polynucleotides follow IUB/TUPAC Recommendations [see Eur.…”