Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution

Abstract

NMR studies were carried out on samples of the non-self-complementary tetramers d(C-A-C-A), d(T-G-T-G) d(G-A-G-A) and d(T-C-T-C) and of 1 : 1 mixtures of the complementary tetramers d(C-A-C-A) .cntdot. d(T-G-T-G) and d(G-A-G-A) .cntdot. d(T-C-T-C) at two DNA concentrations and of the self-complementary octamers d(C-A-C-A-T-G-T-G) and d(G-A-G-A-T-C-T-C). Assignments, based upon one-dimensional NOE and homonuclear-decoupling and two-dimensional correlated and NOE spectroscopies are given of the resonances of most of the base and sugar protons. Chemical shift vs. temperature profiles, constructed for all samples, yielded insight into the temperature- and concentration-dependent conformational behaviour of the compounds and were used to obtain thermodynamic parameters pertaining to the stacked-single-strand .dblarw. random-coil and duplex .dblarw. random-coil equilibria. Vicinal proton-proton couplings were analysed in terms of the conformation of the deoxyribose rings in the single-stranded tetramers and duplexed octamers. The NOE patterns, chemical shift profiles, imino-proton resonances and coupling data revealed that the compounds adopt B-DNA-like structures. The ratio duplexed/stacked-single-strand/random coil depends upon external conditions as well as upon base sequence. The thermodynamic data indicate that: (a) in terms of single-helical stacking, the R-R steps (Tm 321-328 K) appear more stable than the Y-R or R-Y steps (Tm 308-316 K) and the Y-Y steps score least (Tm 290-300 K), and (b) the duplexes consisting of alternating, d(Y-R)n, strands are more stable, in terms of .delta.H.degree., compared to the d(R-R)n .cntdot. d(Y-Y)n duplexes. The analyses of the couplings demonstrated that the sugars of the single-stranded tetramers and duplexed octamers occur as a blend of N- and S-type conformers, with a preference for the S-type (C2''-endo)sugar conformation: upon duplex formation, no significant shift in the N-type/S-type ratio was observed. The fraction S-type sugar conformation of a given residue, %S, in the stacked-single strands was found to depend upon the nature of its own base and that of the adjacent residues: sugars in an R-R stretch display high values of %S (90-100), whereas those in Y-Y stretches show relatively low values (.apprxeq. 65). It appears that a good stacking interaction between bases goes hand-in-hand with high values of %S. The geometry of the S-type sugars, and thus of backbone angle .delta.s, in the single-stranded tetramers displays a base-sequence-dependent variation. The observed variation of .delta.s agrees qualitatively with the one predicted from the base sequence via the .SIGMA..delta.-sum function [Mellema, J.-R., Pieters, J. M. L., van der Marel, G. A., van Boom, J. H. and Altona, C, (1984) Eur. J. Biochem. 143, 285-301]. An enhanced variation of .delta.s was found for the residues in the duplex of d(C-A-C-A-T-G-T-G)2. Comparison of the .delta.s values observed for residues of d(C-A-C-A-T-G-T-G)2 and for corresponding residues of the tetramers revealed that the values of .delta.s for pyrimidine residues decrease sharply, whereas those of the purine residues show little change upon duplex formation. This finding is taken to indicate that the sugar rings of the pyrimidine residues, relative to those of the purine residues, have a greater capacity to assimilate structural changes associated with duplex formation of this octamer. The observed variation of .delta.s in the single-stranded tetramers and in d(C-A-C-A-T-G-T-G)2 are compared with those predicted from the base sequence via the .SIGMA..delta. and the .SIGMA.3 sum functions.