A method has been developed to solve structures of DNA oligomers in solution from the experimental NOE data. The method is a combination of two approaches: (1) full matrix NOESY simulations and (2) conformational calculations of DNA double helix based on generalized helical parameters. The process of the refinement of a solution structure does not involve NMR-derived interproton distance constraints; rather it consists of a direct fitting of a structure to the experimental NOE data, a weighted sum of energy, and R factor being under minimization. A helical parameters-based generation of DNA forms makes it possible to organize the search for the optimal structure more effectively, systematically varying starting conformations. The method has been used to calculate a structure for the self-complementary DNA hexamer GGATCC, which is consistent with the available experimental data. The structure belongs to the B family of forms, although the local structural heterogeneity is very strong. Sugar puckers vary from O4'-exo to C3'-exo; helical steps are open with different magnitudes toward the minor groove. Next, we have addressed the question of how uniquely the structure is defined by the existing NMR data. Different structural parameters have been systematically varied, and their effect on individual NOE's and the R factor has been studied. Two energetically conjugated parameters, sugar puckers and glycosidic angles, can be determined very reliably, because of the strong dependences of the intraresidue H6/H8 to H2'/H2''/H3' NOE's. In contrast, the local helical conformation of DNA and the geometry of base pairs proved to be underdetermined by the existing NOE information, because the effect of any helical parameter on interproton distances can be compensated by the concerted changes in other parameters.

Extensive studies using one- and two-dimensional 1H NMR at 500 MHz revealed that the oligonucleotide d(CGCCGCAGC) in solution at 5 degrees C forms a double helix under conditions of high salt (500 mM in NaCl, 1 mM sodium phosphate), low pH (pH 4.5), and high DNA concentration (4 mM in duplex). The presence of very strong nuclear Overhauser effects (NOEs) from base H8/H6 to sugar H2',H2" and the absence of NOE from base H8/H6 to sugar H3' suggested that the oligomer under these solution conditions forms a right-handed B-DNA double helix. The following lines of experimental evidence were used to conclude that C4 and A7 form an integral part of the duplex: (i) the presence of a NOESY cross-peak involving H8 of A7 and H8 of G8, (ii) the presence of a two-dimensional NOE (NOESY) cross-peak between H6 of C3 and H6 of C4, (iii) base protons belonging to C4 and A7 forming a part of the H8/H6---H1' cross-connectivity route, and (iv) the pattern of H8/H6---H2',H2" NOESY cross-connectivity based upon a B-DNA model requiring that both C4 and A7 form an integral part of the duplex. The possibility of an A-C pair involving H bonds was also examined. Two possible structural models of the duplex at pH 4.5 are proposed: in one model A-C pairing involves two H bonds, and in the other A-C pairing involves a single H bond.

Intrinsic DNA bending is caused by specific DNA sequences. The decamer d(GA4T4C)2, when it repeats in a synthetic polymer or in kinetoplast DNA, results in a macroscopic bending of the molecule as a whole. We employed high-resolution two-dimensional NMR methods to examine the intrinsic structural properties of the d(GA4T4C)2 duplex in solution. Examination of the NOESY data at 50- and 100-ms mixing times indicated that the kinds of observed NOEs can originate if each of the ten nucleotidyl residues belongs to the B-DNA family, i.e., C2'-endo,anti. However, the degree of observed NOE intensities from the A-T junction as well as the observed AH2-AH2 cross-peaks from adjacent AT pairs could not be rationalized on the basis of a straight B-DNA model but could be explained by only a B-DNA model with some structural discontinuity at the A-T junction--the site of 2-fold symmetry in the molecule. In view of the fact that the degree of observed NOE intensities can be complicated by spin diffusion and by fine structural distortion, we have resorted to the use of quantitative theoretical NOESY simulation (which takes into account primary, secondary, and higher orders of NOE) to delineate the structural discontinuity at the A-T junction and to arrive at a structure for the duplex d(GA4T4C)2. We propose a "junction B-DNA model" which can quantitatively explain the 2D NOESY data at 100- and 50-ms mixing times. In this model the two structural blocks in the molecule, i.e., d(GA4).d(T4C) and d(T4C).d(GA4), are conformationally equivalent and are connected at the A-T junction where the base pairs are stably stacked, but the two local structural frames do not coincide in space. This model can create an overall bending of 10 degrees with a center of curvature 50 A away from the center of the duplex. It is the thesis of this paper that the observed bending in polymers with a repeat of d(GA4T4C)2 and the bending in natural DNAs where AnTn.AnTn repeats are present originate at the oligonucleotide repeat level.

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A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz 1H NMR studies in H2O and D2O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2", it was concluded that in d(CGCCGCAGC) and d(CGCCGTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins.

Magnetic shielding constants were calculated for the synthetic deoxyribonucleic acid (DNA) double helix poly(dG-dC).poly(dG-dC) from the x, y, and z coordinates of Z-DNA of Rich and co-workers [Wang, A. H-J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G., & Rich, A. (1979) Nature (London) 282, 680-686)] and B-DNA of Arnott & Hukins [Arnott, S., & Hukins, D. W. L. (1972) Biochem. Biophys. Res. Commun. 47, 1504-1509], taking into account the contribution to shielding from ring current effects and effects from the diamagnetic and paramagnetic components of the atomic magnetic anisotropy. Comparison of the calculated shielding values with the experimentally observed nuclear magnetic resonance shift data for poly(dG-dC).poly(dG-dC) in high salt solution shows striking agreement for Z-DNA and considerable deviation for B-DNA, indicating that this synthetic DNA double helix is high salt solution can assume the spatial configuration of the left-handed Z-DNA double helix known to occur in crystals.

It is very well documented that the presence of an An.Tn tract causes intrinsic DNA bending. Hagerman demonstrated that the sequence in which the An.Tn tracts are joined plays a very crucial role in determining DNA bending. For example, Hagerman showed that the polymer with a repeat of d(GA4T4C)n greater than or equal to 10 is bent but the polymer with a repeat of d(GT4A4C)n greater than or equal to 10 is not bent [Hagerman, P. J. (1986) Nature (London) 326, 720-722]. Earlier we have shown that the decamer repeat d(GA4T4C)2 is itself bent with a finite structural discontinuity at the A----T sequence [Sarma, M. H., Gupta, G., & Sarma, R. H. (1988) Biochemistry 27, 3423-3432]. In the present article, we summarize our studies on the decamer repeat d(GT4A4C)2 structure in solution. By employment of 1D and 2D 1H NMR studies at 500 MHz a complete sequential assignment has been made for the exchangeable and nonexchangeable protons belonging to the ten nucleotides. NOESY data were collected for d(GT4A4C)2 at 17 degrees C in D2O for three mixing times, 150, 100, and 50 ms. A quantitative NOESY simulation technique was employed to arrive at a structural model of d(GT4A4C)2 in solution. Our detailed analyses revealed the following structural features: (i) The duplex adopts the gross morphology of a B-DNA. (ii) All the A.T pairs are propeller twisted (less than or equal to -15 degrees). (iii) Although both A and T nucleotides belong to the C2'-endo,anticonformational domain, there is a mild variation in the actual conformation of the A and T residues. (iv) Even though there is a subtle conformational difference in the A and T nucleotides, two structural frames of T4.A4 segments are joined at the T----A sequence in such a way that there is no finite discontinuity at the junction; i.e., two neighboring frames exactly coincide at the T----A junction. Thus, our studies on d(GA4T4C)2 (Sarma et al., 1988) and on d(GT4A4C)2 (this article) reveal the structural peculiarity of the An.Tn tract and the effect of A----T/T----A sequence in causing DNA bending.

Secondary structures of poly(dG).poly(dC) and poly(dG).poly(dm5C) in solution are determined by nuclear Overhauser effect (NOE) measurements on GH8-deuterated and -nondeuterated DNAs with low presaturation pulse lengths (10-25 ms) and low-power and prolonged accumulations in the range of 50,000-72,000 scans. Under these conditions, the NOE difference spectra were free from diffusion. Primary NOEs between base protons GH8/CH6 and sugar protons H1', H2'/H2'', and H3' suggest that in poly(dG).poly(dC) both guanine and cytosine nucleotides adopt a C3'-endo, low anti X = 200-220 degrees conformation. Computer modeling of the NOE data enable identification for the first time, in terms of the geometry of the nucleotide repeat, handedness, and helix geometry, of the structure of poly(dG).poly(dC) to be the A form, and the derived structure for the polymer duplex is very close to the single crystal structure of the double-helical d-GGGGCCCC [McCall, M., Brown, T., & Kennard, O. (1985) J. Mol. Biol. 183, 385-396]. Similar nuclear Overhauser effect data on poly(dG).poly(dm5C) revealed that G and m5C adopt a C2'endo, anti X = 240-260 degrees conformation, which indicates that this DNA exhibits the B form in solution. In summary, the results presented in this paper demonstrate that methylation of cytosines in poly(dG).poly(dC) causes A----B transition in the molecule.