The applicability of NMR methods to solution structure of nucleic acids

Study by (23)Na-NMR, (1)H-NMR, and ultraviolet spectroscopy of the thermal stability of an 11-basepair oligonucleotide

23Na-NMR, (1)H-NMR, and ultraviolet (UV) spectroscopy have been used to study the thermal stability of the double helix structure of an 11-basepair oligonucleotide. The denaturation curves obtained by (23)Na-NMR and UV are analyzed using a two-state model. The melting temperature and DeltaH(0) obtained are identical within experimental error, suggesting that modifications in the ionic atmosphere, probed by (23)Na-NMR, and the modifications in the basepair stacking, probed by UV, occur at the same temperature. Additional dynamical information on the denaturation process has been obtained by (1)H-NMR: slow exchange is observed between the thymine methyl resonances, and the disappearance of imino protons shows that a single basepair opening does not contribute significantly to proton exchange.

The intrinsic curvature of a 51 bp K-DNA fragment of Leishmania tarentolae: a molecular model

DNA intrinsic structure and curvature is a subject of debate because of the importance of these attributes in processes such as DNA packaging, transcription, and gene regulation. X-ray crystallography of DNA single crystals has provided a wealth of information about the local, short range conformational features of DNA. On the other hand, gel electrophoresis analysis of DNA has not only uncovered the macroscopic curvature of DNA but it also provides most of the available data on DNA intrinsic curvature. However, gel electrophoresis can not identify features of DNA structure at the nucleotide or atomic level. In order to address the problem of DNA intrinsic curvature in an attempt to bridge the gap between X-ray crystallography and gel electrophoresis, we use the computational method of molecular dynamics (MD). In this study, we report the results of 2.0 ns MD simulations on a 51 bp fragment of the K-DNA of Leishmania tarentolae containing several A-tracts. The K-DNA double helix is very stable and remains in an intermediate state between the canonical A and B forms of the duplex. The magnitude of global curvature (75 degrees) agrees well with the experimental estimate (72 degrees) available. Analysis of local (every base triplet) and sublocal (every helix turn) curvature shows that the 51 bp K-DNA fragment has curvature features also present in the Wedge, Junction and Calladine's models of DNA intrinsic curvature. We further characterize the flexibility of individual nucleotides in the molecule and find the sugar flexibility within the A-tracts to be strongly correlated with the pattern of A-tract cleavage by the hydroxyl radical. Differential curvature and flexibility at the 5' and 3'junctions between A-tracts and general-sequence DNA are found to modulate the global curvature of the K-DNA fragment.

The secondary structure of a fourteen-nucleotide fragment of the hairpin ribozyme

A fourteen nucleotide RNA has been synthesized and its secondary structure investigated by non-denaturing polyacrylamide gel electrophoresis and 1H nuclear magnetic resonance spectroscopy. This fourteen nucleotide RNA corresponds to the hairpin loop end of the proposed secondary structure of the (-)sTRSV hairpin ribozyme. Non-denaturing polyacrylamide gel electrophoresis indicates that the fourteen nucleotide RNA exists predominantly as a monomer at a 1 mM strand concentration. Four peaks are found in the imino hydrogen region of the 1H NMR spectrum of the fourteen nucleotide RNA at this concentration. One-dimensional nuclear Overhauser effect spectroscopy of the imino hydrogen region of the 1H NMR spectrum gives results consistent with a model of the secondary structure of the fourteen nucleotide RNA having a three nucleotide hairpin loop and two double-stranded stems separated by a single bulged adenosine.

NMR studies and restrained-molecular-dynamics calculations of a long A+T-rich stretch in DNA. Effects of phosphate charge and solvent approximations

The nonamer duplex d(GCAAAAACG).d(CGTTTTTGC) was studied by 1H-NMR at 500 MHz. With the exception of the H5' and H5" sugar protons, all protons were assigned by two-dimensional NMR experiments [NOE spectroscopy (NOESY), double-quantum-filtered J-correlated spectroscopy (DQF-COSY) and total correlation spectroscopy (TOCSY)]. The exchange kinetics of the imino protons of the Watson-Crick base pairing were studied at 15 degrees C by measuring inversion-recovery rates under conditions of extensive ammonia base catalysis. Extrapolation to infinite base concentration gave anomalous long lifetimes for the A-tract in accordance with previous results [Leroy, J.-L., Charettier, E., Kochoyan, M. & Guéron, M. (1988) Biochemistry 27, 8894-8898]. On average, 11 NOESY distance constraints/nucleotide were evaluated using the complete relaxation matrix approach. Deoxyribose coupling constants were obtained from simulations of the DQF-COSY cross-peaks, assuming a rapid two-state equilibrium between a C2'-endo and C3'-endo conformer. The sugars were found to be predominantly in the C2'-endo conformation. The NMR-derived distance and torsion constraints were implemented into three different restrained-molecular-dynamics (rMD) protocols, two in vacuo, with different charges on the phosphate group and the third with the solvent explicitly included. All protocols displayed good convergence from different starting structures. The structures derived from the three protocols satisfied experimental restraints equally well and had similar final energies. Although the overall pattern of sequence dependence of helical parameters shows some resemblance in all structures, we find that the absolute amplitudes of the parameters are largely dependent on the rMD protocols, particularly the twist parameters. The minor groove distance P(n + 2)-P(m + 2) varies from 0.7 nm to 1.2 nm in the three protocols. Still the NOESY-derived anomalously short distances AH2(n)-H1'(m + 1) and AH2(n)-H1'(n + 1), n and m denote complementary residues, which are assumed to be indicative of a compressed minor groove, are kept in all calculated structures.

Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG)

We have presented a detailed analysis for structure determinations for the DNA duplex d(CGCAAAAATGCG) obtained from X-ray crystallography, nuclear magnetic resonance, and molecular dynamics simulation. Each of the structures for the duplex deviates from the structure of the canonical form of B-DNA in a number of observable characteristics. Specifically, the three determinations all contain DNA axis deflections at the junctions of the A-tract with the flanking sequences. The analysis provided shows that the general characteristics of the structures obtained for d(CGCAAAAATGCG) from X-ray, NMR, and MD methods turn out to be quite similar. The extent to which this result can be generalized remains to be established by consideration of similar cross-comparisons on diverse oligonucleotide structures.

Base dependence of B-DNA sugar conformation in solution and in the solid state

Analysis of 1H-NOESY solution data for eight short DNA duplexes has revealed pronounced differences between the sugar conformations of purine and pyrimidine nucleotides. It was found that the H1'-H4' interproton distance is less than ca. 3.0 A in pyrimidine sugars, while in purine sugars it is more than ca. 3.0A. This difference has been analyzed by comparison with the sugar conformations of highly resolved B-DNA crystal structures and model sugar conformations. The conclusion can be drawn that the deoxyribose conformation is of the general C2'-endo type but pyrimidine sugars are characterized by smaller phase angles of pseudorotation P (90 degrees < P < 150 degrees), while purine sugars have larger P values that are greater than ca. 140 degrees (140 degrees < P < 180 degrees). There is no such clear base dependence of sugar conformation in highly resolved B-DNA crystal structures; however the similar trend can be seen as in the solution studies. Based on B-type DNA crystal structures, J-coupling constants have been calculated, and the applicability of experimental coupling measurements to the determination of sugar conformation is discussed.