Phosphorus-31 nuclear magnetic resonance of double- and triple-helical nucleic acids. Phosphorus-31 chemical shifts as a probe of phosphorus-oxygen ester bond torsional angles

Random coil phosphorus chemical shift of deoxyribonucleic acids

Random coil phosphorus chemical shift has been studied using 16 17-nucleotide DNA sequences. Due to the presence of residual base stacking in these sequences, the temperature and sequence effects were investigated at 50 and 55 degrees C. The phosphorus chemical shifts of random coil DNA sequences have been found to be independent of temperature. Sequence effect analysis shows that the phosphorus chemical shift of a nucleotide in a random coil DNA sequence depends on both its 5'- and 3'-nearest neighbors. A trimer model has been used to establish the random coil 31P chemical shift prediction protocol which shows an accuracy of 0.02 ppm.

Evidence for similar structural changes on binding of platinum anti-tumor agents to DNA and nucleosomes

The influence of Pt(II) compounds on the 31P NMR spectra of natural DNA, synthetic polynucleotides, and nucleosomes was investigated. With Pt complexes which are anti-tumor agents, a new peak or shoulder centered at approximately 1.2 ppm downfield from the untreated DNA signal was observed. When Pt compounds known not to be anti-tumor agents were studied, no such new signal was observed. The most reasonable explanation for the downfield resonance is that it is a consequence of a structural change induced in the DNA by the anti-tumor agent. Since the effect of the Pt compounds on nucleosomes was similar, the same structural change is probably occurring in DNA in solution and in nucleosomes. A nonalternating dG . dC polymer, but not alternating G . C or any A . T polymers, exhibited a similar spectral change and this finding suggests that the structural change in the DNA arises primarily from reaction of Pt anti-tumor agents with adjacent G residues.

An A-type double helix of DNA having B-type puckering of the deoxyribose rings

DNA usually adopts structure B in aqueous solution, while structure A is preferred in mixtures of trifluoroethanol (TFE) with water. However, the octamer d(CCCCGGGG) and other d(C(n)G(n)) fragments of DNA provide CD spectra that suggest that the base-pairs are stacked in an A-like fashion even in aqueous solution. Yet, d(CCCCGGGG) undergoes a cooperative TFE-induced transition into structure A, indicating that an important part of the aqueous duplex retains structure B. NMR spectroscopy shows that puckering of the deoxyribose rings is of the B-type. Hence, combination of the information provided by CD spectroscopy and NMR spectroscopy suggests an unprecedented double helix of DNA in which A-like base stacking is combined with B-type puckering of the deoxyribose rings. In order to determine whether this combination is possible, we used molecular dynamics to simulate the duplex of d(CCCCGGGG). Remarkably, the simulations, completely unrestrained by the experimental data, provided a very stable double helix of DNA, exhibiting just the intermediate B/A features described above. The double helix contained well-stacked guanine bases but almost unstacked cytosine bases. This generated a hole in the double helix center, which is a property characteristic for A-DNA, but absent from B-DNA. The minor groove was narrow at the double helix ends but wide at the central CG step where the Watson-Crick base-pairs were buckled in opposite directions. The base-pairs stacked tightly at the ends but stacking was loose in the duplex center. The present double helix, in which A-like base stacking is combined with B-type sugar puckering, is relevant to replication and transcription because both of these phenomena involve a local B-to-A transition.

High-resolution NMR study of a synthetic oligoribonucleotide with a tetranucleotide GAGA loop that is a substrate for the cytotoxic protein, ricin

Ricin is a cytotoxic protein that inactivates ribosomes by hydrolyzing the N-glycosidic bond at position A4324 in eukaryotic 28S rRNA. Its substrate domain forms a double helical stem and a 17-base loop that includes the sequence GAGA, the second adenosine of which corresponds to A4324. Recently, studies of mutant RNAs have shown that the four-nucleotide loop, GAGA, can function as a substrate for ricin. To investigate the structure that is recognized by ricin, we studied the properties of a short synthetic substrate, the dodecaribonucleotide r-CUCAGAGAUGAG, which forms a RNA hairpin structure with a GABA loop and a stem of four base pairs. The results of NMR spectroscopy allowed us to construct the solution structure of this oligonucleotide by restrained molecular-dynamic calculations. We found that the stem region exists as an A-form duplex. 5G and 8A in the loop region form an unusual G:A base pair, and the phosphodiester backbone has a turn between 5G and 6A. This turn seems to help ricin to gain access to 6A which is the only site of depurination in the entire structure. The overall structure of the GAGA loop is similar to those of the GAAA and GCAA loops that have been described but that are not recognized by ricin. Therefore, in addition to the adenosine at the depurination site, the neighboring guanosine on the 3' side (7G) may also play a role in the recognition mechanism together with 5G and 8A.

Solution structure of lariat RNA by 500 MHz NMR spectroscopy and molecular dynamics studies in water

A 500 MHz NMR study of the lariat RNA tetramer 1 and pentamer 2 mimicking the naturally occurring lariat RNA is reported. The conformational properties of 1 and 2 were compared with those of a linear branched RNA tetramer 3, which show that the conformational features of the two lariat RNAs, 1 and 2, are quite constrained and significantly different from those observed for the linear branched RNA tetramer 3. The conformation of all sugar residues forming the lariat ring in 1 and 2 are locked in a rigid South-type conformation. All residues in both lariat RNAs have a high population of gamma+ (67-85%) and beta t (95-100%) rotamers except guanosine where the gamma+ population is low. The conformation around the glycosidic bond is anti for all residues except for guanosine where NOE data indicates an equilibrium of syn<-->anti. In both lariat RNAs, 1 and 2, the temperature dependent 1H and 31P chemical shifts as well as the oligomerization shifts, with respect to adenosine 2',3',5'-triethyl-phosphate (Sund et al., 1992, Tetrahedron 48, 695) suggests that the 3'-->5' linked U4 or C4 residue is stacked on guanosine. Subsequently, 1H-1H, 1H-31P and 13C-31P coupling constants derived torsional constraints were used for molecular dynamics study in water with counter sodium ions for a total of 226 ps. The MD simulations were first carried out with harmonic torsional constraints which were derived from J couplings (0-86 ps) and then completely without constraints (96-226 ps). The lack of any major changes in the conformation of the two lariat-RNA structures upon releasing the NMR constraints indicate that the conformers generated in the MD simulation in water agree well with the structural features suggested by experimental observables. This means that the ensemble of conformers generated during the MD trajectory of 226 ps are not artificially held in these conformations due to the NMR constraints, suggesting that these conformers can be considered to be good representatives of the actual NMR observed solution structures.

Molecular and crystal structure of Sp-thymidin-3'-yl 4-thiothymidin-5'-yl methylphosphonate

The molecular structure of one diastereomer of the dinucleoside methylphosphonate Tp(Me)sT (1) has been determined by X-ray diffraction methods. The crystal asymmetric unit contains one molecule of 1 and one methanol in an orthorhombic unit cell of dimensions a = 13.241(4), b = 13.844(3), c = 14.944(7) A, space group P2(1)2(1)2(1). Both pyrimidine bases in 1 are oriented anti relative to the 2'-deoxyribose rings, and the sugar conformations are 2E and 2(3)T in the 4-thiothymidine and thymidine moieties, respectively. The deoxyribose-phosphonate backbone has an extended conformation with the bases completely unstacked and almost parallel. The absolute configuration at the phosphorus center in 1 is Sp.

On the metastability of left-handed DNA motifs

Alternating purine-pyrimidine DNA sequences such as poly [d(C-G)] or poly[d(m5C-G)] undergo a cooperative, salt-induced structural transition from a right-handed B conformation, which prevails at relatively low ionic strength, into a left-handed Z form, generally believed to be stabilized by high salt concentrations. We report here that upon a monotonous increase of the ionic strength, the well-established B to Z transition is followed by a second, hitherto unobserved conformational change leading from Z-DNA back into a right-handed B-like form. This observation indicates that, in contrast with the current convention, the Z motif represents an unstable configuration relative to the B form at both low and high salt concentrations and that the occurrence of a left-handed DNA structure, presently depicted as a step function of the ionic strength, should rather be treated in terms of a pulse. The reported transition underscores the inherent metastability of the Z configuration, and indicates, consequently, that this motif is ideally suited to act as a structural regulatory element, as such an element should be endowed with a large susceptibility to cellular parameters.

Spectroscopic study of the interaction between poly-(9-vinyladenine) and single or multistrand RNA

The interaction between poly(9-vinyladenine) (PVAd) and poly[r(U)] was investigated by means of uv, CD, 1H-, and 31P-nmr spectroscopies. The interaction was dependent on the molecular weight of PVAd determined by uv and CD spectroscopies. Based on imino proton nmr, it was clearly found that PVAd formed the complex with poly[r(U)] by complementary hydrogen bonding. The interaction of PVAd with double- and triple-stranded helices of RNA was also investigated by uv melting behavior and 31P-nmr spectroscopy. The results suggested that PVAd could not interact with the double-stranded poly[r(A)].poly[r(U)] but did with the triple-stranded RNA.

Molecular mechanics studies of dinucleoside methylphosphonates: influence of methylphosphonate and its chirality on the phosphodiester conformation

Molecular mechanics studies are performed on single stranded as well as base paired forms of dinucleoside methylphosphonates comprising different base sequences for both the S- and R-isomers of methylphosphonate (MP). S-MP produces noticeable distortions in the geometry, locally at the phosphate center, and this enables the stereochemical feasibility of compact g- g- phosphodiester. Besides, it tends to perturb the conformations around the P-O3' and glycosyl bonds, causing minor variations in stacking interactions. In single stranded dinucleosides, the gain in adjacent base stacking interaction energies seems to be sufficient to overcome the barrier to P-O3' bond rotation arising due to S-MP...sugar interaction, and this results in transition to a compact phosphodiester (BI-type) from an initial extended phosphodiester (BII-type) conformation. Such a thing seems rather difficult in base pair constrained duplexes. Dinucleosides with R-MP behave analogous to normal phosphate duplexes as the methyl group is away from the sugar. It is found that dinucleoside methylphosphonates are energetically less favoured than the corresponding dinucleoside phosphates mainly due to the depletion of contributions from electrostatic attractive interactions involving the base and sugar with the methylphosphonate consequent to the nonionic nature of the latter. Neither S-MP nor R-MP seem to significantly alter the stereochemistry of duplex structure.

Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides

A tridecaribonucleotide, r-UGAGCUUCGGCUC, and two analogues r(UGAGC)d(UUCG)r(GCUC) and r-UGAGCUUCIGCUC, which form a hairpin structure with a four-base-paired stem and a UUCG loop, were synthesized by the solid-phase phosphoramidite method. Properties of these three oligomers and d-TGAGCTTCGGCTC, the DNA analogue, were studied by UV, CD and NMR spectroscopy. The melting temperature (Tm) data suggest that the 2'-hydroxy1 groups and the 2-amino group of guanosine in the loop (9G) stabilize the CUUCGG hairpin which is known to have an unusually high Tm. NMR studies show that this 9G takes a syn conformation and the phosphodiester backbone has a turn at 9G-10G which is a junction of the stem and loop.

Oligodeoxyribonucleoside methylphosphonates. NMR and UV spectroscopic studies of Rp-Rp and Sp-Sp methylphosphonate (Me) modified duplexes of (d[GGAATTCC])2

1H NMR chemical shift assignments for the title compounds were made for most of the 1H signals using two-dimensional nuclear Overhauser effect (2D-NOE) data, which were also used to establish the absolute configuration at the modified phosphorus. The chemical shifts were similar to those reported [Broido, M.S., et al. (1985) Eur. J. Biochem. 150, 117-128] for the unmodified, parent, B-type duplex [d(GGAATTCC)]2. Differences in chemical shifts were mostly localized to the nucleotides on the 5'- and 3'-sides of the modified phosphorus. The Rp-Rp isomers exhibited UV-derived Tm values similar to that of the parent duplex. On the other hand, the Sp-Sp isomers generally exhibited lower Tm values which correlated with P-CH3--H3' (n-1 nucleotide) cross peak intensities and 31P spectral parameters. The combined data argue for increased steric interactions with the Sp-P-Me methyl group as the modification position is moved toward the center of the oligomer. All of the Tm results can be explained in terms of three factors which result from replacement of a phosphate by a methylphosphonate group: reduction of oligomer charge; electronic and other substituent effects; steric interactions.

Synthesis and characterization of oligodeoxyribonucleotides containing terminal phosphates. NMR, UV spectroscopic and thermodynamic analysis of duplex formation of [d(pGGAATTCC)]2, [d(GGAATTCCp)]2 and [d(pGGAATTCCp)]2

Derivatives of the oligomer [d(GGAATTCC)]2 with 5' (5'-P), 3' (3'-P) and both 5' and 3' (5',3'-P2) terminal phosphate groups have been synthesized and studied by temperature dependent UV and NMR spectroscopic methods. Thermodynamic studies of the helix to strand transition indicate that addition of 3' phosphate groups has very little effect on the delta G degree for helix formation at 37 degrees C while addition of 5' phosphate groups adds approximately -0.5 kcal/mole to the delta G degree for duplex formation. The helix stabilization by 5' phosphate groups occurs at salt concentrations of 0.1 M and above, and is primarily enthalpic in origin. Tm studies as a function of ionic strength also indicate that the oligomers fall into two groups with the parent and 3'-P derivatives being similar but less stable than the 5'-P and 5',3'-P2 derivatives. Imino proton and 31P NMR studies also divide the oligomers into these same two groups based on spectral comparisons and temperature induced chemical shift and linewidth changes. 31P NMR analysis suggests that addition of 5' phosphate groups results in a small change in phosphodiester torsional angles in the g,t to g,g direction, indicating improved base stacking at the 5' end of the modified oligomer. No such changes are seen at the 3' end of the oligomer on adding 3' phosphate groups.

Poly(8-bromo-2'-deoxyadenylic acid): the syn/anti relationship

The synthesis of a high-molecular-weight, putatively all-syn DNA analogue, poly(8-bromo-2'-deoxyadenylic acid), is described. The syn----anti transition was shown to be both salt and temperature dependent. Conditions were found which favored 'normal' Watson-Crick pairing and duplex formation with poly(dT).

31P-NMR analysis of the B to Z transition in double-stranded (dC-dG)3 and (dC-dG)4 in high salt solution

In 4M NaCl solutions (dC-dG)n (n = 3,4; approximately 9 mM) exist as a mixture o +/- B and Z forms. The low and high field components of two 31P NMR resonances originating from internal phosphodiester groups are assigned to the GpC and CpG linkages, respectively. Low temperatures stabilize the Z-forms, which completely disappear above 50 degrees C (n = 3) and 65 degrees C (n = 4). delta H = -44 and -17 kJ/mol for B to Z transition in the hexamer and octamer duplexes, respectively. Temperature dependent changes (0-50 degrees C range) in the spin-lattice relaxation times at 145.7 MHz are distinctly different for the 31P nuclei o +/- GpC and CpG groups. The relaxation data can be explained by assuming that the GpC phosphodiester groups undergo more local internal motion than do the CpG groups.

Conformation and dynamics of short DNA duplexes: (dC-dG)3 and (dC-dG)4

Natural abundance 13C NMR spectra of duplexed (dC-dG)3 and (dC-dG)4 exhibit resolved resonances for most of the carbons at 0.1M NaCl in aqueous solution. Large transitions in chemical shift for many of the hexamer carbons (up to 1.8 ppm) are observed in variable temperature measurements. Determination of spin-lattice relaxation times and nuclear Overhauser enhancements in 0.1M NaCl indicate that the duplexes tumble almost isotropically, with overall correlation times near 5 nsec; the sugar carbons experience more rapid local motions than do the base carbons. The relaxation data are also consistent with the most rapid local motions occurring at the chain-terminal residues, especially in the Cyd(1) sugar. 4M NaCl causes changes in the 13C chemical shifts of most of the guanine base carbons, and rearrangements in the deoxyribose carbon shifts; this is consistent with changes predicted by a salt-induced B to Z transition, viz. conversion of the guanylates from the anti to syn range about the glycosyl bond, and from the S to N pseudorotational state of the deoxyribose ring.

Short oligodeoxynucleotides with d(G-C)n sequence do not assume left-handed conformation in high salt conditions

d(G-C)n oligodeoxynucleotides (with n varying from 3 to 7) were studied by the circular dichroism technique in 5 M-NaCl. Contrary to what was previously found with the d(C-G)n series in the same solvent, the left-handed double-stranded Z-conformation appears less stable than the B-form for low n values. The influence of base sequence on the relative stability of B- and Z-conformations for the two series is discussed.

Zinc Z-DNA

Circular dichroism spectra of poly(dG-dC) in the presence of some zinc complexes exhibit the characteristic inversion associated with the formation of a left handed helix. The transition of B to Z DNA is cooperative and slow. The concentration of zinc complex at the mid point of the transition is strongly dependent upon the nature of the ligand bound to zinc. The most efficient species is one with a tetradentate amine for which the mid point is observed at a zinc:nucleotide ratio of 1:24. 31P spectra of one of these complexes confirm the presence of a left handed helix.

Theoretical study of the geometrical arrangement of GT and GA wobble pairs in two short duplexes, Proton NMR chemical shifts and interaction energy calculations

NMR shielding constants are calculated for the base protons of duplexes formed by the dodecamer d(CGTGAATTCGCG) and the decamer d(CCAAGATTGG). A good agreement with experimental data is obtained for B-DNA helices in which the wobble GT and GA pairs are in the plane of the corresponding GC pairs of the parent duplexes formed by d(CGCGAATTCGCG) and d(CCAAGCTTGG), if the glycosyl bonds of T and G or A and G are symmetrical with respect to the dyad axis of the Watson-Crick GC pair. Interaction energy calculations show that this type of geometrical arrangement, which implies a distortion of the ribonphosphate backbone of both strands of the duplexes are more stable than those in which only one strand has its conformation modified by the presence of the wobble pair. For the duplex containing the GA pair, NMR chemical shifts as well as interaction energy computations favour the Watson-Crick hydrogen bonding scheme. The variation of the different contributions (intrastrand, interstrand, pair-pair) to the interaction energy between the bases of the duplexes, with the geometrical arrangement of the wobble pairs, is reported.

NMR studies of conformational states and dynamics of DNA

The application of high resolution NMR techniques to the investigation of DNA double helices in solution is currently in a rapid state of change as a result of advances in three different fields. First, new methods (cloning, enzymatic degradation, sonication, and chemical synthesis) have been developed for producing large quantities of short DNA suitable for NMR studies. Second, there have been major advances in the field of NMR in terms of the introduction of new pulse techniques and improvements in instrumentation. Finally, as a result of recent X-ray diffraction studies on short DNA helices and the discovery of left-handed Z-DNA there is heightened interest in the study of DNA structures in solution and the effect of sequence on structure. In the present review, we discuss the way in which NMR techniques have been used to probe various aspects of the DNA properties, including base pairing structure, dynamics of breathing, effect of sequence on DNA structure, internal molecular motions, the effect of environment on the DNA, and the interaction of DNA with small ligands.

Spectroscopic studies of (m5dC-dG)3: thermal stability of B- and Z-forms

The hexanucleoside pentaphosphate d(m5CpGpm5CpGpm5CpG) has been studied in solution by ultra-violet absorption, circular dichroism and 31P nuclear magnetic resonance under various experimental conditions. In 0.2 M NaClO4 at low temperature, an hexamer duplex is formed which has a B or B-like conformation. As the salt concentration is increased, a transition from a B-form to the Z-form occurs and is complete in 3 M NaClO4. In 3 M NaClO4, the behavior of the Z double helix is complex as a function of temperature. The variation of the circular dichroism at 295 nm is biphasic. A first transition occurs over a large range of temperature and corresponds to a conformational change due to a non-cooperative intramolecular process. Ultra-violet absorption and 31P nuclear magnetic resonance show that the new conformation arising from a distortion of the backbone is not similar to that observed in low salt conditions (B-form). At high hexanucleotide concentration, aggregates are formed. The second transition is cooperative and corresponds to the melting of a double stranded helix into single strands.

A 1H nOe and CD study of the salt-concentration dependence of the structure of d(G-C)

Intra- and internucleotide 1H nuclear Overhauser effects (nOes) have been observed in the synthetic decancleoside nonaphosphate d(G-C)5 at low and high salt concentrations, and in conditions under which duplex formation is complete. Comparison of the nOes with interproton distances derived from model and X-ray structures suggest that the duplex is right-handed up to a sodium chloride concentration of 4M, in contrast to the behaviour of poly [d(G-C)]. C.D. spectra are consistent with this suggestion.

31P NMR and viscometric studies of the interaction of meso-tetra(4-N-methylpyridyl) porphine and its Ni(II) and Zn(II) derivatives with DNA

The interactions of meso-tetra(4-N-methylpyridyl) porphine (TMPyP) and its Zn(II) and Ni(II) derivatives with DNA have been investigated by 31P NMR and viscometric titrations. TMPyP and its Ni derivative increase the viscosity of linear DNA, cause unwinding and reverse coiling of superhelical DNA, and induce a separate downfield peak in the 31P NMR spectrum of DNA. The Zn derivative slightly decreases the viscosity of linear DNA, does not unwind superhelical DNA, and does not give a downfield NMR peak. The main DNA 31P NMR signal is shifted slightly upfield on either the addition of TMPyP or the Ni compound. These results indicate that TMPyP and the Ni(II), but not the Zn(II), derivative bind to DNA by intercalation.