On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. II. Proton shifts in the ribose ring of purine nucleosides as a function of the torsion angle about the glycosyl bond

8-Oxo-7,8-dihydroadenine and 8-Oxo-7,8-dihydroadenosine-Chemistry, Structure, and Function in RNA and Their Presence in Natural Products and Potential Drug Derivatives

A description and history of the role that 8-oxo-7,8-dihydroadenine (8-oxoAde) and 8-oxo-7,8-dihydroadenosine (8-oxoA) have in various fields has been compiled. This Review focusses on 1) the formation of this oxidatively generated modification in RNA, its interactions with other biopolymers, and its potential role in the development/progression of disease; 2) the independent synthesis and incorporation of this modified nucleoside into oligonucleotides of RNA to display the progress that has been made in establishing its behavior in biologically relevant systems; 3) reported synthetic routes, which date back to 1890, along with the progress that has been made in the total synthesis of the nucleobase, nucleoside, and their corresponding derivatives; and 4) the isolation, total synthesis, and biological activity of natural products containing these moieties as the backbone. The current state of research regarding this oxidatively generated lesion as well as its importance in the context of RNA, natural products, and potential as drug derivatives is illustrated using all available examples reported to date.

Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions

Oxidative DNA damage has been implicated in mutagenesis, carcinogenesis and aging. Endogenous cellular processes such as aerobic metabolism generate reactive oxygen species (ROS) that interact with DNA to form dozens of DNA lesions. If unrepaired, these lesions can exert a number of deleterious effects including the induction of mutations. In an effort to understand the genetic consequences of cellular oxidative damage, many laboratories have determined the patterns of mutations generated by the interaction of ROS with DNA. Compilation of these mutational spectra has revealed that GC-->AT transitions and GC-->TA transversions are the most commonly observed mutations resulting from oxidative damage to DNA. Since mutational spectra convey only the end result of a complex cascade of events, which includes formation of multiple adducts, repair processing, and polymerase errors, it is difficult if not impossible to assess the mutational specificity of individual DNA lesions directly from these spectra. This problem is especially complicated in the case of oxidative DNA damage owing to the multiplicity of lesions formed by a single damaging agent. The task of assigning specific features of mutational spectra to individual DNA lesions has been made possible with the advent of a technology to analyze the mutational properties of single defined adducts, in vitro and in vivo. At the same time, parallel progress in the discovery and cloning of repair enzymes has advanced understanding of the biochemical mechanisms by which cells excise DNA damage. This combination of tools has brought our understanding of DNA lesions to a new level of sophistication. In this review, we summarize the known properties of individual oxidative lesions in terms of their structure, mutagenicity and repairability.

Oligonucleotide-mediated triple helix formation using an N3-protonated deoxycytidine analog exhibiting pH-independent binding within the physiological range

Triple helix formation with pyrimidine deoxyoligonucleotides for the sequence-specific recognition of DNA duplex targets suffers from a decrease in affinity as the pH of the medium increases to that of physiological fluids. A solution to this problem has been identified and entails the substitution of N6-methyl-8-oxo-2'-deoxyadenosine (M) for the 5-methyl-deoxycytosine base residues. The triple helix forming ability of an oligonucleotide consisting of thymidine and M residues is pH independent in the physiological range. Furthermore, M has been found to be superior to the previously used 5-methyldeoxycytidine and deoxyguanosine in conferring increased affinity for duplex DNA under physiological salt conditions.

Correlation between NMR spectral parameters of nucleosides and its implication to the conformation about the glycosyl bond

Analyses of high resolution proton and carbon NMR spectra of a series of guanine nucleosides in DMSO have revealed a near linear correlation between the chemical shift of the H2, atom of the sugar moiety and the vicinal coupling constant 3JC4-H1'. This unexpected result provides evidence that the variations in the glycosyl torsion angle between nucleosides in solution are less that those which have previously been reported in crystals and it is an experimental basis for analyzing the syn and anti populations from chemical shift and coupling constant data.

The three-dimensional structure of a DNA hairpin in solution two-dimensional NMR studies and structural analysis of d(ATCCTATTTATAGGAT)

The hairpin formed by d(ATCCTATTTATAGGAT) was studied by means of two-dimensional NMR spectroscopy and conformational analysis. Almost all 1H resonances of the stem region could be assigned, while the 1H and 31P spectra of the loop region were interpreted completely; this includes the stereospecific assignment of the H5' and H5" resonances. The derivation of the detailed loop structure was carried out in a stepwise fashion including some improved and new methods for structure determination from NMR data. In the first step, the mononucleotide structures were examined. The conformational space available to the mononucleotide was scanned systematically by varying the glycosidic torsion angle and pseudorotational parameters. Each generated conformer was tested against the experimental J coupling constants and NOE parameters. In the following stage, the structures of dinucleotides and longer fragments were derived. Inter-residue distances between protons were calculated by means of a procedure in which the simulated NOEs, obtained via a relaxation-matrix approach, were fitted to the experimental NOEs without the introduction of a molecular model. In addition, the backbone torsion angles beta, gamma and epsilon were deduced from homocoupling and heterocoupling constants. These data served as constraints in the next step, in which the loop sequence was subjected to a multi-conformer generation procedure. The resulting structures were tested against the mentioned constraints and disregarded if these constraints were violated. This yielded a family of structures for the loop region, confined to a relatively narrow conformational space. A representative conformation was subsequently docked on a B-type stem which fulfilled the structural constraints (derived from the NMR experiments for the stem region) to yield the hairpin structure. Results obtained from subsequent restrained-molecular-mechanics as well as free-molecular-mechanics calculations are in accordance with those obtained by means of the analysis described above. The structure of the hairpin loop is a compactly folded conformation and the first base of the central TTTA region forms a Hoogsteen T-A pair with the fourth base. This Hoogsteen base pair is stacked upon the sixth base pair of the B-type double-helical stem. The second base of the loop is folded into the minor groove, whereas the third base of the loop is partly stacked on the first and fourth bases. The phosphate backbone exhibits a sharp turn between the third and fourth nucleotides of the loop. The peculiar structure of this hairpin loop is discussed in relation to loop folding in DNA and RNA hairpins and in relation to a general model for loop folding.

Structure of oxidatively damaged nucleic acid adducts. 3. Tautomerism, ionization and protonation of 8-hydroxyadenosine studied by 15N NMR spectroscopy

Natural abundance 15N NMR spectroscopy and ancillary spectroscopic techniques have been employed to study the solution structure of 8-hydroxyadenosine. 8-Hydroxyadenosine is a naturally occurring oxidized nucleic acid adduct that is generally implied to have an 8-hydroxy tautomeric structure. 15N NMR chemical shifts and coupling constants, however, indicate that the modified base exists as an 8-keto tautomer. The pH dependence of 15N NMR and UV spectra showed the presence of two pKa's, at 2.9 and 8.7, corresponding to protonation at N1 and ionization at N7, respectively. The latter results in the formation of an 8-enolate structure. Unusual upfield shifts of the 1H and 15N resonances of the NH2 group, and a reduction in the one-bond coupling constant 1JN6-H6, is indicative of an unfavorable steric or electronic interaction between the NH2 group and the adjacent N7-H proton. This interaction results in a subtle change in the structure of the NH2 group. In addition to being a possible mechanism for alteration of hydrogen bonding in oxidized DNA, this type of interaction gives a better understanding into N7-N9 tautomerism of adenine. Furthermore, the structure of 8-hydroxyadenosine has been related to possible mechanisms for mutations.

Quantum mechanical calculations of NMR chemical shifts in nucleic acids

During the last twenty-five years the development of quantum mechanical calculations and experimental measurements of chemical shifts of the different type of nuclei present in nucleic acids have run parallel in close relation to each other. The first calculations dealt with intramolecular effects on base proton shifts (Veillard, 1962) but the real breakthrough of the theory occurred with the advent of computations of intermolecular shielding due to the ring current effect of the nucleic acid bases (Giessner-Prettre & Pullman, 1970).

13C-NMR of ribosyl ApApA, ApApG and ApUpG

The chemical shifts as well as the 13C-31P coupling constants of the carbon-13 nuclei in single-stranded ApApA, ApApG, and ApUpG are sensitive to sequence and temperature. ApApA and ApApG have similar properties with large shielding (up to 1.7 ppm) of many of the base carbons upon decreasing the temperature from 70 degrees C to 11 degrees C; the base carbons have smaller shielding changes in ApUpG. Large shielding and deshielding effects are observed for the 1', 3', 4' and 5'-carbons over this temperature range. Analysis of the 13C-31P couplings measured at the 4' ribose carbons show that the population of the anti rotamer about O5'-C5' varies from 98 to 75%, and is higher in ApApA and ApApG than in ApUpG. The CCOP coupling data at 2' and 4' is consistent with a blend of the -antiperiplanar/-synclinal nonclassical rotamers about the C3'-O3' bond, varying from 89/11% in ApApG to 55/45% in ApUpG. The coupling and chemical shift data support the thesis that ApUpG is stacked much less than the other two molecules. The stacked forms of all three trinucleotides is most easily interpreted by a standard A-RNA model. It is not necessary to invoke the "bulged base" hypothesis [Lee, C.-H. and Tinoco, Jr., I. (1981) Biophysical Chemistry 1, 283-294; Lankhorst, P.P., Wille, G., van Boom., J.H., Altona, C., and Haasnoot, C.A.G. (1983) Nucleic Acids Research 11, 2839-2856] to explain the contrast in 13C spectroscopic properties of ApUpG in comparison to ApApG and ApApA.

Intramolecular conformation of puromycin in solution as studied by proton magnetic resonance

The intramolecular conformation of puromycin, a broad spectrum antibiotic, in solution has been investigated by proton magnetic resonance (PMR) spectroscopy. A comparison of the proton chemical shift and proton-proton coupling constant data of puromycin with puromycin aminonucleoside suggests that puromycin in solution exists as an equilibrium blend of extended and folded conformers. These folded conformers are the result of flexibility around the C alpha -C beta bond of the aminoacyl segment of puromycin. One of the folded conformers predicted by PMR is in excellent agreement with the x-ray data.

Conformational studies of 13 trinucleoside bisphosphates by 360-MHz 1H-NMR spectroscopy. 1. Ribose protons

The ribose protons of 13 trinucleoside bisphosphates (trimers) were studied, using 360-MHz proton nuclear magnetic resonance spectroscopy. Complete assignments and analyses of the NMR signals of these protons were carried out by the methods of homonuclear decoupling and computer line-shape simulations. It was shown that the trinucleotides preferred the anti, 3' endo, gamma +, beta t and epsilon t/epsilon- conformations for the glycosidic torsions, the ribose rings, the C4'-C5' bonds, the C5'-O5' bonds, and the C3'-O3' bonds, respectively. It was also found that the trimers, especially those which had noticeable population of 'bulged' structures, did not necessarily have a higher population of these preferred local conformations than their component dimers. The overall conformations of the trinucleotides are classified into two categories. The conformations in the first category involve the nearest-neighbor interactions. Each dinucleotide moiety can assume one of the four stable conformations (I, I', II and III) or the open forms of dinucleoside monophosphates. However, due to steric hindrance, there are only four cases in which both dinucleotide moieties can assume one of the four stable conformations at the same time. These four combinations of conformations are I-I, I'-I', I-II and III-I', where the first Roman numeral represents the conformation of the NpN'p-moiety and the second one, that of the -pN'pN'' moiety of the trimers. Among them, I-I and I'-I' are helical structures, capable of forming a double helix. The second category contains conformations with bulged structures which have the two dinucleotide moieties in open forms (i.e. no nearest-neighbor interactions) and the bases of the two terminal residues stacking on each other while the middle residue is bulged out. These bulged conformations may serve as structural models for frame-shift mutations.

Thermodynamics of stacking and of self-association of the dinucleoside monophosphate m2(6)A-U from proton NMR chemical shifts: differential concentration temperature profile method

Chemical shifts of base and sugar protons of the modified ribodinucleoside monophosphate N6-dimethyladenylyl(3'-5')uridine (m2(6)A-U) were measured at 100, 360 and 400 MHz in aqueous solution. Seven different samples were used with concentrations ranging from 0.28 mM to 32.7 mM. The temperature was varied from -5 degrees C to 105 degrees C. An internal temperature calibration was used. The effects of intermolecular self-association and of intramolecular stacking on the chemical shifts were quantitatively separated by means of a new approach: differential concentration/temperature profiles (DCTP). Several computational models were tested and the analysis allowed deeper insight into the behaviour of m2(6)A-U at the molecular level. The simple two-state approach for both self-association and stacking already afforded a significant improvement over models in which the association is entirely neglected. A computer least-squares analysis of the chemical shift behaviour of each individual proton yielded thermodynamic parameters for self-association and stacking. However, the two-state model did not suffice to reproduce accurately all of the observations. A satisfactory fit required two additional assumptions: (a) the aromatic protons experience different association shifts in stacked and in unstacked molecules: (b) a temperature-dependent conformational equilibrium exists between sets of unstacked microstates. The stacked state is taken to represent a single conformational species. The implementation of this extended model in the least-squares optimization allowed the reproduction of over one thousand chemical shift observations within experimental error. Thermodynamic equilibrium parameters deduced for intramolecular stacking are: delta H degrees x = -28.8 kJ mol-1, delta S degrees x = -93 J mol-1 K-1. These numbers agree well with those obtained earlier by us from circular dichroism spectra. The equilibrium enthalpy and entropy values deduced for the association process are: delta H degrees A = -35 kJ mol-1 and delta S degrees A = -95 J mol-1 K-1.

Alternate g-g- conformation for dinucleoside phosphates in solution

An alternative g-g- conformation (conformer I') for dinucleosides in solution has been deduced, based on potential energy calculations and nuclear magnetic resonance spectroscopy. This conformation is characterized by larger glycosidic torsional angles (chi = 94-111 degrees) than those of conformer I (chi = 8-35 degrees), although the other torsional angles are similar. There are thus four stable conformers (I, I', II and III) for dinucleosides in equilibrium with the open forms. The structure of conformer I' supports that of the 'vertical' double helix constructed by Olson (W.K. Olson, Proc. Natl. Acad. Sci. U.S.A. 74, (1977) 1775). Our data may suggest the possibility of interconversion between the vertical double helix and the regular double helix of A-form DNA, RNA or A'-form RNA.

Synthesis and properties of CpG analogues containing an 8-bromoguanosine residue. Evidence for Z-RNA duplex formation

Three dinucleoside monophosphates containing 8-bromoguanosine (br8G), (2'-5')C-br8G, (3'-5')C-br8G, and dC-br8G, were synthesized and characterized by UV absorption, CD, and 1H NMR spectroscopy. The 1H NMR data show that all the br8G residues in these dimers take a syn glycosidic conformation. At low dimer strand concentration (5 X 10(-5) M), the UV hypochromicity data suggest that the degree of base stacking decreases in the following order, (2'-5')C-br8G greater than C-G approximately equal to dC-br8G greater than (3'-5')C-br8G. The CD data also suggest little stacking in (3'-5')C-br8G. At high dimer strand concentration (5 X 10(-3) M), only (3'-5')C-br8G shows duplex formation in 0.1 M NaCl. The duplex is assumed to take a left-handed helical structure similar to that of Z-DNA. The Tm of this duplex is surprisingly high for a dimer (about 35 and 45 degrees C at 5 X 10(-3) and 10(-2) M dimer strand concentration, respectively). The above results and the similarity between the CD spectra of (3'-5')C-br8G and poly(G-C) suggest the possible existence of Z-form structure in ribooligo- and ribopolynucleotides with alternating purine-pyrimidine sequences.

Force field conformational analysis of aminofluorene and acetylaminofluorene substituted deoxyguanosine

The hepatocarcinogen N-hydroxy-2-acetylaminofluorene forms two C8-substituted deoxyguanosine adducts in vivo. The conformation of these adducts, as well as 2'-deoxyguanosine and 8-amino-2'-deoxyguanosine has been studied with Allinger's force field. Using the glycoside rotation as a reaction coordinate, multidimensional potential energy surface were determined by relaxing all internal degrees of freedom. The calculations indicate the 2'-deoxyguanosine should exist as a mixture of syn and anti forms, that the syn form is slightly favored for 8-amino-2'-deoxyguanosine, that N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) will only be found in the syn conformation and that, although the syn form is also more stable for N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF), it will have a substantially greater proportion of the anti-conformer than is found with dG-C8-AAF. The results of the force field calculations are discussed in relation to the effects these adducts may have on DNA structure.

Binding of mercury(II) to poly(dA-dT) studied by proton nuclear magnetic resonance

The binding of Hg(II) to poly(dA-dT) has been examined with proton NMR spectroscopy. Addition of HgCl2 between r (Hg2+/nucleotide) = 0 and 0.25 results in loss of the exchangeable imino N3H resonance of thymine, indicating preferential binding at this site. The nonexchangeable base resonances AH8, AH2, and TH6 shift their intensity downfield in a cooperative manner, indicating complexation which is slow on the NMR time scale and changes in the polymer conformation upon binding. At r = 0.25, the polymer is cross-linked, and an increase in temperature does not result in denaturation of the polymer, as evidenced by the thymine proton resonance chemical shifts. The chemical shifts of the AH2 and T(CH3)5 base resonances allow some general conclusions to be made about the stereochemistry of this complex.

Left-handed deoxyribonucleic acid double helix in solution

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.

NMR studies in the syn-anti dynamic equilibrium in purine nucleosides and nucleotides

The syn in equilibrium anti equilibrium conformation about the glycosidic bond of purine nucleosides and 5'-nucleotides in different solvent systems has been investigated by means of 1H NMR spectroscopy. Quantitative values for the conformer populations were improved, relative to previous results, by a detailed study of, and a resultant derived correction for, the influence of the sugar exocyclic group conformation on the chemical shifts of the sugar ring protons. This was achieved with the aid of nucleosides and nucleotides fixed in the conformations gauche-trans [derivatives of 8,5'-(R)-cyclo] and trans-gauche [derivatives of 8,5'-(S)-cyclo]. The results of 13C NMR confirmed those obtained by 1H NMR. The measured values of the vicinal coupling constants between H-1' and the C-8 and C-4 carbons were employed to evaluate approximately the glycosidic angles chi of the nucleosides in the conformations syn and anti. A critical examination is made of the applicability of relaxation methods, involving analysis of spin-lattice relaxation time of protons (T1) and the Overhauser effect, to determine the conformation of the base about the glycosidic bond; interpretations are provided for the lack of agreement between these methods and those based on chemical shifts in the present study. The foregoing resuls are also applied to an examination of the effect of the conformation of the base about the glycosidic bond on the enzymatic reactions catalyzed by 5'-nucleotidase and adenosine deaminase.

Comparative conformations of uridine and pseudouridine and their derivatives

Stimulated by the suggestion that pseudouridine psi-39 in yeast tRNAPhe could be in a syn conformation [R. E. Hurd and B. R. Reid (1977) Nucleic Acid Research 4, 2747-2755], we have made a comparative study of the solution conformations of psi and U derivatives, using the proton-proton Overhauser effect. Rotation around the glycosidic bond is observed for pseudouridine and 3 psi MP as well as for uridine and 3'UMP. However pseudouridine an 3 psi MP are mostly syn, whereas uridine, 3'-UMP and 5'UMP are mostly anti. There is no evidence for a correlation between sugar conformation and orientation around the glycosidic bond. The results are confirmed by relaxation measurements. They are discussed in the light of earlier studies. They tend to support the suggestion of Hurd and Reid. They raise the question of the orientation of the pseudouridine found elsewhere in tRNA (e.g. in the T psi C loop).

Spatial configuration of mRNA 5'-terminus

Nuclear magnetic resonance investigation has revealed that the 5'-terminus m7G5'ppp5'Am of mRNA displays a spatial configuration in which the bases form stacked arrays. Details of the conformation as derived from coupling constants, shift trends and ring current considerations are discussed.