Conformational studies on pyrimidine 5'-monophosphates and 3',5'-diphosphates. Effect of the phosphate groups on the backbone conformation of polynucleotides

A complete conformational map for RNA

A simple stereochemical framework for understanding RNA structure has remained elusive to date. We present a comprehensive conformational map for two nucleoside-5',3'-diphosphates and for a truncated dinucleotide derived from a grid search of all potential conformers using hard sphere steric exclusion criteria to define allowed conformers. The eight-dimensional conformational space is presented as a series of two-dimensional projections. These projections reveal several well-defined allowed and disallowed regions which correlate well with data obtained from X-ray crystallography of both large and small RNA molecules. Furthermore, the two-dimensional projections show that consecutive and ribose ring-proximal torsion angles are interdependent, while more distant torsion angles are not. Remarkably, using steric criteria alone, it is possible to generate a predictive conformational map for RNA.

Stereochemical studies on nucleic acid analogues. I. Conformations of alpha-nucleosides and alpha-nucleotides: interconversion of sugar puckers via O4'-exo

The preferred conformations of ribo and deoxyribo alpha-nucleosides and alpha-nucleotides, the stereoisomers of the naturally occurring beta-isomers, are worked out by minimizing the conformational energy as a function of all the major parameters including the sugar ring conformations along the pseudorotation path. The results of the studies bring out certain distinct conformational features that are at variance with their beta counterparts. The range of glycosyl conformations are found to be not only quite restricted here but favor predominantly the anti conformation. The syn glycosyl conformation for the entire region of P values are found to be energetically less favorable, with the barrier to anti in equilibrium with syn interconversion being higher especially in alpha-ribonucleosides. The energetically preferred range of pseudorotation phase angles (P) is also considerably restricted and P values corresponding to the C1'-exo range of sugars are highly unfavorable for alpha-nucleosides, in sharp contrast to the broad range of sugar ring conformations favored by beta-isomers. While both trans congruent to 180 degrees and skew congruent to 270 degrees conformations around the C3'-O3' (phi') bond are favored for alpha-3'-nucleotides with deoxyribose sugars, ribose sugars seem to favor only the skew values of phi'. Most interestingly and in sharp contrast to beta-stereoisomers, an energy barrier is encountered at P values corresponding to O4'-endo sugars. This suggests that the possible sugar pucker interconversion between C2'-endo/C3'-exo and C3'-endo/C2'-exo in alpha-anomers could take place only through the O4'-exo region. Likewise the possible path of anti in equilibrium with syn interconversion in alpha-nucleosides is not via high anti, in sharp contrast to beta-nucleosides. These observations should be borne in mind while assigning the sugar ring conformers in alpha-nucleosides and those containing them from nmr investigations. Comparison of the results with beta-anomers seem to suggest on the whole a lack of conformational variability or the restricted nature of alpha-stereoisomers. This could be one of the reasons for its nonselection in the naturally occurring nucleic acids.

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.

Flexibility of 3',5' deoxyribonucleoside diphosphates

In 3',5' deoxyribonucleoside diphosphates, in addition to the nature of the base and the sugar puckering, there are six single bond rotations. However, from the analysis of crystal structure data on the constituents of nucleic acids, only three rotational angles, that are about glycosyl bond, about C4'-C5' and about C3'-O3' bonds, are flexible. For a given sugar puckering and a base, potential energy calculations using non-bonded, electrostatic and torsional functions were carried out by varying the three torsion angles. The energies are represented as isopotential energy surfaces. Since the availability of the real-time color graphics, it is possible to analyse these isopotential energy surfaces. The calculations were carried out for C3' exo and C3' endo puckerings for deoxyribose and also for four bases. These calculations throw more light not only on the allowed regions for the three rotational angles but also on the relationships among them. The dependence of base and the puckering of the sugar on these rotational angles and thereby the flexibility of the 3',5' deoxyribonucleoside diphosphates is discussed. From our calculations, it is now possible to follow minimum energy path for interconversion among various conformers.

Conformational analysis of arabinonucleosides and nucleotides. A comparison with the ribonucleosides and nucleotides

Conformations of arabino nucleosides and nucleotides have been analyzed by semiempirical energy calculations. It is found that the change in the configuration of the O(2')-hydroxyl group in arabinoses compared to riboses exerts significant influence on the conformational priorities of the glycosyl and the exocyclic C(4')-C(5') bond torsions. While the anti conformations for the bases are preferred, the anti in equilibrium or formed from syn interconversion is considerably hampered compared to ribosides due to large energy barrier. Further the preferred anti glycosyl torsions are shifted to higher values for C(3')-endo puckers and in ribosides. While the gauche+ conformation around the C(4')-C(5') bond is favored for C(3')-endo arabinosides, it is strongly stabilized for C(2')-endo arabinosides only in the presence of the intrasugar hydrogen bond O(2')-H ... O(5'). The net attractive electrostatic interactions between the phosphate and the base stabilizes the preferred conformations of 5'-arabinonucleotides also.

Conformation of pyridazine nucleosides: the molecular structure of 4-hydroxy-1-(beta-D-ribofuranosyl)pyridazin-6-one (3-deaza-6-azauridine)

The glycosyl torsiona angle in 4-hydroxy-1-(beta-D-ribofuranosyl)-pyridazin-6-one (or 3-deaza-6-azauridine) is in the "high-anti" region. This is similar to the torsional angles observed for 6-azapyrimidine and 8-azapurine nucleosides, but in marked contrast to those found in uridine, 3-deazauridine and other pyrimidine nucleosides.

RNA structure

This review is concerned primarily with the physical structure and changes in the structure of RNA molecules. It will be evident that we have not attempted comprehensive coverage of what amounts to a vast literature. We have tried to stay away from particular areas that have been recently reviewed elsewhere. Citations to and information from them are included, however, so that access to the literature is available. Much of what we treat in depth deals with the crystal structures and solution behaviour of model RNA compounds, including synthetic polymers and molecular fragments such as dinucleoside phosphates. Sequence data on natural RNA are cited, but not in detail. Similarly, apart from tRNA, natural RNAs the structural determinations of which are presently not so far advanced, are not dwelt upon. We have tried to present in detail the available structural data with scaled drawings that permit facile comparisons of molecular geometries.

Proton magnetic resonance study of the intramolecular association and conformation of the alpha and beta pyridine mononucleotides and nucleosides

The chemical shifts and coupling constants are reported for the proton nuclear magnetic resonance (NMR) spectra of the alpha and beta anomers of the oxidized and reduced pyridine mononucleotides and nucleosides. The pseudorotational conformational analyses of the ribose coupling constants indicate that the ribose conformation for beta-nicotinamide mononucleotide, beta NMN, can best be described by a 3:1 mixture of interconverting 3'-exo (S) and 2'-exo (N) conformers. Reduction of betaNMN to betaNMNH results in phase angles consistent with interconverting 2'-endo (S) and 3'-endo (N) conformers without changes in the conformer populations. Cleavage of the 5'-phosphate from betaNMN has a significant effect on the phase angles (becoming more like those for betaNMNH), conformer population (the N and S conformers become nearly equal), and the distribution of the rotational isomers around the ribose 4'-5' bond to the exocyclic methylene (the gauche-gauche population decreases by about 25%). In contrast, for betaNMNH these parameters are all insensitive to dephosphorylation. The pseudorotational analysis has been extended to define the conformational parameters of alpha nucleotides. Analysis of the coupling constants for the alpha anomers indicates that the phase angles, conformer populations, and rotational isomers are generally insensitive to dephosphorylation, whereas both the phase angle and conformer populations are strongly dependent on the redox state of the base, alphaNMN being predominantly 2'-endo and alphaNMNH exclusively 2'-exo. The rotational isomers around the 4'-5' and 5'- O bonds are found to be insensitive to.the large changes in ribose conformation in the absence of any interaction with the base. The results are discussed in terms of relative contributions from base-ribose, ribose-side chain, and base-side chain interactions to the general conformational restraints imposed by the cis-2'-3'-hydroxyl interaction in beta nucleotides and the additional cis-2'-hydroxyl-base interaction in alpha nucleotides. The significance of these interactions with respect to the enzymatic and nonenzymatic properties of the pyridine nucleotides is also considered.

A possible conformation for double-stranded polynucleotides

A model is presented for double-stranded polynucleotides which involves side-by-side meshing of the two strands rather than double helical intertwining. The sugar-phosphate backbone has a twisted strip-like character, yet base-pairing of the Watson-Crick type is still possible. Structural features of the basic model are described and coordinates are presented for a representative example. The structure has, on the whole, reasonable sterochemical contacts, and can be shown to produce a fiber diffraction pattern with x-rays not unlike that of the B form of DNA.

Hydrolysis in 2'-chloro-2'-deoxy nucleosides, -nucleotides and -polynucleotides to arabinose-derivatives

The rate of hydrolysis of 2'-chloro-2'-deoxycytidine and -uridine, and their 5'-phosphates, -diphosphates and polymers to the corresponding arabinocytidine and arabinouridine derivatives in the presence of Tris-HCL pH 8.9 is determined. This rate is highest for the nucleosides, less for the 5'-phosphates and 5'-diphosphates and even less for the polynucleotides. In the the 2'-chloro-2'-deoxyuridine series the O2, 2'-cyclonucleoside was formed in addition to the arabinonucleoside.

The solution conformation of nicotinamide mononucleotide: a quantitative application of the nuclear Overhauser effect

Torsion about the glycosidic linkage in nicotinamide mononucleotide has been investigated by quantitative application of the nuclear Overhauser effect. These measurements show that the syn (chi congruent to 20 degrees) and anti (chi congruent to 200 degrees) conformers of the title compound are isoenergetic, or nearly so, and interconverting rapidly. The syn/anti partition is not measurably affected by either changes in pH or temperature.