Assignment and conformational properties of the sugar-ring hydroxyl protons of the common nucleosides

Davies, David B.; Danyluk, S.

doi:10.1139/v70-526

Cited by 23 publications

(4 citation statements)

References 8 publications

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“…Similar considerations suggest that 6 is represented by two rather rigid conformations at equilibrium which are best characterized as C(4')-endo and C(4')-exo, respectively.10 Hydroxyl Coupling. The values of /H(2'),oh of 4.0 and 4.4 Hz for 3a and 4a, respectively, are similar to those measured in nucleosides in general (Davies, 1978;Davies & Danyluk, 1970 and suggest no conformational preference around the C(l,)-C(2')-0(2,)-H torsional angle so that all three staggered rotamers are about equally populated.…”

Section: Resultssupporting

confidence: 77%

Structure and conformation of pseudouridine analogs

Lipnick¹,

Fissekis²,

O'Brien³

1981

Biochemistry

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The structural and conformational features of the "anomeric" DL-trans- and DL-cis-5-(3-hydroxytetrahydrofuran-2-yl)uracils (3a, 4a) and five similar analogues were studied in order to determine their applicability as models of beta- and alpha-pseudouridine. The 270-MHz proton NMR spectra were measured for all analogues to define their ring geometries in solution and to estimate the solution population of model N, S conformers in a two-state dynamic equilibrium treatment. Two sets of calculations were employed to evaluate the relative contributions of these states to the observed vicinal coupling constants related to the C(3')-C(4') fragment. In the first, similar geometries were assumed for each pair of conformers, while in the second, limited to 3, the geometries were those derived from X-ray crystallographic data; both gave comparable results. The cis analogues 4a and 4b are excellent conformational models for alpha-pseudouridine. In the trans series (3a-c), the equilibrium is weighted toward the N conformer (approximately 80%), differing from that found in beta-pseudouridine for which each model conformer is equally populated. Possible implications of the conformational effects upon the pairing properties of pseudouridine in tRNA are discussed.

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Section: Resultssupporting

confidence: 77%

Structure and conformation of pseudouridine analogs

Lipnick¹,

Fissekis²,

O'Brien³

1981

Biochemistry

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“…In the absence of acid or base catalysis, the exchange of hydroxyl protons in (CD3)2SO is slow on the NMR time scale and thus they appear as sharp, well-resolved resonances that can show vicinal scalar coupling to protons on an adjacent atom (24). As a result, not only can the number of free hydroxyls in a compound be determined, but also, by using homonuclear spin decoupling, they can be specifically assigned.…”

Section: Proton Assignmentmentioning

confidence: 99%

Structure of a poly (adenosine diphosphoribose) monomer: 2'-(5"-hosphoribosyl)-5'-adenosine monophosphate.

Ferro¹,

Oppenheimer²

1978

Proc. Natl. Acad. Sci. U.S.A.

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A preparation of poly(adenosine diphosphoribose) synthase obtained from pigeon liver nuclei has been used to make poly(adenosine diphosphoribose) with an average chain length of 20. Digestion of the purified poly(adenosine diphosphoribose) with snake venom phosphodiesterase (oligonucleate 5'-nucleotidohydrolase; EC 3.1.4.1) gave the monomer, 2'-5"-phosphoribosyl-5'-AMP. After purification of the monomer on a Dowex-1 column, further digestion with alkaline phosphatase [orthophosphoric-monoester phosphohydrolase (alkaline optimum); EC 3.1.3.1] yielded the dephosphorylated product, 2'-ribosyl adenosine. Nuclear magnetic resonance spectra at 360MHz of the 2'-ribosyl adenosine were obtained in [2H6Jdi-methylsulfoxide, which allows direct observation of the hydroxyl protons. These spectra show the absence of the adenosine 2'-hydroxyl proton, thus confirming the 2' position as the site of attachment of the ribose to the adenosine moiety. Comparison of the coupling constants and the chemical shifts of the ribose hydroxyl protons of 2'-ribosyl adenosine with the model compounds a-and fl-methylribofuranoside establishes an a (1" 2') glycosidic linkage in the monomer. No evidence was found for heterogeneity in either the site of attachment or configuration of the linkage in the 2'(5"-phosphoribosyl)5'-AMP. The nuclei of eukaryotic cells contain an enzyme that converts NAD+ into a homopolymer of repeating adenosine diphosphoribose (ADP-Rib) units with a concomitant release of nicotinamide (1-3). The poly(ADP-Rib) formed has a variable chain length and is covalently attached to histones and other nuclear proteins (4, 5). Although poly(ADP-Rib) has been shown to occur in vivo (5), its specific biological function is as yet undetermined, however there is possible evidence for its implication in DNA replication (5).Doly and Petek (6) exists that poly(ADP-Rib) may be heterogeneous with regard to the site of attachment of the ribosyl moiety. Further heterogeneity is possible since the anomeric configuration at R1" is unknown, although a fi configuration has been drawn (1, 5, 7). The implications arising from possible heterogeneity makes a structural determination imperative.Two classes of enzymes are known that can degrade poly(ADP-Rib): poly(ADP-Rib) glycohydrolases, which attack the ribosyl-adenosine bond (8, 9) liberating ADP-Rib, and pyrophosphatases, such as endogenous pyrophosphatases (10, 11) or snake venom phosphodiesterase (oligonucleate 5'-nucleotidohydrolase; EC 3.1.4.1) (12), which cleave the pyrophosphate linkage. The resulting monomer from the latter reactions, 2'-(5"-phosphoribosyl)-5'-AMP [AMP(P-Rib)], retains the glycosidic linkage and thus allows structural analysis. We report the 360 MHz 1H nuclear magnetic resonance (NMR) spectra of AMP(P-Rib) and 2'-ribosyladenosine (Rib-Ado). The analysis of these spectra allow6 the determination of both the site and configuration of the glycosidic linkage for poly(ADP-Rib) synthesized in uitro and provides evidence for the homogeneity of poly(ADP-Rib).MATERIALS AND...

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“…6 In methylcyclopentane, however, a considerable proportion of the molecules is likely to have an axial methyl group because, even in methylcyclohexane, the less favorable conformation constitutes ca. 8 % of the mixture at room temperature,8 **and the difference between the conformational free energies of an equatorial and an axial methyl group is certainly larger for cyclohexane than for cyclopentane. Each of the second three compounds in Table II has two equally favored but rapidly interconverting forms.…”

mentioning

confidence: 98%

Nuclear magnetic resonance spectroscopy. Carbon-13 chemical shifts of methycyclopentanes, cyclopentanols, and cyclopentyl acetates

Roberts¹,

Christl²,

Reich³

1971

J. Am. Chem. Soc.

195

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The 13Cchemical shifts of the title compounds have been determined by high-resolution nmr spectroscopy with the aid of proton decoupling. Substituent effects have been computed and compared to those obtained for some corresponding cyclohexane compounds, with the hope of providing information about steric interactions and conformations of cyclopentane derivatives. Rather large downfield a (up to ~24 ppm) and ß (up to ~7 ppm) shifts were observed on dissolution of up to 0.5 M europium tris(dipivalomethane) in cyclopentanols. The cis-and trans-1 -methyl-and 1,3-dimethylcyclopentanols showed somewhat different chelate shifts which could be used to help assign the stereochemical configuration of these substances. The 13C chemical-shift changes produced by chain branching in some aliphatic acetates and ethers are compared and rationalized.Carbon-13 magnetic resonance spectroscopy has been shown to be a very useful method for conformational analysis. In cyclohexanes, the influence of an equatorial substituent on the chemical shifts of the ring carbons 1, 2, 3, 5, and 6 is about 5 ppm different from the effect of the same substituent in the axial position. This behavior has been found for cyclohexanols,3•4 methylcyclohexanes,5 and cyclohexyl methyl ethers.4 The origins of these substituent effects are discussed in detail elsewhere.3 6 We now wish to report the results of similar investigations in the cyclopentane series.

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Assignment and conformational properties of the sugar-ring hydroxyl protons of the common nucleosides

Cited by 23 publications

References 8 publications

Structure and conformation of pseudouridine analogs

Structure and conformation of pseudouridine analogs

Structure of a poly (adenosine diphosphoribose) monomer: 2'-(5"-hosphoribosyl)-5'-adenosine monophosphate.

Nuclear magnetic resonance spectroscopy. Carbon-13 chemical shifts of methycyclopentanes, cyclopentanols, and cyclopentyl acetates

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