The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.

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Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy.

Recommendations for the presentation of NMR structures of proteins and nucleic acids

NMR investigation of RNA structure

The chemical synthesis of oligo- and poly-nucleotides by the phosphotriester approach

A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-pro ton couplings. The coupling data required for this analysis consist of sums...

Conformational Analysis of the Deoxyribofuranose Ring in DNA by means of Sums of Proton-proton Coupling Constants: A Graphical Method

A data file was created containing internal coordinates and derived parameters for 178 β-D-furanoside fragments, occurring in X-ray structures of ribo-, 2′-deoxyribo- and arabinonucleoside derivatives. The variability in bond angles and torsion angles can be described by four conformational parameters; the kind and degree of ring puckering as expressed in phase angle of pseudorotation P and puckering amplitude vm, the conformation of the side-chain δ and the glycosidic torsion angle χ. Comparison between out-of-plane and torsion angle methods for calculation of pseudorotation parameters revealed that the latter method is better suited to describe the internal coordinates of the non-equilateral five-membered ring. Inspection of the distribution of phase angles and puckering amplitudes lends additional support to the hypothesis that conformational interconversion of the familiar N and S type ring conformers is a process of hindered pseudorotation, proceeding through the O4′endo conformation (P = 90°) and maintaining a constant puckering amplitude. Both syn-anti distribution and preferred ranges of χ are correlated with furanose conformation in ribonucleosides; the distribution is also affected by the type of base, purines showing higher syn/anti ratios than pyrimidines. Three modes are observed for the backbone torsion angle δ(C4′–C5′); the most abundant rotamer is δ+, followed by δa. The δ− rotamer has so far been found only in S-type furanosides. Regressions based on existing or modified equations were used to express variations in internal coordinates in terms of the four parameters involved. As a consequence of its anomeric character, the glycosidic bond length can be described by a cyclic function of χ. Endocyclic bond angles' and torsion angles show small but systematic deviations from the pseudorotation equations derived for equilateral rings. Based on observed correlations with the four parameters, reasonably accurate coordinates for exocyclic atoms, including hydrogen atoms, could also be obtained. Coordinates for model β-D-furanoside fragments with preferred χ and δ orientations and variable pseudorotation parameters, covering a part of the N ⇌ S interconversion pathway, are presented. Their usefulness in future theoretical and experimental studies on nucleic acid conformations, both in the solid state and in solution, is discussed.

Empirical Correlations Between Conformational Parameters in β‐D‐Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents Full Description of Nucleoside Molecular Geometries in Terms of Four Parameters

Interpretation of vicinal proton-proton coupling constants by a generalized Karplus relation. Conformational analysis of the exocyclic C4′-C5′ bond in nucleosides and nucleotides: Preliminary Communication

The rates of deacylation of 5′-O-acetyl-, -methoxyacetyl-, -phenoxyacetyl-, -formyl-, and -chloroacetyl-uridines (10a–e, respectively) in aqueous and methanolic ammonia have been measured. From these data, a procedure has been developed for the general preparation of 2′-O-(methoxytetrahydropyranyl)-3′-O-acyl ribonucleosides (9) by selective deacylation of suitably designed 2′-O-(methoxytetrahydropyranyl)-3′,5′-di-O-acyl derivatives (8).Two series of 2′-acetal 3′-esters (9), designed as building blocks for oligoribonucleotide synthesis, have been prepared from each of the four main ribonucleosides: one series (derived from uridine, 4-N-benzoylcytidine, adenosine, and 2-N-benzoylguanosine) consists of 3′-acetates or -benzoates and the other series (derived from uridine, 4-N-p-anisoylcytidine, 6-N-p-anisoyladenosine, and 2-N-benzoylguanosine) consists of 3′-methoxy-acetates. All these 2′-O-(methoxytetrahydropyranyl)-3′-O-acyl ribonucleosides (9) have been obtained in satisfactory yields and all except one have been isolated as pure crystalline solids.

The synthesis of oligoribonucleotides. Part XI. Preparation of ribonucleoside 2'-acetal 3'-esters by selective deacylation.

Proton NMR studies at 360 MHz are reported on the adenine dinucleoside monophosphates N6-dimethyladenyly(3'-5')-N6-dimethyladenosine (m(6)(2)Apm(6)(2)A), ApA, rApdA, dAprA and on the methyl phosphate esters of the monomers m(6)(2)Ap, pm(6)(2)A, Ap and pA. Complete 1H-NMR spectral assignments are given. The dimers were also investigated by means of circular dichroism to obtain accurate thermodynamic parameters of the stacking equilibrium. With the aid of the thermodynamic data NMR coupling constants are extrapolated to values appropriate to the stacked conformers. A modernized version of pseudorotation analysis is used to delineate the conformational behaviour of the ribose and 2'-deoxyribose rings. It is shown that the unmethylated dimers can be arranged in two groups (dApdA/dAprA vs ApA/rApdA) according to their melting temperatures. ApA and the fully N6-methylated dimer m(6)(2)Apm(6)(2)A prefer to adopt the classical right-handed N-N stacked conformation. Both dimers with a 2'-deoxyribose ring at the 5'-OH end (dApdA and dAprA) behave similarly and occur in solution as a 75:25 mixture of S-S and S-N stacked states. The fully stacked hybrid dimer rApdA displays an unexpectedly large amount of S conformers (greater than 40%) in both sugar rings. This finding is rationalized by the postulation of a right-handed helical S-S stacked state on the basis of NMR and circular dichroic data.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1982.tb06693.x

Influence of the 2'-hydroxyl group and of 6-N-methylation on the conformation of adenine dinucleoside monophosphates in solution. A nuclear magnetic resonance and circular dichroism study.

Crystals of the title compound are orthorhombic, space group P212121, with Z= 4 in a unit cell of dimensions: a= 16.48(1), b= 4.752(4), and c= 15.94(1)A. The structure was determined from three-dimensional diffractometer data by direct methods, and refined by least-squares methods to R 4.04%. The dioxolan and ribofuranose rings are cis-connected about the C(2′)–C(3′) bond. The relatively flattened ribose ring (ϕmax. 23°) has the C(2′)-endo S-conformation, the glycosidic torsion angle lies in the normal anti range (χCN 56.5°) and the orientation of the C(5′)–O(5′) side-chain is gauche–gauche. The crystal packing is governed by O(2)⋯ N(3)(2.896 A) and O(4)⋯ O(5′)(2.907 A) hydrogen bonds.
 1
 H n.m.r. spectroscopy reveals the existence of various conformational equilibria in solution. Vicinal coupling constants between ribose protons are consistent with an N [C(3′)-endo]⇌ S [C(2′)-endo] equilibrium with a slightly more puckered ribose ring than occurs in the crystal structure. The C(5′)–O(5′) side-chain shows almost equal populations of gauche–gauche- and gauche–trans-rotamers with a minor contribution of the trans–gauche-conformation. The c.d. spectrum and the chemical shifts of the base protons H(5) and H(6) indicate a preference for the anti-conformation about the glycosidic bond.

Harry P. M. de Leeuw

Papers

Empirical Correlations Between Conformational Parameters in β‐D‐Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents Full Description of Nucleoside Molecular Geometries in Terms of Four Parameters

Interpretation of vicinal proton-proton coupling constants by a generalized Karplus relation. Conformational analysis of the exocyclic C4′-C5′ bond in nucleosides and nucleotides: Preliminary Communication

The synthesis of oligoribonucleotides. Part XI. Preparation of ribonucleoside 2'-acetal 3'-esters by selective deacylation.

Influence of the 2'-hydroxyl group and of 6-N-methylation on the conformation of adenine dinucleoside monophosphates in solution. A nuclear magnetic resonance and circular dichroism study.

Crystal structure and molecular conformation of 2′,3′-O-methoxymethyleneuridine: X-ray and nuclear magnetic resonance investigation