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A data file was created containing internal coordinates and derived parameters for 178~-D-furanoside fragments, occurring in X-ray structures of ribo-, 2'-deoxyriboand 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 " m , the conformation of the side-chain 0 and the glycosidic torsion angle X. 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 Nand S type ring conformers is a process of hindered pseudorotation, proceeding through the 04'endo conformation (P = 90°) and maintaining a constant puckering amplitude. Both syn-anti distribution and preferred ranges of X 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 0(C4'-C5'); the most abundant rotamer is 0., followed by 0•. The O. 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 X. 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 {3-D-furanoside fragments with preferred X and 0 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.• This paper is part XIII in the series Nucleic Acid Constituents from this laboratory. For part XII sec Nature, 281, 235 (1<)79).

13C-31P coupling constants of 10 oligoribonucleoside phosphates, measured at a number of temperatures, are presented. The combination of these data with 1H-31P couplings of the same compounds leads to the derivation of two new and mutually consistent sets of Karplus parameters: J(CCOP) = 6.9cos2 phi--3.4cos phi + 0.7 J(HCOP) = 15.3cos2 phi--6.1cos phi + 1.6 At the same time new values for the base sequence dependent magnitude of the trans conformer of the backbone angle epsilon (C4'-C3'-O3'-P) are calculated. The present results show that the magnitude of epsilon(t) in right-handed ribo helices is confined to the range 214 degrees-226 degrees (average 219 degrees), which is in much better agreement with single crystal X-ray studies (average 218 degrees) than were previous deductions from NMR spectroscopic results (average 208 degrees).

High-resolution NMR and UV-melting experiments have been used to study the hairpin formation of partly self-complementary DNA fragments in an attempt to derive rules that describe the folding in these molecules. Earlier experiments on the hexadecanucleotide d(ATCCTA-TTTT-TAGGAT) had indicated that within the loop of four thymidines a wobble T-T pair is formed (Blommers et al., 1987). In the present paper it is shown that if the first and the last thymines of the intervening sequence are replaced by complementary bases, sometimes base pairs can be formed. Thus for the intervening sequences -CTTG- and -TTTA- with the pyrimidine in the 5'-position and the purine in the 3'-position, a base pair is formed leading to a loop consisting of two residues. For the intervening sequences -GTTC- and -ATTT- with the purine in the 5'-position and the pyrimidine in the 3'-position, this turns out not to be the case. It was found that it made no difference when the four-membered sequence was closed by a G-C base pair or an A-T base pair. Replacement of the two central thymidine residues by the more bulky adenine residues limits the hairpin to a four-membered loop scheme. Very surprisingly, it was found from 2D NOE experiments that the T-A base pair, formed in the loop consisting of the -TTTA- sequence, is a Hoogsteen pair. It is argued that the pairing of the bases in this scheme may facilitate the formation of a loop of two residues, since the distance of the C1' atoms in this base pair is 8.6 A instead of 10.4 A found in the canonical Watson-Crick base pair. Combination of the data obtained for the series of DNA fragments studied shows that the results can be explained by a simple, earlier proposed, loop folding principle which assumes that the folding of the four-membered loop is dictated by the stacking of the double-helical stem of the hairpin.

SynopsisThe relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-~-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substituents on 35HH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and T, is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N ( x 2 positive sign) and type S (XZ negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, TN, Ps, 7s) and the equilibrium constant K . The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:l conformational equilibrium between well-defined N-and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond a t the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4'-8" in most cases. In all, the proline ring is far less "floppy" than hitherto assumed.

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The relationship between vicinal N M R proton-proton coupling constants and the pseudorotational properties of the sugar ring in nucleosides and nucleotides is reinvestigated. Compared with our earlier study several important improvements are introduced: first, a new empirical generalization of the classical Karplus equation is utilized, which allows an accurate correction for the effects of electronegativity and orientation of substituents on 3J(EIH); second, empirical correlations between the parameters governing the conformation of p-D-furanosides (taken from an analysis of 178 crystal stmctores) were used to define proton-proton torsion angles as a fnnctiou of the pseudorotation parameters P and a,,,; and, third an iterative least-squares computer program was devised to obtain the best fit of the conformational parameters to the experimental coupling constants. N M R data for the sugar ring in the following compounds were taken from the literature and analysed: 3',5'-cy&c nudeotides, a base-stacked nionucleotide, 2'-~ydroarabinonucleosides, or-~-2',2-0-cyclouridine, 2'-and 3'-aminosubstituted ribonucleosides, 2'-and 3'-deoxyribonucleosides. The present results confirm that the conformational properties found in the solid state are, on the whole, preserved in solution.