Crystal structure of a naturally occurring dinucleoside phoaphate: uridylyl 3',5'-adenosine phosphate model for RNA chain folding

Mechanisms of chain folding in nucleic acids. The (omega, omega) plot and its correlation to the nucleotide geometry in yeast tRNAPhe1

The (omega', omega) polot depicting the internucleotide P-O bond rotation angles in yeast phenylalanyl transfer RNA has established the interdependence of the phosphodiesters and the nucleotide geometries in the folding of the polynucleotide backbone. The plot distinguishes the regions characteristic of secondary helical structures and tertiary structural loops and bends. The folding of the polynucleotide chain is accomplished either solely by rotations around the P-O bonds or in concert with rotations around the nucleotide C4'-C5' bond with or without changes in the sugar ring pucker. In spite of differences in nucleotide sequence and intraloop tertiary interactions in the anticodon and pseudouridine loops, a characteristic repeating structural unit is found for the sugar-phosphate backbone of the tetranucleotide segment around the sharp turns.

Molecular orbital calculations on the conformation of phosphodiesters. An extended correlation between the geometry and the conformation of the phosphate group

An extension of our previous correlation (C.R. Acad. Sci. Paris, Ser. D (1973) 277, 2257; Biochim. Biophys. Acta (1974) 340, 299) between the geometry of the phosphate group and the conformation of phosphodiesters established by PCILO computations, shows that the probability of gauche-trans or trans-gauche conformations should become appreciable for low values (100-101) of the 33'-P-O5', angle and may even become predominant when the C-O-P angles have also a low value (congruent to 117 degrees). The results agree satisfactorily with available X-ray crystallographic data.

Backbone conformations in secondary and tertiary structural units of nucleic acids. Constraint in the phosphodiester conformation

The possible backbone phosphodiester conformations in a dinucleoside monophosphate and a dinucleoside triphosphate have been investigated by semiempirical energy calculations. Conformational energies have been computed as a function of the rotations omega' and omega about the internucleotide P-O(3') and P-O(5') linkages, with the nucleotide residues themselves assumed to be in one of the preferred [C(3')-endo] conformations. The terminal phosphates in a dinucleoside triphosphate greatly limit the possible conformations for the backbone (in a polynucleotide) compared to a dinucleoside monophosphate. There appear to be two major types of conformations that are favored for the backbone. The phosphodiester conformation (omega',omega) approximately (290 degrees ,290 degrees ) characteristic of helical structures is one of them, indicating that the polynucleotide backbone shows an inherent tendency for the helical conformation. The other favored conformation is centered at (omega',omega) approximately (190 degrees ,300 degrees ) and results in an extended backbone structure with unstacked bases. A third possible conformation centered at (omega', omega) approximately (200 degrees , 60 degrees ) and the (190 degrees , 300 degrees ) conformation appear to be important for the folding of a polynucleotide chain. The conformation (omega',omega) approximately (80 degrees ,80 degrees ), observed in a dinucleoside monophosphate and believed to be a candidate for producing an abrupt turn in a polynucleotide chain, is found to be stereochemically unfavorable in a dinucleoside triphosphate and a polynucleotide.

Structure of a dinucleotide: thymidylyl-(5'-3')-thymidylate-5' (pTpT)

The crystal and molecular structure of the naturally occurring deoxyribose dinucleotide sodium thymidylyl-(5'-->3')-thymidylate-5' has been determined by x-ray diffraction. There are four molecules of dinucleotide and 52 water molecules in an orthorhombic unit cell of dimensions (in angstroms) a = 16.06, b = 15.13, c = 15.65, space group P2(1)2(1)2. There is a very high degree of conformational consistency between the two halves of the molecule when the dinucleotide is viewed as the combination of two 5'-mononucleotides. The planes of the two thymines are not parallel, but are tilted 38 degrees with respect to each other. An extensive system of hydrogen bonding exists involving the bases, waters, phosphates, and sodiums; no base-base hydrogen bonding occurs. The dinucleotide structural parameters should be of assistance in interpreting DNA fiber diagrams in terms of possible structures.

A crystalline fragment of the double helix: the structure of the dinucleoside phosphate guanylyl-3',5'-cytidine

The sodium salt of guanylyl-3',5'-cytidine crystallizes in a monoclinic unit cell with one molecule in the asymmetric unit. Each molecule is related to another molecule by a 2-fold rotation axis which results in the formation of an antiparallel, right-handed double helix with complementary hydrogen bonding between the guanine and cytosine residues. The crystal is heavily hydrated with 36 water molecules in the unit cell. The geometry of this crystalline double helix is very similar to those which have been derived from studies of fiber x-ray diffraction patterns of double-stranded RNA, even though the latter do not yield data at atomic resolution.

The dimensions and shapes of the furanose rings in nucleic acids

A survey was made of the geometry of furanose rings in beta-nucleotides and beta-nucleosides (as monomers related to nucleic acids) for which structures have been determined by X-ray crystallography. Mean values, and estimated standard deviations from them, were calculated for bond-lengths, bond-angles and conformation-angles. For parameters with values dependent on ring-puckering, separate calculations were made for each ring type. (The rings are puckered in one of three conformations: C-2- or C-3-endo or C-3-exo; C-2-exo has not been observed.) The results were used to compute standard furanose rings with C-2-endo, C-3-endo and C-3-exo conformations for use in nucleic acid molecular model-building. The survey also showed that the only other conformation-angle in nucleotides dependent on the furanose ring conformation corresponds to the relative orientation of the purine (or pyrimidine) base and the ring.