Geometric parameters in nucleic acids: nitrogenous bases (original) (raw)
Related papers
Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents
Journal of the American Chemical Society, 1996
A statistical survey of the torsion angles, bond angles, and bond lengths in the sugar and phosphate groups of well-refined mononucleoside, mononucleotide, dinucleoside monophosphate, and trinucleoside diphosphate crystal structures contained in the Cambridge Structural Database and the Nucleic Acid Database is reported. The mean values of the geometrical parameters in these structures and their estimated standard deviations are separated according to their chemistry and conformation. These new parameters serve as a basis for a dictionary of standard nucleic acid geometry.
Acta Crystallographica Section B Structural Science, 1988
The probability distributions of the N-H...O=C and O-H...O=C hydrogen-bond lengths observed in the crystal structures of the purines, pyrimidines, nucleosides and nucleotides have been fitted to a onedimensional hydrogen-bond potential-energy function. In order to obtain a quantitative correspondence between the experimental and theoretical distributions, it is necessary to include with the usual hydrogenbond-type potential-energy function, an effective crystal-packing force and two thermodynamical parameters of the crystal lattice, the Debye temperature and the Gruneisen constant.
New parameters for the refinement of nucleic acid-containing structures
Acta Crystallographica Section D Biological Crystallography, 1996
Structures at atomic resolution (up to 1.0,&) which contain bases, sugars or the phosphodiester linkage, were selected from the Nucleic Acid Database or the Cambridge Structural Database to build a nucleic acid dictionary from X-ray refined structures. The dictionary consists of the average values for bond distances, bond angles and dihedral angles. The variance of the sample is used to provide information about the expected r.m.s, deviations of the refined parameters. A dictionary was constructed for refinement trials in X-PLOR. The dictionary includes RNA and DNA in C2'-endo and C3'-endo sugar pucker conformations, as well as values for the backbone dihedrals. Tests were performed on the dictionary using three structures: a B-DNA, a Z-DNA and a protein-DNA complex. During the course of refinement, all three structures showed significant improvements as measured by r.m.s, deviations and R factors when compared to the previous DNA dictionary.
Journal of Computer-Aided Molecular Design, 2006
Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more nonplanar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA.
Nucleic Acids Research, 2009
We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-highresolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides-it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.
Conformational analysis of nucleic acids revisited: Curves+
2009
Abstract We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis.
Open Structural Biology Journal, 2008
The author has found recently that the lengths of chemical bonds are sums of the covalent and or ionic radii of the relevant atoms constituting the bonds, whether they are completely or partially covalent or ionic. This finding has been tested here for the skeletal bond lengths in the molecular constituents of nucleic acids, adenine, thymine, guanine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On collecting the existing data and comparing them graphically with the sums of the appropriate covalent radii of C, N, O, H and P, it is found that there is a linear dependence with effectively unit slope and zero intercept. This shows that the bond lengths in the above molecules can be interpreted as sums of the relevant atomic covalent radii. Based on this result, the author has presented here the atomic structures of the above molecules in terms of the atomic radii (for the first time).
J Phys Chem B, 2000
In the present paper, we have analyzed the conformational energy and geometrical parameters of the isolated 2′-deoxyribonucleosides and ribonucleosides. Geometry optimization of these nucleic acid constituents has been undertaken by means of density functional theory with the Becke-Lee-Yang-Parr exchange and correlation functional and split valence basis sets, 6-31G (/) , including nonstandard polarization functions on carbon, nitrogen, and oxygen atoms. For each nucleoside, three major conformers, i.e., C2′-endo/anti, C3′endo/anti, and C3′-endo/syn, have been taken into consideration, where C3′-endo and C2′-endo refer to the north (N)-type and south (S)-type sugar puckering, respectively, and anti and syn designate the orientation of the base with respect to the sugar. In both families (2′-deoxyribonucleosides and ribonucleosides) the anti orientation of the base stabilized by an intramolecular C-H‚‚‚O hydrogen bond formed between the base and the O5′ atom of the sugar moiety corresponds to the lowest energy states. In the 2′-deoxyribonucleosides including uracil, guanine, and adenine bases the lowest energy conformer is C2′-endo/anti, whereas in 2′deoxycytidine the most stable conformer is C3′-endo/anti. In ribonucleosides, the C3′-endo/anti and C2′endo/anti conformers nearly have the same energy, except in cytidine, where the most stable conformer is C3′-endo/anti. Therefore, a general discussion has been devoted to the exceptional cases of 2′-deoxycytidine and cytidine compared to the other nucleosides. The present calculated results have also been compared with those recently reported at the MP2 level by other authors on the 2′-deoxyribonucleosides or smaller model compounds on one hand, and with the experimental results based on a statistical survey of nucleoside crystal structures on the other hand.