Nucleic Acid Crystal Structures Research Articles

A unified dinucleotide alphabet describing both RNA and DNA structures.

By analyzing almost 120 000 dinucleotides in over 2000 nonredundant nucleic acid crystal structures, we define 96+1 diNucleotide Conformers, NtCs, which describe the geometry of RNA and DNA dinucleotides. NtC classes are grouped into 15 codes of the structural alphabet CANA (Conformational Alphabet of Nucleic Acids) to simplify symbolic annotation of the prominent structural features of NAs and their intuitive graphical display. The search for nontrivial patterns of NtCs resulted in the identification of several types of RNA loops, some of them observed for the first time. Over 30% of the nearly six million dinucleotides in the PDB cannot be assigned to any NtC class but we demonstrate that up to a half of them can be re-refined with the help of proper refinement targets. A statistical analysis of the preferences of NtCs and CANA codes for the 16 dinucleotide sequences showed that neither the NtC class AA00, which forms the scaffold of RNA structures, nor BB00, the DNA most populated class, are sequence neutral but their distributions are significantly biased. The reported automated assignment of the NtC classes and CANA codes available at dnatco.org provides a powerful tool for unbiased analysis of nucleic acid structures by structural and molecular biologists.

Phosphorus SAD Phasing for Nucleic Acid Structures: Limitations and Potential

Phasing of nucleic acid crystal diffraction data using the anomalous signal of phosphorus, P-SAD, at Cukα wavelength has been previously demonstrated using Z-DNA. Since the original work on P-SAD with Z-DNA there has been, with a notable exception, a conspicuous absence of applications of the technique to additional nucleic acid crystal structures. We have reproduced the P-SAD phasing of Z-DNA using a rotating-anode source and have attempted to phase a variety of nucleic acid crystals using P-SAD without success. A comparison of P-SAD using Z-DNA and a representative nucleic acid, the Dickerson-Drew dodecamer, is presented along with a S-SAD using only two sulfurs to phase a 2’-thio modified DNA decamer. A theoretical explanation for the limitation of P-SAD applied to nucleic acids is presented to show that the relatively high atomic displacement parameter of phosphorus in the nucleic acid backbone is responsible for the lack of success in applying P-SAD to nucleic acid diffraction data.

Nucleic‐acid structural deformability deduced from anisotropic displacement parameters

The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, which suggest how the protein may direct enzymatic action.

The role of quality in providing seamless access to information and data in e-science; the experience gained in crystallography

The determination of molecular structures of biological and chemical interest is a major role of applied crystallography worldwide today. Where once each new structure represented a hard-won research result, improvements in technique, technology and computational power have brought large-scale structure determination efforts well into the realm of e-science. Half a million crystal structures of 'small' molecules and over 35,000 protein and nucleic-acid crystal structures are publicly available. Many more structures have been determined but never published; increasingly these are being disseminated over the web. The crystallographic community is energetic through the activities of the International Union of Crystallography (IUCr) in its efforts to uphold quality standards in a diverse scientific environment. The IUCr has developed a data exchange standard, the crystallographic information file (CIF), and associated data dictionaries. These have allowed the seamless transfer of information from the experimental apparatus, through computation analysis, to database deposition and publication. The formal data language of CIF also allows the definition of quality standards for data deposition and publication, and the deployment of mechanisms for checking compliance with such standards, such as the checkCIF web service. This article discusses the role of the crystallographic journals owned by the IUCr in maintaining quality of information and data for effective peer-reviewed publishing of advances in crystallographic science, and the possibilities provided by the CIF dictionaries for future semantic web applications.

Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation.

The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improvements in coordinate accuracy of NMR structures of RNA can be obtained by making use of two conformational database potentials of mean force: a nucleic acid torsion angle database potential consisting of various multidimensional torsion angle correlations; and an RNA specific base-base positioning potential that provides a simple geometric, statistically based, description of sequential and nonsequential base-base interactions. The former is based on 416 nucleic acid crystal structures solved at a resolution of </=2 A and an R-factor </=25%; the latter is based on 131 RNA crystal structures solved at a resolution of </=3 A and an R-factor of </=25%, and includes both the large and small subunits of the ribosome. The application of these two database potentials is illustrated for the structure refinement of an RNA aptamer/theophylline complex for which extensive NOE and residual dipolar coupling data have been measured in solution.

New Tools and Data for Improving Structures, Using All-Atom Contacts

Publisher Summary This chapter reviews new techniques to make significant improvements in the accuracy and reliability of protein and nucleic acid crystal structures. Three major circumstances are responsible for motivating to update the traditional geometric criteria for protein structure validation: (1) the development of the all-atom contact method that can discriminate one major category of physically impossible from possible conformations, (2) the need to omit high B-factor examples that surprisingly has seldom been done before, and (3) the greatly expanded number of structures now available at high resolution. The all-atom contact technique depends on adding the hydrogen atoms, most of which are completely determined to a suitable accuracy by the positions of the heavier atoms. The methodology of macromolecular crystallography is mature, powerful, and effective, and it has transformed the understanding of biology at the molecular level. Macromolecular structures are improved significantly (i.e., made more accurate for a given resolution and data quality) by the use of validation tools, such as the free R factor and Ramachandran plot criteria. A detailed and critical analysis of the contacts and geometry inside macromolecules shows that the structures are remarkably relaxed and, at the same time, remarkably well packed.

Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: A Quantum Mechanical Study

The glycosyl torsion ( χ) in nucleic acids has long been recognized to be a major determinant of their conformational properties. χ torsional energetics were systematically mapped in deoxyribonucleosides using high-level quantum mechanical methods, for north and south sugar puckers and with γ in the g + and trans conformations. In all cases, the syn conformation is found higher in energy than the anti. When γ is changed from g + to trans, the anti orientation of the base is strongly destabilized, and the energy difference and barrier between anti and syn are significantly decreased. The barrier between anti and syn in deoxyribonucleosides is found to be less than 10 kcal/mol and tends to be lower with purines than with pyrimidines. With γ = g +/ χ = anti, a south sugar yields a significantly broader energy well than a north sugar with no energy barrier between χ values typical of A or B DNA. Contrary to the prevailing view, the syn orientation is not more stable with south puckers than with north puckers. The syn conformation is significantly more energetically accessible with guanine than with adenine in 5-nucleotides but not in nucleosides. Analysis of nucleic acid crystal structures shows that γ = trans/ χ = anti is a minor but not negligible conformation. Overall, χ appears to be a very malleable structural parameter with the experimental χ distributions reflecting, to a large extent, the associated intrinsic torsional energetics.

Checking nucleic acid crystal structures.

The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of the backbone. One of the local indicators, the density index, is particularly useful in spotting regions of the model that fit poorly in the electron density. Using this parameter, the quality of crystallographic water positions in the analyzed structures was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. The possibility that cases of poorly positioned water molecules are symptomatic of more widespread problems with the structure as a whole is also raised.

The Role of Backbone Oxygen Atoms in the Organization of Nucleic Acid Tertiary Structure: Zippers, Networks, Clamps, and C‐H…︁O Hydrogen Bonds

AbstractTight packing between structural elements is a prerequisite for molecular recognition and catalysis. In proteins, α‐helices and β‐sheets present the amino acid side chains on the surface while the polar amide bonds are buried. The opposite is found in double‐ and polystranded nucleic acids, where negatively charged phosphates occupy the surface and the side chains are hydrogen bonded in the core. Thus the question arises: How do densely packed nucleic acid molecules achieve close approach, despite the repulsion between phosphates that would appear to preclude tight contacts? One obvious answer is by mediating interstrand contacts through coordinated cations that can screen the negative charges. In this contribution, however, we highlight a variety of alternative direct interactions involving atoms of the sugar‐phosphate backbone that can promote tight packing of RNA and DNA into functional molecules. We have analyzed the existing nucleic acid crystal structures in terms of the presence of close contacts between backbone regions. In RNA, ribose 2′‐hydroxyl groups were observed to mediate such contacts in the majority of cases. However, their absence in DNA does not prevent oligodeoxynucleotides from packing tightly, aided by various interactions between backbone atoms.