A DNA structural alphabet provides new insight into DNA flexibility

DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson–Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.

Analysis of XFEL serial diffraction data from individual crystalline fibrils

Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.

Fibre Diffraction and Whole Powder Pattern Fitting in Polymers

Crystal structure determination using a single crystal of any material has become a routine exercise. However in the case of fibres, the micro-crystallites are randomly arranged with their axis parallel to the fibre axis giving rise to poor reflections which are due to diffuse scattering, crystal structure determination is not possible. Hence crystal structure determination using poor fibre diffraction data is a challenging one. Model based correlations of X-ray diffraction data from fibrous materials are extensively discussed in a book by Fraser and MacRue(1973). The crux of the problem in fibre diffraction analysis is that the number of X-ray diffraction data is less than what could have been obtained for a single crystal. This aspect has limited the use of existing well developed crystallographic method such as Fourier synthesis of electron density or least squares refinement of atomic parameters.

The phase problem for one-dimensional crystals

The phase problem for diffraction amplitudes measured from a one-dimensional crystal is examined. In the absence of anya prioriinformation, the solution to this problem is shown to be unique up to a parameterized, low-dimensional set of solutions. Minimal additionala prioriinformation is expected to render the solution unique. The effects of additional information such as positivity, molecular envelope and helical symmetry on uniqueness are characterized. The results are pertinent to structural studies of polymeric and rod-like biomolecular assemblies that form one-dimensional, rather than three-dimensional, crystals. This shows the potential forab initiophasing of diffraction data from single such assemblies measured using new X-ray free-electron laser sources. Such an approach would circumvent the complicated inversion of cylindrically averaged diffraction that is necessary in traditional X-ray fibre diffraction analysis.