Challenges and surprises that arise with nucleic acids during model building and refinement

Using Molecular Replacement Phasing to Study the Structure and Function of RNA

In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are likely to be determined in the years to come. The broader availability of experimentally determined RNA structures implies that molecular replacement (MR) will be used more and more frequently as a method for phasing future crystallographic structures. In this report we describe various aspects relative to RNA structure determination by MR. First, we describe how to select and create MR search models for nucleic acids. Second, we describe how to perform MR searches on RNA using available crystallographic software. Finally, we describe how to refine and interpret the successful MR solutions. These protocols are applicable to determine novel RNA structures as well as to establish structural-functional relationships on existing RNA structures.

Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing

Head-to-head fusions of two identical double-stranded fragments of RNA can be designed to self-assemble from a single RNA species and form a double-stranded helix with a twofold rotation axis relating the two strands. These symmetrical RNA molecules are more likely to crystallize without end-on-end statistical packing disorder because the two halves of the molecule are identical. This approach can be used to study many fragments of double-stranded RNA or many isolated helical domains from large single-stranded RNAs that may not yet be amenable to high-resolution studies by crystallography or NMR. We used fusion RNAs to study one (the U-helix) of three functional domains formed when guide RNA binds to its cognate pre-edited mRNA from the trypanosome RNA editing system. The U-helix forms when the 3' oligo(U) tail of the guide RNA (gRNA) binds to the purine-rich, pre-edited mRNA upstream from the current RNA editing site. Fusion RNAs 16-and 32-base pairs in length formed crystals that gave diffraction to 1.37 and 1.05 Å respectively. We provide the composition of a fusion RNA crystallization screen and describe the X-ray data collection, structure determination, and refinement of the crystal structures of fusion RNAs.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

New model-fitting and model-completion programs for automated iterative nucleic acid refinement

In the past decade many structures of nucleic acids have been determined, which have contributed to our understanding of their biological functions. However, crystals containing nucleic acids often diffract X-rays poorly. This makes electron-density interpretation difficult and requires a great deal of expertise in crystallography and knowledge of nucleic acid structure. Here, new programs called NAFIT and NABUILD for fitting and extending nucleic acid models are presented. These programs can be used as modules in the automated refinement system LAFIRE, as well as acting as independent programs. NAFIT performs sequential grouped fitting with empirical torsion-angle restraints and antibumping restraints including H atoms. NABUILD extends the model using a skeletonized map in a coarse-grained manner. It has been shown that NAFIT greatly improves electron-density fit and geometric quality and that iterative refinement with NABUILD significantly reduces the Rfree factor.