Structural studies of a group I intron splicing factor and a continuous three-dimensional DNA lattice

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns by stabilizing the catalytically active structure of the intron RNA. I determined 1.95 Å X-ray crystal structure of a C-terminally truncated CYT-18 protein (∆C423-669) that efficiently splices the Neurospora crassa ND1 intron and other group I introns. The structure shows that CYT-18’s nucleotide-binding fold and intermediate α-helical domain are essentially the same as those of closely related bacterial TyrRSs, except for an α-helical N-terminal extension (H0) and two small insertions (I and II) in the nucleotide-binding fold. The X-ray crystal structure in conjunction with site-directed hydroxyl radical cleavage data enabled the construction of a refined model of the CYT-18/group I intron RNA complex. The model shows that the group I intron RNA, like tRNATyr, binds across the surface of the two subunits of the homodimer, but interacts with the side opposite the aminoacylation active site. Though CYT-18 contains a tRNATyr binding site, and there are structural similarities between group I introns and tRNAs, these results demonstrate that CYT-18 adapted to function in intron splicing by acquiring a distinct binding site for group I introns. DNA has proved to be a versatile material for the rational design and assembly of nanometer scale objects. I solved the crystal structure of a continuous three-dimensional DNA lattice formed by the self-assembly of a DNA 13-mer to 2.1 Å resolution. The structure consists of stacked layers of parallel helices with adjacent layers linked through parallel-stranded base pairing. The hexagonal lattice geometry contains solvent channels large enough to allow 3’-linked guest molecules into the crystal. I have successfully used these parallel base pairs to design and produce crystals with greatly enlarged solvent channels. This lattice may have applications as a molecular scaffold for structure determination of guest molecules, as a molecular sieve, or in the assembly of molecular electronics. Predictable non-Watson-Crick base pairs may serve as a new tool in structural DNA nanotechnology.