An in Vitro Peptide Complementation Assay for CYT-18-Dependent Group I Intron Splicing Reveals a New Role for the N‑Terminus

The mitochondrial tyrosyl tRNA synthetase from <i>Neurospora crassa</i> (CYT-18 protein) is a bifunctional group I intron splicing cofactor. CYT-18 is capable of splicing multiple group I introns from a wide variety of sources by stabilizing the catalytically active intron structures. CYT-18 and mt TyrRSs from related fungal species have evolved to assist in group I intron splicing in part by the accumulation of three N-terminal domain insertions. Biochemical and structural analysis indicate that the N-terminal insertions serve primarily to create a structure-stabilizing scaffold for critical tertiary interactions between the two major RNA domains of group I introns. Previous studies concluded that the primarily α-helical N-terminal insertion, H0, contributes to protein stability and is necessary for splicing the <i>N. crassa</i> ND1 intron but is dispensable for splicing the <i>N. crassa</i> mitochondrial LSU intron. Here, we show that CYT-18 with a complete H0 deletion retains residual ND1 intron splicing activity and that addition of the missing N-terminus <i>in trans</i> is capable of restoring a significant portion of its splicing activity. The development of this peptide complementation assay has allowed us to explore important characteristics of the CYT-18/group I intron interaction including the stoichiometry of H0 in intron splicing and the importance of specific H0 residues. Evaluation of truncated H0 peptides in this assay and a re-examination of the CYT-18 crystal structure suggest a previously unknown structural role of the first five N-terminal residues of CYT-18. These residues interact directly with another splicing insertion, making H0 a central structural element responsible for connecting all three N-terminal splicing insertions

Designed DNA Crystal Habit Modifiers

DNA is now one of the most widely used molecules for programmed self-assembly of discrete nanostructures. One of the long-standing goals of the DNA nanotechnology field has been the assembly of periodic, macroscopic 3D DNA crystals for controlled positioning of guest molecules to be used in a variety of applications. With continuing successes in assembling DNA crystals, there is an enhanced need to tailor macroscopic crystal propertiesincluding morphologyto enable their integration into more complex systems. Here we describe the ability to alter and control crystal habits of a 3D DNA crystal formed by self-assembly of a DNA 13-mer. The introduction of “poison” oligonucleotides that specifically disrupt critical noncanonical base-pairing interactions in the crystal lattice leads to predictably modified crystal habits. We demonstrate that the poison oligomers can act as habit modifiers both during the initial crystallization and during growth of shell layers on a crystal macroseed

Three-Dimensional DNA Crystals with pH-Responsive Noncanonical Junctions

Three-dimensional (3D) DNA crystals have been envisioned as programmable biomaterial scaffolds for creating ordered arrays of biological and nonbiological molecules. Despite having excellent programmable properties, the linearity of the Watson–Crick B-form duplex imposes limitations on 3D crystal design. Predictable noncanonical base pairing motifs have the potential to serve as junctions to connect linear DNA segments into complex 3D lattices. Here, we designed crystals based on a template structure with parallel-stranded noncanonical base pairs. Depending on pH, the structures we determined contained all but one or two of the designed secondary structure interactions. Surprisingly, a conformational change of the designed Watson–Crick duplex region resulted in crystal packing differences between the predicted and observed structures. However, the designed noncanonical motif was virtually identical to the template when crystals were grown at pH 5.5, highlighting the motif’s predictability. At pH 7.0 we observed a structurally similar variation on this motif that contains a previously unobserved C–G•G–C quadruple base pair. We demonstrate that these two variants can interconvert <i>in crystallo</i> in response to pH perturbations. This study spotlights several important considerations in DNA crystal design, describes the first 3D DNA lattice composed of A-DNA helical sheets, and reveals a noncanonical DNA motif that has adaptive features that may be useful for designing dynamic crystals or biomaterial assemblies