Nucleic acid nanostructures as tags for cryo-electron microscopy

Cryo-electron microscopy (cryo-EM) is an indispensable tool for structural biologists, allowing the reconstruction of biomolecules in their native, hydrated state to nanometre, or sub-nanometre, resolution. Unfortunately in situ cryo-EM characterisation is currently limited by our ability to interpret micrographs and tomograms, as a low signal-to-noise ratio means different structures are usually difficult to distinguish. To overcome this limitation, microscopists often use cryo-EM tags: electron-dense, nano-scale objects with specific targeting properties. This thesis presents two related projects involving the use of nucleic acid nanostructures as cryo-EM tags.
In Project 1, I introduce functionalised DNA-origami nanostructures as tags. I begin with the cryo-EM characterisation of various nanostructures in cell lysate to assess their imaging properties in a biological context. I find that solid lattice-based nanostructures provide high contrast in this environment. By cryo-EM, the outline of nanostructures is often difficult to visualise, whereas the internal arrangement of helices results in a distinctive stripy′effect.Asarest̲,ho≠ycomb-laiceorigaminanostructureswithd⇔erentshapescanbed⇔ict̲→dist∈guish,whereasnanostructuresofd⇔erentlaicetypesareeasilyidentifiab≤.Basedonthisprelim∈arywork,Ipresentasignpostorigaminanostructuresfortagg∈g,comprisingahigh-contr∗,asymmetricsign' for identification, and a six-helix bundle `post' for targeting. To functionalise nanostructures for targeting, I have characterised an RNA aptamer which binds green fluorescent protein (GFP) and quantified its binding affinity to GFP analogues. The aptamer is attached to a signpost nanostructure by hybridisation and in situ binding is demonstrated with a murine leukaemia virus test system. High-contrast, high-efficiency labelling of viral glycoproteins is observed. Electroporation of polyamine-stabilised nanostructures into E. coli is also shown for intracellular labelling applications.
In Project 2, I present methods for designing 3D RNA nanostructures for co-transcriptional folding. This provides the groundwork for the development of genetically-encoded cryo-EM tags. I firstly introduce a grid-like architecture, where an RNA nanostructure consists of a set of interacting units arranged on a square lattice. Each unit is a branched hairpin structure, with units connected by a path of single-stranded linkers and through kissing interactions between complementary hairpin arms. For this design, six different nanostructures are synthesised. Supermolecular assembly of nanostructures into finite super-structures is demonstrated, as is the incorporation of an aptamer sequence for GFP binding. Finally, I investigate an origami-like route toward RNA nanostructure design, by introducing two new assembly motifs for incorporation into an already-established 2D RNA origami architecture in an effort to build in 3D. My first origami-like design uses paranemic crossovers formed between bulge loops situated on adjacent sheets. I show that these nanostructures do not fold into the intended 3D structure and suggest explanations for this observation. In my second origami-like design, I introduce the combined bulge-loop/kissing-loop motif. Two-sheet nanostructures, held together through these motifs, have been designed. Although a more promising prospect than the previous design, the yield of well-folded structures is low. Based on these observations, the grid-like architecture will provide a more promising launching pad for the development of genetic tags.

Advisor: Turberfield, A