Reversible and Controllable Nanolocomotion of an RNA-Processing Machinery

Molecular motors have inspired many avenues of research for nanotechnology but most molecular motors studied so far allow only unidirectional movement. The archaeal RNA-exosome is a reversible motor that can either polymerize or degrade an RNA strand, depending on the chemical environments. We developed a single molecule fluorescence assay to analyze the real time locomotion of this nanomachine on RNA. Despite the multimeric structure, the enzyme followed the Michaelis−Menten kinetics with the maximum speed of ∼3 nucleotides/s, showing that the three catalytic cylinders do not fire cooperatively. We also demonstrate rapid directional switching on demand by fluidic control. When the two reaction speeds are balanced on average, the enzyme shows a memory of the previous reaction it catalyzed and stochastically switches between primarily polymerizing and primarily degrading behaviors. The processive, reversible, and controllable locomotion propelled by this nanomachine has a promising potential in environmental sensing, diagnostic, and cargo delivery applications

Impact of Heterogeneity and Lattice Bond Strength on DNA Triangle Crystal Growth

One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and co-workers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson–Crick base pairing. However, 3D crystallization of larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem. Larger objects would offer more degrees of freedom and design options with respect to tailoring lattice geometry and for positioning other objects within a crystal lattice. The greater rigidity of multilayer DNA origami could also positively influence the diffractive properties of crystals composed of such particles. Here, we rationally explore the role of heterogeneity and Watson–Crick interaction strengths in crystal growth using 40 variants of the original DNA triangle as model multichain objects. Crystal growth of the triangle was remarkably robust despite massive chemical, geometrical, and thermodynamical sample heterogeneity that we introduced, but the crystal growth sensitively depended on the sequences of base pairs next to the Watson–Crick sticky ends of the triangle. Our results point to weak lattice interactions and high concentrations as decisive factors for achieving productive crystallization, while sample heterogeneity and impurities played a minor role

Interaction of the antibody with TWEAK.

<p>A) Ribbon representation of one Fab fragment binding to one TWEAK protomer (orange:TWEAK, blue:light chain, green:heavy chain). B) Stereo representation of the epitope recognition with interacting residues as labeled stick model and important hydrogen bond interaction highlighted as dashed lines. The binding is mainly mediated by CDR loop 1 and 2 of the heavy chain interacting with residues of the loops connecting strands D/E and B’/B and residues of strand G. In addition Y93 of CDR3 of the light chain interacts with a main chain N and stacks with the guanidinium group of R130 of TWEAK. C) Interestingly not only canonical CDR loops are involved in TWEAK binding, but an additional hydrogen bond is formed between light chain R68 of a non CDR loop with D75 of a second subunit of the trimeric TWEAK complex (gray).</p

Cross blocking assay.

1<p>The Molar Ratio (MR %) was calculated as the quotient of the secondary antibody binding signal to the primary antibody binding signal, both binding to the surface-presented TWEAK ligand.</p

Structure of human TWEAK.

<p>A) Ribbon representations of the TWEAK trimer with one protomer colored orange and the symmetry related ones in gray (crystallographic 3-fold axis indicated as black triangle). On the left top view oriented as in 1A with N- and C-Terminus on the top. In the middle side view oriented as in 1B with labeled N- and C-Terminus. In the situation of the uncleaved precursor the membrane is located on top of the molecule. The disulfide bond is highlighted as stick model and beta strands are labeled according to TNF superfamily nomenclature. The dashed lines indicate flexible loops E-F and A-A’’ not visible in the electron density. On the right, bottom view of the TWEAK trimer. B) Solvent accessible electrostatic surface potential (red −4 kT to blue +4 kT) of the TWEAK trimer with the same orientations as in A. Resembling the high pI of TWEAK with 9.62 the complete upper surface is highly positively charged. A second basic patch is located at the side of the TWEAK trimer (dashed ellipse middle picture). This positively charged region is also found in other members of the TNF family (i.e. APRIL, BAFF) and coincides with their receptor binding site. C) Overview of the TWEAK-TWEAK interface as found in the homotrimer in the same orientation and labeled as in A (middle picture). Notable hydrogen bonds involved in the trimerization are indicated as dashed lines with the respective interacting amino acids as sticks. The hydrogen bonds with interacting atoms and distances are listed in the table.</p

Model of the TWEAK – Fn14 receptor interaction.

<p>A) Side view of the TWEAK trimer showing the solvent accessible electrostatic surface potential (red −4 kT to blue +4 kT). The positively charged patch indicating the possible receptor binding site (dashed ellipse) is covered by the antibody selected for inhibiting TWEAK-Fn14 interaction (cartoon model of Hv in green and Lv in blue). B) Same view as in A with the antibody and TWEAK surface set transparence. After superposition of cytokine-receptor structures APRIL-BCMA (blue; PDB ID 1XU2), APRIL-TACI (brown; PDB ID 1XU1), TALL-BCMA (red; PDB ID 1OQD) and TALL-BAFFR (green; PDB ID 1OQE) the CRD of the receptors co-localize and mark the putative binding site of Fn14 on TWEAK (only the CRD of the receptors is shown as colored cartoon model). C) The NMR model of the Fn14 CRD (blue; PDB ID 2RPJ) is placed at the putative receptor binding site of TWEAK according to the complex structures shown in B. The basic patch is indicated with the dashed ellipse. Only one of the three receptors is shown. D) Stereo view of the modeled TWEAK-Fn14 CRD interface. Upon rigid body and positional refinement of the putative TWEAK-Fn14 CRD complex a dense hydrogen bond network is formed at the interface. The perfect complementarities of charged and hydrophobic patches, as well as the involvement of Fn14 side chains already shown to play an important role in TWEAK binding support this model.</p

Biochemical analysis of selected anti TWEAK antibodies.

<p>Biochemical analysis of selected anti TWEAK antibodies.</p

Crystallographic data collection and model refinement statistics.

<p>Crystallographic data collection and model refinement statistics.</p

Analysis of <i>in vitro</i> transcribed RNA of the measles virus genome.

<p>Sequences were generated according to deep sequencing data. The transcripts were either transfected into 293T ISRE-FF reporter cells in order to validate the immunostimulatory potential or ATPase hydrolysis experiments were performed in presence of recombinant <i>m</i>MDA5. <b>A:</b> Comparison of relative luciferase activities (black) and relative ATPase activities (grey) of <i>in vitro</i> transcribed RNAs (n = 3 and n = 2 respectively, values were normalized to the highest mean value of each replicate). <b>B:</b> Pearson correlation between (+) RNA maximal coverage and relative luciferase activity. <b>C:</b> Pearson correlation between (+) RNA maximal coverage and relative ATPase activity. <b>D:</b> Correlation analysis between AU content and luciferase or ATPase activity, and between ATPase and luciferase activity.</p

Strand separation of sequencing libraries into (+) and (−) MeV RNA.

<p>RNA deep sequencing libraries were generated based on the strand-specific mRNA sample preparation protocol from Epicentre. The Epicentre protocol encompasses sequential ligation of 5′ and 3′ adapters to RNA molecules, thus preserving strandness information. <b>A:</b> RIG-I-associated sequences in comparison to the control mapped to the viral antigenome. (+) RNA is shown in red; (−) RNA is shown in magenta; the control library is shown in black and grey. <b>B:</b> MDA5-associated sequences in comparison to the control mapped to the viral antigenome. (+) RNA is shown in blue, (−) RNA is shown in cyan; the control library is shown in black and grey.</p