Non-Enzymatic RNA Backbone Proofreading through Energy-Dissipative Recycling

Non-enzymatic oligomerization of activated ribonucleotides leads to ribonucleic acids that contain a mixture of 2′,5′- and 3′,5′-linkages, and overcoming this backbone heterogeneity has long been considered a major limitation to the prebiotic emergence of RNA. Herein, we demonstrate non-enzymatic chemistry that progressively converts 2′,5′-linkages into 3′,5′-linkages through iterative degradation and repair. The energetic costs of this proofreading are met by the hydrolytic turnover of a phosphate activating agent and an acylating agent. With multiple rounds of this energy-dissipative recycling, we show that all-3′,5′-linked duplex RNA can emerge from a backbone heterogeneous mixture, thereby delineating a route that could have driven RNA evolution on the early earth.     

A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay

Protein in, DNA out: A "binding-induced molecular translator" is able to convert an input target protein into an output DNA that can be readily detected and potentially be used to assemble DNA nanodevices. Successful molecular translation is mediated by binding-induced DNA assembly on a gold nanoparticle (AuNP) scaffold, thereby achieving efficient target-dependent strand displacement.     

Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

Toehold‐mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold‐mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold‐mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one‐to‐many and many‐to‐one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold‐mediated DNA strand displacement.     

A General Treatment to Study Molecular Complexes Stabilized by Hydrogen‐, Halogen‐, and Carbon‐Bond Networks: Experiment and Theory of (CH2F2)n⋅⋅⋅(H2O)m

Rotational spectra of several difluoromethane–water adducts have been observed using two broadband chirped‐pulse Fourier‐transform microwave (CP‐FTMW) spectrometers. The experimental structures of (CH₂F₂)???(H₂O)₂, (CH₂F₂)₂???(H₂O), (CH₂F₂)???(H₂O)₃, and (CH₂F₂)₂???(H₂O)₂ were unambiguously identified with the aid of 18 isotopic substituted species. A subtle competition between hydrogen, halogen, and carbon bonds is observed and a detailed analysis was performed on the complex network of non‐covalent interactions which stabilize each cluster. The study shows that the combination of stabilizing contact networks is able to reinforce the interaction strength through a cooperative effect, which can lead to large stable oligomers.