Activated Ribonucleotides Undergo a Sugar Pucker Switch upon Binding to a Single-Stranded RNA Template

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5′-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3′-<i>endo</i> sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2′-<i>endo</i> conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2′-<i>endo</i> and C3′-<i>endo</i> conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5′-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2′-<i>endo</i> in the free state to C3′-<i>endo</i> upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2′-deoxyribonucleotides maintain a C2′-<i>endo</i> sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions

Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms

Mass spectrometry (MS) is a powerful technique for characterizing noncanonical nucleobases and other chemical modifications in small RNAs, yielding rich chemical information that is complementary to high-throughput indirect sequencing. However, mass spectra are often prohibitively complex when fragment ions are analyzed following either solution phase hydrolysis or gas phase fragmentation. For all but the simplest cases, ions arising from multiple fragmentation events, alternative fragmentation pathways, and diverse salt adducts frequently obscure desired single-cut fragment ions. Here we show that it is possible to take advantage of predictable regularities in liquid chromatographic (LC) separation of optimized RNA digests to greatly simplify the interpretation of complex MS data. A two-dimensional analysis of extracted compound chromatograms permits straightforward and robust de novo sequencing, using a novel Monte Carlo algorithm that automatically generates bidirectional paired-end reads, pinpointing the position of modified nucleotides in a sequence. We demonstrate that these advances permit routine LC–MS sequencing of RNAs containing noncanonical nucleotides, and we furthermore examine the applicability of this approach to the study of oligonucleotides containing artificial modifications as well as those commonly observed in post-transcriptionally modified RNAs

Revealing the Self-Generated Heterointerface of NaV₂O₅ in Zn Storage via a Scalable Production Method

Solid-state sintering has been widely used as the most typical preparation method for nanomaterials. However, it usually requires high-pressure and high-temperature conditions because a slow solid-state diffusion kinetics and the presence of pores would impede proper ion diffusion. Herein, a simple and scalable method, so-called template-assisted solid-state sintering, has been utilized to synthesize a two-dimensional (2D) lamellar NaV2O5 as a cathode for aqueous zinc-ion batteries (AZIBs), and its mechanism of the improved preparation method is explored. A combined series of in situ/ex situ measurements and density functional theory (DFT) calculation reveal the Zn storage mechanism of the Zn//NaV2O5 system. A new phase of Zn3(OH)2V2O7(H2O)2 will be irreversibly generated, resulting in a self-generated heterointerface of Zn3(OH)2V2O7(H2O)2/NaV2O5. It will tune the electronic structure of NaV2O5 and accelerate the diffusion of Zn in the bulk phase, which inspires regulation of its generation for beneficial effects. In addition, a self-healing quasi-solid battery using the designed cathode has been assembled to demonstrate its application in the field of flexible wearables. This work offers a novel concept and path for creating the cathode materials for high-performance aqueous/nonaqueous batteries