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The development of unnatural base pairs (UBPs) has greatly increased the information storage capacity of DNA, allowing for transcription of unnatural RNA by the heterologously expressed T7 RNA polymerase (RNAP) in Escherichia coli. However, little is known about how UBPs are transcribed by cellular RNA polymerases. Here, we investigated how synthetic unnatural nucleotides, NaM and TPT3, are recognized by eukaryotic RNA polymerase II (Pol II) and found that Pol II is able to selectively recognize UBPs with high fidelity when dTPT3 is in the template strand and rNaMTP acts as the nucleotide substrate. Our structural analysis and molecular dynamics simulation provide structural insights into transcriptional processing of UBPs in a stepwise manner. Intriguingly, we identified a novel 3-RNA binding site after rNaM addition, termed the swing state. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.

Any search for present or past life beyond Earth should consider the initialprocesses and related environmental controls that might have led to its start.As on Earth, such an understanding lies well beyond how simple organicmolecules become the more complex biomolecules of life, because it must alsoinclude the key environmental factors that permitted, modulated, and mostcritically facilitated the prebiotic pathways to life's emergence. Moreover, weask how habitability, defined in part by the presence of liquid water, wassustained so that life could persist and evolve to the point of shaping its ownenvironment. Researchers have successfully explored many chapters of Earth'scoevolving environments and biosphere spanning the last few billion yearsthrough lenses of sophisticated analytical and computational techniques, andthe findings have profoundly impacted the search for life beyond Earth. Yetlife's very beginnings during the first hundreds of millions of years of ourplanet's history remain largely unknown--despite decades of research. Thisreport centers on one key point: that the earliest steps on the path to life'semergence on Earth were tied intimately to the evolving chemical and physicalconditions of our earliest environments. Yet, a rigorous, interdisciplinaryunderstanding of that relationship has not been explored adequately and oncebetter understood will inform our search for life beyond Earth. In this way,studies of the emergence of life must become a truly interdisciplinary effort,requiring a mix that expands the traditional platform of prebiotic chemistry toinclude geochemists, atmospheric chemists, geologists and geophysicists,astronomers, mission scientists and engineers, and astrobiologists.

Numerous long-standing questions in origins-of-life research center on the history of biopolymers. For example, how and why did nature select the polypeptide backbone and proteinaceous side chains? Depsipeptides, containing both ester and amide linkages, have been proposed as ancestors of polypeptides. In this paper, we investigate cationic depsipeptides that form under mild dry-down reactions. We compare the oligomerization of various cationic amino acids, including the cationic proteinaceous amino acids (lysine, Lys; arginine, Arg; and histidine, His), along with nonproteinaceous analogs of Lys harboring fewer methylene groups in their side chains. These analogs, which have been discussed as potential prebiotic alternatives to Lys, are ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid (Orn, Dab, and Dpr). We observe that the proteinaceous amino acids condense more extensively than these nonproteinaceous amino acids. Orn and Dab readily cyclize into lactams, while Dab and Dpr condense less efficiently. Furthermore, the proteinaceous amino acids exhibit more selective oligomerization through their α-amines relative to their side-chain groups. This selectivity results in predominantly linear depsipeptides in which the amino acids are α-amine-linked, analogous to today's proteins. These results suggest a chemical basis for the selection of Lys, Arg, and His over other cationic amino acids for incorporation into proto-proteins on the early Earth. Given that electrostatics are key elements of protein-RNA and protein-DNA interactions in extant life, we hypothesize that cationic side chains incorporated into proto-peptides, as reported in this study, served in a variety of functions with ancestral nucleic acid polymers in the early stages of life.

Nicotinamide adenine dinucleotide (NAD+) is a redox active molecule that is universally found in biology. Despite the importance and simplicity of this molecule, few reports exist that investigate which molecular features are important for the activity of this ribodinucleotide. By exploiting the nonenzymatic reduction and oxidation of NAD+ by pyruvate and methylene blue, respectively, we were able to identify key molecular features necessary for the intrinsic activity of NAD+ through kinetic analysis. Such features may explain how NAD+ could have been selected early during the emergence of life. Simpler molecules, such as nicotinamide, that lack an anomeric carbon are incapable of accepting electrons from pyruvate. The phosphate moiety inhibits activity in the absence of metal ions but facilitates activity at physiological pH and model prebiotic conditions by recruiting catalytic Mg2+. Reduction proceeds through consecutive single electron transfer events. Of the derivatives tested, including nicotinamide mononucleotide, nicotinamide riboside, 3‐(aminocarbonyl)‐1‐(2,3‐dihydroxypropyl)pyridinium, 1‐methylnicotinamide, and nicotinamide, only NAD+ and nicotinamide mononucleotide would be capable of efficiently accepting and donating electrons within a nonenzymatic electron transport chain. The data are consistent with early metabolic chemistry exploiting NAD+ or nicotinamide mononucleotide and not simpler molecules. [ABSTRACT FROM AUTHOR]

The prebiotic generation of sugars in the context of origins of life studies is of considerable interest. Among the important intramolecular processes of sugars are carbonyl migrations and accompanying epimerizations. Herein we describe the carbonyl migration‐epimerization process occurring down the entire carbon chain of chirally pure d‐tetroses sugars under mild conditions. Employing chirally pure 1‐13C‐erythrose, 4‐13C‐erythrose and 1‐13C‐threose, we (1) identify all the species formed as the carbonyl migrates down the four‐carbon chain and (2) assess the rates associated with the production of each of these species. Competing aldol reactions and oxidative fragmentation processes were also observed. Further observations of self‐condensation of glycolaldehyde mainly yielding 2‐keto‐hexoses (sorbose and tagatose) and tetrulose also provides a basis for understanding the effect of carbonyl migrations on the product distribution in plausible prebiotic scenarios. [ABSTRACT FROM AUTHOR]

The prebiotic origins of ribose, nucleosides, and eventually RNA are enduring questions whose answers are central to the RNA world hypothesis. The abiotic synthesis of sugars was first demonstrated over a century ago, but no known prebiotic reaction produces ribose (an aldose sugar) selectively and in good yield. In contrast, ribulose, and fructose (ketose sugars) and other monosaccharides are formed in high yield by several robust abiotic reactions. It is reported here that ketose sugars ‐ both ketopentoses and ketohexoes ‐ serve as precursors for the formation of ribosides and other aldosides, as demonstrated by glycoside‐forming reactions involving barbituric acid, a plausibly prebiotic nucleobase. Moreover, a one‐pot reaction of glyceraldehyde and barbituric acid was discovered which under mild conditions, and without special minerals or other catalysts, results in the formation of glycosides. These results reveal that an exclusive or high‐yielding generation of free ribose was not required for its incorporation into processes that provided the foundations for life. [ABSTRACT FROM AUTHOR]