a b s t r a c tThe T box mechanism is widely used in Gram-positive bacteria to regulate expression of aminoacyltRNA synthetase genes and genes involved in amino acid biosynthesis and uptake. Binding of a specific uncharged tRNA to a riboswitch element in the nascent transcript causes a structural change in the transcript that promotes expression of the downstream coding sequence. In most cases, this occurs by stabilization of an antiterminator element that competes with formation of a terminator helix. Specific tRNA recognition by the nascent transcript results in increased expression of genes important for tRNA aminoacylation in response to decreased pools of charged tRNA.

The nature of the first genetic polymer is the subject of major debate in the origin of life field 1 . Although the common 'RNA world' theory suggests RNA as the first replicable information carrier at the dawn of life, other evidence implies that life may have started with a heterogeneous nucleic acid genetic system including both RNA and DNA 2 . Such a theory streamlines the eventual 'genetic takeover' of homogeneous DNA from RNA as the principal information storage molecule in the central dogma, but requires a selective abiotic synthesis of both RNA and DNA building blocks in the same local primordial geochemical scenario. Herein, we demonstrate a high-yielding, completely stereo-, regio-, and furanosyl-selective prebiotic synthesis of the purine deoxyribonucleosides, 2 deoxyadenosine and deoxyinosine. Our synthesis utilizes key intermediates in the prebiotic synthesis of the canonical pyrimidine ribonucleosides, and we show that, once generated, the pyrimidines persist throughout the synthesis of the purine deoxyribonucleosides, ultimately leading to a mixture of deoxyadenosine, deoxyinosine, cytidine, and uridine. These results support the notion that purine deoxyribonucleosides and pyrimidine ribonucleosides may have coexisted before the emergence of life 3 .

Breakthroughs in the study of the origin of life have demonstrated how some of the building blocks essential to biology could have been formed under various primordial scenarios, and could therefore have contributed to the chemical evolution of life. Missing building blocks are then sometimes inferred to be products of primitive biosynthesis, which can stretch the limits of plausibility. Here, we demonstrate the synthesis of 2'-deoxy-2-thiouridine, and subsequently 2'-deoxyadenosine and 2-deoxyribose, under prebiotic conditions. 2'-Deoxy-2-thiouridine is produced by photoreduction of 2,2'-anhydro-2-thiouridine, which is in turn formed by phosphorylation of 2-thiouridine–an intermediate of prebiotic RNA synthesis. 2'-Deoxy-2-thiouridine is an effective deoxyribosylating agent and may have functioned as such in either abiotic or proto-enzyme-catalysed pathways to DNA, as demonstrated by its conversion to 2'-deoxyadenosine by reaction with adenine, and 2-deoxyribose by hydrolysis. An alternative prebiotic phosphorylation of 2-thiouridine leads to the formation of its 5'-phosphate, showing that hypotheses in which 2-thiouridine was a key component of early RNA sequences are within the bounds of synthetic credibility.

The T box transcription antitermination system is a riboswitch found primarily in Gram-positive bacteria which monitors the aminoacylation of the cognate tRNA and regulates a variety of amino acid-related genes. Novel 4,5-disubstituted oxazolidinones were identified as high affinity RNA molecular effectors that modulate the transcription antitermination function of the T box riboswitch.Identifying RNA ligands that modulate transcription regulation is an important area for drug discovery that has been only minimally explored to date. One potential therapeutic target is the T box transcription antitermination mechanism. This mechanism regulates many amino acid-related genes, including aminoacyl-tRNA synthetase genes, and is found predominantly in Gram-positive bacteria. 1 The T box RNAs are members of the "riboswitch" family in which nascent RNAs directly sense effector molecules to control gene expression. 2-4 The T box genes contain a complex set of structural elements within the 5′ untranslated region of their mRNAs (the "leader region"). These elements include a transcription termination signal that abrogates synthesis of the full-length mRNA and a competing antiterminator element. Readthrough of the terminator, and expression of the downstream gene, is dependent on binding of a specific uncharged tRNA to the nascent RNA transcript; each gene in the T box family responds independently to the cognate uncharged tRNA. 5 The T box antitermination mechanism can function in the absence of additional cellular factors, 6 and the antiterminator RNA element is a critical component of the mechanism. 5 The leader RNA-tRNA interaction stabilizes the antiterminator element, thereby preventing formation of the competing terminator element (Figure 1). The antiterminator element is highly conserved and has been extensively characterized by genetic, biochemical and structural biology approaches. 7-9 A significant challenge in rational ligand design for RNA structure-specific binding is to achieve both high affinity and excellent tertiary structure specificity. Aminoglycosides, the most widely studied RNA ligands, bind primarily in divalent cation binding sites. 10-12 The electrostatic attraction between the multiple protonated amino groups and the negatively charged RNA phosphate backbone leads to very high affinities. However, due to the ubiquitous presence of divalent cation binding sites in RNA, primarily for tertiary fold stabilization, 13 the aminoglycosides readily bind many RNAs 14 thus reducing their utility for RNA structurespecific ligand design. A variety of other RNA ligands have been investigated, 15-21 but few Correspondence to: Jennifer V. Hines. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the produ...

High-yielding and selective prebiotic syntheses of RNA and DNA nucleotides involve UV irradiation to promote the key reaction steps and eradicate biologically irrelevant isomers. While these syntheses were likely enabled by UV-rich prebiotic environment, UV-induced formation of photodamages in polymeric nucleic acids, such as cyclobutane pyrimidine dimers (CPDs), remains the key unresolved issue for the origins of RNA and DNA on Earth. Here, we demonstrate that substitution of adenine with 2,6-diaminopurine enables repair of CPDs with yields reaching 92%. This substantial self-repairing activity originates from excellent electron donating properties of 2,6-diaminopurine in nucleic acid strands. We also show that the deoxyribonucleosides of 2,6-diaminopurine and adenine can be formed under the same prebiotic conditions. Considering that 2,6-diaminopurine was previously shown to increase the rate of nonenzymatic RNA replication, this nucleobase could have played critical roles in the formation of functional and photostable RNA/DNA oligomers in UV-rich prebiotic environments.