Evaluation of cytosine base editing and adenine base editing as a potential treatment for alpha-1 antitrypsin deficiency.

Alpha-1 antitrypsin deficiency (AATD) is a rare autosomal codominant disease caused by mutations within the SERPINA1 gene. The most prevalent variant in patients is PiZ SERPINA1, containing a single G > A transition mutation. PiZ alpha-1 antitrypsin (AAT) is prone to misfolding, leading to the accumulation of toxic aggregates within hepatocytes. In addition, the abnormally low level of AAT secreted into circulation provides insufficient inhibition of neutrophil elastase within the lungs, eventually causing emphysema. Cytosine and adenine base editors enable the programmable conversion of C⋅G to T⋅A and A⋅T to G⋅C base pairs, respectively. In this study, two different base editing approaches were developed: use of a cytosine base editor to install a compensatory mutation (p.Met374Ile) and use of an adenine base editor to mediate the correction of the pathogenic PiZ mutation. After treatment with lipid nanoparticles formulated with base editing reagents, PiZ-transgenic mice exhibited durable editing of SERPINA1 in the liver, increased serum AAT, and improved liver histology. These results indicate that base editing has the potential to address both lung and liver disease in AATD.

Storing and Reading Information in Mixtures of Fluorescent Molecules.

The rapidly increasing use of digital technologies requires the rethinking of methods to store data. This work shows that digital data can be stored in mixtures of fluorescent dye molecules, which are deposited on a surface by inkjet printing, where an amide bond tethers the dye molecules to the surface. A microscope equipped with a multichannel fluorescence detector distinguishes individual dyes in the mixture. The presence or absence of these molecules in the mixture encodes binary information (i.e., "0" or "1"). The use of mixtures of molecules, instead of sequence-defined macromolecules, minimizes the time and difficulty of synthesis and eliminates the requirement of sequencing. We have written, stored, and read a total of approximately 400 kilobits (both text and images) with greater than 99% recovery of information, written at an average rate of 128 bits/s (16 bytes/s) and read at a rate of 469 bits/s (58.6 bytes/s).

Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA.

The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.

Reversible Transformation of a Supramolecular Hydrogel by Redox Switching of Methylene Blue-A Noncovalent Chain Stopper.

The simple and reversible control of the degree of polymerization, and thereby the bulk material properties, of a supramolecular polymer is reported. Noncovalent capping agents (chain stoppers) modulate the length of supramolecular polymers by stacking on the surfaces of the polymer's ends. Methylene blue (MB) is a positively charged, planar polycyclic dye that acts as a chain stopper. It can be reversibly switched between its colored, planar, cationic state and a colorless, nonplanar, neutral state (leucomethylene blue, LMB) by reduction with ascorbic acid and then reoxidized to MB by O2. LMB does not act as a chain stopper. This behavior was utilized to reversibly trigger the gel to sol transformation of supramolecular polymers formed by the self-assembly of hexameric rosettes comprising 2,4,6-triaminopyrimidine and a hexanoic acid-substituted cyanuric acid (CyCo6) in aqueous media. The results of our experiments highlight the ability of this approach to reversibly switch between the gel and solution states of materials formed from supramolecular polymers and thereby control their bulk properties.

Storage of Information Using Small Organic Molecules.

Although information is ubiquitous, and its technology arguably among the highest that humankind has produced, its very ubiquity has posed new types of problems. Three that involve storage of information (rather than computation) include its usage of energy, the robustness of stored information over long times, and its ability to resist corruption through tampering. The difficulty in solving these problems using present methods has stimulated interest in the possibilities available through fundamentally different strategies, including storage of information in molecules. Here we show that storage of information in mixtures of readily available, stable, low-molecular-weight molecules offers new approaches to this problem. This procedure uses a common, small set of molecules (here, 32 oligopeptides) to write binary information. It minimizes the time and difficulty of synthesis of new molecules. It also circumvents the challenges of encoding and reading messages in linear macromolecules. We have encoded, written, stored, and read a total of approximately 400 kilobits (both text and images), coded as mixtures of molecules, with greater than 99% recovery of information, written at an average rate of 8 bits/s, and read at a rate of 20 bits/s. This demonstration indicates that organic and analytical chemistry offer many new strategies and capabilities to problems in long-term, zero-energy, robust information storage.

Robustness, Entrainment, and Hybridization in Dissipative Molecular Networks, and the Origin of Life.

How simple chemical reactions self-assembled into complex, robust networks at the origin of life is unknown. This general problem-self-assembly of dissipative molecular networks-is also important in understanding the growth of complexity from simplicity in molecular and biomolecular systems. Here, we describe how heterogeneity in the composition of a small network of oscillatory organic reactions can sustain (rather than stop) these oscillations, when homogeneity in their composition does not. Specifically, multiple reactants in an amide-forming network sustain oscillation when the environment (here, the space velocity) changes, while homogeneous networks-those with fewer reactants-do not. Remarkably, a mixture of two reactants of different structure-neither of which produces oscillations individually-oscillates when combined. These results demonstrate that molecular heterogeneity present in mixtures of reactants can promote rather than suppress complex behaviors.

Charge Transport through Self-Assembled Monolayers of Monoterpenoids.

The nature of the processes at the origin of life that selected specific classes of molecules for broad incorporation into cells is controversial. Among those classes selected were polyisoprenoids and their derivatives. This paper tests the hypothesis that polyisoprenoids were early contributors to membranes in part because they (or their derivatives) could facilitate charge transport by quantum tunneling. It measures charge transport across self-assembled monolayers (SAMs) of carboxyl-terminated monoterpenoids (O2 C(C9 HX)) and alkanoates (O2 C(C7 HX)) with different degrees of unsaturation, supported on silver (AgTS ) bottom electrodes, with Ga2 O3 /EGaIn top electrodes. Measurements of current density of SAMs of linear length-matched hydrocarbons-both saturated and unsaturated-show that completely unsaturated molecules transport charge faster than those that are completely saturated by approximately a factor of ten. This increase in relative rates of charge transport correlates with the number of carbon-carbon double bonds, but not with the extent of conjugation. These results suggest that polyisoprenoids-even fully unsaturated-are not sufficiently good tunneling conductors for their conductivity to have favored them as building blocks in the prebiotic world.

Spontaneous Symmetry Breaking in the Formation of Supramolecular Polymers: Implications for the Origin of Biological Homochirality.

Aqueous solutions of the achiral, monomeric, nucleobase mimics (2,4,6-triaminopyrimidine, TAP, and a cyanuric acid derivative, CyCo6) spontaneously assemble into macroscopic homochiral domains of supramolecular polymers. These assemblies exhibit a high degree of chiral amplification. Addition of a small quantity of one handedness of a chiral derivative of CyCo6 generates exclusively homochiral structures. This system exhibits the highest reported degree of chiral amplification for dynamic helical polymers or supramolecular helices. Significantly, homochiral polymers comprised of hexameric rosettes with structural features that resemble nucleic acids are formed from mixtures of cyanuric acid (Cy) and ribonucleotides (l-, d-pTARC) that arise spontaneously from the reaction of TAP with the sugars. These findings support the hypothesis that nucleic acid homochirality was a result of symmetry breaking at the supramolecular polymer level.

Autocatalytic Cycles in a Copper-Catalyzed Azide-Alkyne Cycloaddition Reaction.

This work describes the autocatalytic copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction between tripropargylamine and 2-azidoethanol in the presence of Cu(II) salts. The product of this reaction, tris-(hydroxyethyltriazolylmethyl)amine (N(C3N3)3), accelerates the cycloaddition reaction (and thus its own production) by two mechanisms: (i) by coordinating Cu(II) and promoting its reduction to Cu(I) and (ii) by enhancing the catalytic reactivity of Cu(I) in the cycloaddition step. Because of the cooperation of these two processes, a rate enhancement of >400× is observed over the course of the reaction. The kinetic profile of the autocatalysis can be controlled by using different azides and alkynes or ligands (e.g., ammonia) for Cu(II). When carried out in a layer of 1% agarose gel, and initiated by ascorbic acid, this autocatalytic reaction generates an autocatalytic front. This system is prototypical of autocatalytic reactions where the formation of a product, which acts as a ligand for a catalytic metal ion, enhances the production and activity of the catalyst.

Silicate-Promoted Phosphorylation of Glycerol in Non-Aqueous Solvents: A Prebiotically Plausible Route to Organophosphates.

Phosphorylation reactions of glycerol were studied using different inorganic phosphates such as sodium phosphate, trimetaphosphate (a condensed phosphate), and struvite. The reactions were carried out in two non-aqueous solvents: formamide and a eutectic solvent consisting of choline-chloride and glycerol in a ratio of 1:2.5. The glycerol reacted in formamide and in the eutectic solvent with phosphate to yield its phosphorylated derivatives in the presence of silicates such as quartz sand and kaolinite clay. The reactions were carried out by heating glycerol with a phosphate source at 85 °C for one week and were analyzed by 31P-nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). The yield of the phosphorylated glycerol was improved by the presence of silicates, and reached 90% in some experiments. Our findings further support the proposal that non-aqueous solvents are advantageous for the prebiotic synthesis of biomolecules, and suggest that silicates may have aided in the formation of organophosphates on the prebiotic earth.

Darwin's Warm Little Pond: A One-Pot Reaction for Prebiotic Phosphorylation and the Mobilization of Phosphate from Minerals in a Urea-Based Solvent.

The poor reactivity of insoluble phosphates, such as apatite-group minerals, has been a long-appreciated obstacle for proposed models of prebiotic organophosphate formation. This obstacle presents a significant challenge to the nascent development of an RNA world and other models for the origins of life on Earth. Herein, we demonstrate that a scenario based on the formation of a urea/ammonium formate/water (UAFW) eutectic solution leads to an increase in phosphorylation when compared to urea alone for phosphate sources of varying solubility. In addition, under evaporative conditions and in the presence of MgSO4 , the UAFW eutectic mobilizes the phosphate sequestered in water-insoluble hydroxyapatite, giving rise to a marked increase in phosphorylation. These results suggest that the prebiotic concentrations of urea in a geologically plausible evaporitic environment could solve the problem of organic phosphorylation on a prebiotic Earth.

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant ß-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

The Synthesis of Cyclic Poly(ethylene imine) and Exact Linear Analogues: An Evaluation of Gene Delivery Comparing Polymer Architectures.

The delivery of genetic material to cells offers the potential to treat many genetic diseases. Cationic polymers, specifically poly(ethylene imine) (PEI), are promising gene delivery vectors due to their inherent ability to condense genetic material and successfully affect its transfection. However, PEI and many other cationic polymers also exhibit high cytotoxicity. To systematically study the effect of polymer architecture on gene delivery efficiency and cell cytotoxicity, a set of cyclic PEIs were prepared for the first time and compared to a set of linear PEIs of the exact same molecular weight. Subsequent in vitro transfection studies determined a higher transfection efficiency for each cyclic PEI sample when compared to its linear PEI analogue in addition to reduced toxicity relative to the branched PEI "gold standard" control. These results highlight the critical role that the architecture of PEI can play in both optimizing transfection and reducing cell toxicity.

Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology.

For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.

Spontaneous prebiotic formation of a ß-ribofuranoside that self-assembles with a complementary heterocycle.

The RNA World hypothesis is central to many current theories regarding the origin and early evolution of life. However, the formation of RNA by plausible prebiotic reactions remains problematic. Formidable challenges include glycosidic bond formation between ribose and the canonical nucleobases, as well as the inability of nucleosides to mutually select their pairing partners from a complex mixture of other molecules prior to polymerization. Here we report a one-pot model prebiotic reaction between a pyrimidine nucleobase (2,4,6-triaminopyrimidine, TAP) and ribose, which produces TAP-ribose conjugates in high yield (60-90%). When cyanuric acid (CA), a plausible ancestral nucleobase, is mixed with a crude TAP+ribose reaction mixture, micrometer-length supramolecular, noncovalent assemblies are formed. A major product of the TAP+ribose reaction is a ß-ribofuranoside of TAP, which we term TARC. This nucleoside is also shown to efficiently form supramolecular assemblies in water by pairing and stacking with CA. These results provide a proof-of-concept system demonstrating that several challenges associated with the prebiotic emergence of RNA, or pre-RNA polymers, may not be as problematic as widely believed.

The origin of RNA and "my grandfather's axe".

The origin of RNA is one of the most formidable problems facing prebiotic chemists. We consider RNA as a product of evolution, as opposed to the more conventional view of RNA as originally being the product of abiotic processes. We have come to accept that life's informational polymers have changed in chemical structure since their emergence, which presents a quandary similar to the paradox of "My Grandfather's Axe". Here, we discuss reasons why all contemporary components of RNA--the nucleobases, ribose, and phosphate--are not likely the original components of the first informational polymer(s) of life. We also evaluate three distinct models put forth as pathways for how the earliest informational polymers might have assembled. We see the quest to uncover the ancestors of RNA as an exciting scientific journey, one that is already providing additional chemical constraints on the origin of life and one that has the potential to produce self-assembling materials, novel catalysis, and bioactive compounds.

Efficient self-assembly in water of long noncovalent polymers by nucleobase analogues.

Molecular self-assembly is widely appreciated to result from a delicate balance between several noncovalent interactions and solvation effects. However, current design approaches for achieving self-assembly in water with small, synthetic molecules do not consider all aspects of the hydrophobic effect, in particular the requirement of surface areas greater than 1 nm(2) for an appreciable free energy of hydration. With the concept of a minimum hydrophobic surface area in mind, we designed a system that achieves highly cooperative self-assembly in water. Two weakly interacting low-molecular-weight monomers (cyanuric acid and a modified triaminopyrimidine) are shown to form extremely long supramolecular polymer assemblies that retain water solubility. The complete absence of intermediate assemblies means that the observed equilibrium is between free monomers and supramolecular assemblies. These observations are in excellent agreement with literature values for the free energy of nucleic acid base interactions as well as the calculated free energy penalty for the exposure of hydrophobic structures in water. The results of our study have implications for the design of new self-assembling structures and hydrogel-forming molecules and may provide insights into the origin of the first RNA-like polymers.

Nonenzymatic ligation of DNA with a reversible step and a final linkage that can be used in PCR.

Nonenzymatic DNA ligation chemistries containing a reversible step allow thermodynamic control of product formation, but they are not necessarily compatible with polymerase enzymes. We report a ligation system that uses commercially available reagents, includes a reversible step, and results in a linkage that can function as a template for PCR amplification with accurate sequence transfer.