Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template

The Impact of Activating Agents on Non-Enzymatic Nucleic Acid Extension Reactions

Non-enzymatic template-directed primer extension is increasingly being studied for the production of RNA and DNA. These reactions benefit from producing RNA or DNA in an aqueous, protecting group free system, without the need for expensive enzymes. However, these primer extension reactions suffer from a lack of fidelity, low reaction rates, low overall yields, and short primer extension lengths. This review outlines a detailed mechanistic pathway for non-enzymatic template-directed primer extension and presents a review of the thermodynamic driving forces involved in entropic templating. Through the lens of entropic templating, the rate and fidelity of a reaction are shown to be intrinsically linked to the reactivity of the activating agent used. Thus, a strategy is discussed for the optimization of non-enzymatic template-directed primer extension, providing a path towards cost-effective in vitro synthesis of RNA and DNA.

Role of helicity in the nonenzymatic template-directed primer extension of DNA

Complexing a DNA primer with an RNA template showed improved nonenzymatic template-directed primer extension, attributed to a shift in the DNA helicity from a B-type towards an A-type helix. A 2-fold (deoxyadenosine) and 4.5-fold (deoxycytidine) increase in conversion from initial DNA primer to a primer + 1 nucleotide product was observed.

Kinetic Proofreading

Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution-an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment-is shown to be widely employed by biological processes that transmit genetic and regulatory information. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA

Single-stranded regions of RNA are important for folding of sequences into 3D structures and for design of therapeutics targeting RNA. Prediction of ensembles of 3D structures for single-stranded regions often involves classical mechanical approximations of interactions defined by quantum mechanical calculations on small model systems. Nuclear magnetic resonance (NMR) spectra and molecular dynamics (MD) simulations of short single strands provide tests for how well the approximations model many of the interactions. Here, the NMR spectra for UCUCGU at 2, 15, and 30 °C are compared to simulations with the AMBER force fields, OL3 and ROC-RNA. This is the first such comparison to an oligoribonucleotide containing an internal guanosine nucleotide (G). G is particularly interesting because of its many H-bonding groups, large dipole moment, and proclivity for both syn and anti conformations. Results reveal formation of a G amino to phosphate non-bridging oxygen H-bond. The results also demonstrate dramatic differences in details of the predicted structures. The variations emphasize the dependence of predictions on individual parameters and their balance with the rest of the force field. The NMR data can serve as a benchmark for future force fields.

Deadlocks of adenine ribonucleotide synthesis: evaluation of adsorption and condensation reactions in a zeolite micropore space

Herein, we report on adenine, d-ribose, and monophosphate adsorption/co-adsorption into the synthetic analog of the zeolite mineral mordenite followed by drying at 50 °C and thermal activation at 150 °C under an argon atmosphere.

Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates

The identification of nonenzymatic pathways for nucleic acid replication is a key challenge in understanding the origin of life. We have previously shown that nonenzymatic RNA primer extension using 2-aminoimidazole (2AI) activated nucleotides occurs primarily through an imidazolium-bridged dinucleotide intermediate. The reactive nature and preorganized structure of the intermediate increase the efficiency of primer extension but remain insufficient to drive extensive copying of RNA templates containing all four canonical nucleotides. To understand the factors that limit RNA copying, we synthesized all ten 2AI-bridged dinucleotide intermediates and measured the kinetics of primer extension in a model system. The affinities of the ten dinucleotides for the primer/template/helper complexes vary by over 7,000-fold, consistent with nearest neighbor energetic predictions. Surprisingly, the reaction rates at saturating intermediate concentrations still vary by over 15-fold, with the most weakly binding dinucleotides exhibiting a lower maximal reaction rate. Certain noncanonical nucleotides can decrease sequence dependent differences in affinity and primer extension rate, while monomers bridged to short oligonucleotides exhibit enhanced binding and reaction rates. We suggest that more uniform binding and reactivity of imidazolium-bridged intermediates may lead to the ability to copy arbitrary template sequences under prebiotically plausible conditions.

The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis

Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomerization of prebiotically synthesized nucleotides is likely to have led to a highly heterogeneous collection of oligonucleotides comprised of a wide range of types of nucleotides connected by a variety of backbone linkages. How then did relatively homogeneous RNA emerge from this primordial heterogeneity? Here we focus on nonenzymatic template-directed primer extension as a process that would have strongly enriched for homogeneous RNA over the course of multiple cycles of replication. We review the effects on copying the kinetics of nucleotides with altered nucleobase and sugar moieties, when they are present as activated monomers and when they are incorporated into primer and template oligonucleotides. We also discuss three variations in backbone connectivity, all of which are nonheritable and regenerate native RNA upon being copied. The kinetic superiority of RNA synthesis suggests that nonenzymatic copying served as a chemical selection mechanism that allowed relatively homogeneous RNA to emerge from a complex mixture of prebiotically synthesized nucleotides and oligonucleotides.

The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases

RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2'dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2'OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2'dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here, we show that a conserved Arg residue uses a two-pronged strategy to select against 2'dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2'OH group to promote NTP binding, but selectively inhibits incorporation of 2'dNTPs by interacting with their 3'OH group to favor the catalytically-inert 2'-endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs.

Nonenzymatic RNA-templated Synthesis of N3'→P5' Phosphoramidate DNA

The RNA world hypothesis describes a scenario where early life forms relied on RNA to govern both inheritance and catalyze useful chemical reactions. Prior to the emergence of enzymes capable of replicating the RNA genome, a nonenzymatic replication process would have been necessary to initiate Darwinian Evolution. However, the one-pot nonenzymatic RNA chemical copying of templates with mixed-sequences is insufficient to generate strand products long enough to encode useful function. The use of alternate (RNA-like) genetic polymers may overcome hurdles associated with RNA copying, and further our understanding of nonenzymatic copying chemistry. This protocol describes the nonenzymatic copying of RNA templates into N3'→P5' phosphoramidate DNA (3'-NP-DNA). We describe, in detail, the synthesis of 3'-amino-2',3'-dideoxyribonucleotide monomers activated with 2-aminoimidazole (3'-NH₂-2AIpddN), and their use in template-directed polymerization.

Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs

The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in ³ E-envelope C_3' -endo, and B-type in ² E-envelope C_2' -endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.

Crystallographic observation of nonenzymatic RNA primer extension

The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5′-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process.

Enzymes speed up chemical reactions that are essential to life. Most enzymes are proteins, but some are molecules of ribonucleic acid or RNA. Like DNA, RNA is made from a chain of building blocks called nucleotides. In modern organisms, protein-based enzymes build RNAs by linking nucleotides together, while the building blocks of proteins are linked by an RNA-based enzyme at the heart of a structure called a ribosome. The earliest life on Earth most likely relied only on RNA-based enzymes, but during the emergence of life, scientists believe that RNA molecules must have replicated spontaneously before dedicated RNA-based enzymes had evolved.

How RNA could replicate without enzymes has been a puzzle for decades. Recently, scientists discovered a previously unsuspected chemical intermediate that forms during the process, and hypothesized that this molecule’s special structure is what enables the chemical reaction that adds new nucleotides to a growing strand of RNA.

To test this hypothesis, Zhang et al. diffused free RNA nucleotides into a crystalized complex containing template strands of RNA attached to short pieces of RNA called primers, which kick-start replication. Then, the crystals were frozen at various intervals and viewed using X-rays. This allowed Zhang et al. to observe the structural changes that occurred over time as the compounds reacted. The approach first revealed that the free nucleotides had paired with complementary nucleotides on the RNA template strands. Then, pairs of free nucleotides reacted with each other to form the intermediate. Finally, the intermediate reacted with the primer, forming a new bond that connects the RNA primer to one of the nucleotides of the intermediate, while the other nucleotide of the intermediate was released as a free nucleotide.

This experiment confirms that the specific structure of the intermediate molecule promotes RNA replication without help from enzymes. These findings will benefit chemists and biologists who study how RNA evolves and replicates. Future research building upon this work will deepen scientific understanding of the environmental conditions that were required for life to appear on Earth.

The C2'- and C3'-endo equilibrium for AMP molecules bound in the cystathionine-beta-synthase domain

The equilibrium between C2'- and C3'-endo conformations of nucleotides in solution, as well as their polymers DNA and RNA, has been well studied in previous work. However, this equilibrium of nucleotides in their binding state remains unclear. We observed two AMP molecules, in C3'- and C2'-endo conformations respectively, simultaneously bound to a cystathionine-beta-synthase (CBS) domain dimer of the magnesium and cobalt efflux protein CorC in the crystallographic study. The C2'-endo AMP molecule assumes the higher sugar pucker energy and one more hydrogen bond with the protein than the C3'-endo molecule does. The balance between the high sugar pucker energy and the low binding energy suggests an equilibrium or switch between C2'- and C3'-endo conformations of the bound nucleotides. Our work challenge the previous hypothesis that the ribose of the bound nucleotides would be locked in a fixed conformation.

A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations

The computational efficiency of approximate quantum mechanical methods allows their use for the construction of multidimensional reaction free energy profiles. It has recently been demonstrated that quantum models based on the neglect of diatomic differential overlap (NNDO) approximation have difficulty modeling deoxyribose and ribose sugar ring puckers and thus limit their predictive value in the study of RNA and DNA systems. A method has been introduced in our previous work to improve the description of the sugar puckering conformational landscape that uses a multidimensional B-spline correction map (BMAP correction) for systems involving intrinsically coupled torsion angles. This method greatly improved the adiabatic potential energy surface profiles of DNA and RNA sugar rings relative to high-level ab initio methods even for highly problematic NDDO-based models. In the present work, a BMAP correction is developed, implemented, and tested in molecular dynamics simulations using the AM1/d-PhoT semiempirical Hamiltonian for biological phosphoryl transfer reactions. Results are presented for gas-phase adiabatic potential energy surfaces of RNA transesterification model reactions and condensed-phase QM/MM free energy surfaces for nonenzymatic and RNase A-catalyzed transesterification reactions. The results show that the BMAP correction is stable, efficient, and leads to improvement in both the potential energy and free energy profiles for the reactions studied, as compared with ab initio and experimental reference data. Exploration of the effect of the size of the quantum mechanical region indicates the best agreement with experimental reaction barriers occurs when the full CpA dinucleotide substrate is treated quantum mechanically with the sugar pucker correction.

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

The nonenzymatic copying of RNA templates with imidazole-activated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex. The structure shows that GpppG binds the RNA template through two Watson-Crick base pairs, with the primer 3'-hydroxyl oriented to attack the 5'-phosphate of the adjacent G residue. Thus, the GpppG structure suggests that the bound imidazolium-bridged dinucleotide intermediate would be preorganized to react with the primer by in-line S_N2 substitution. The structures of bound GppG and GppppG suggest that the length and flexibility of the 5'-5' linkage are important for optimal preorganization of the complex, whereas the position of the 5'-phosphate of bound pGpG explains the slow rate of oligonucleotide ligation reactions. Our studies provide a structural interpretation for the observed reactivity of the imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.

Enhanced Nonenzymatic RNA Copying with 2-Aminoimidazole Activated Nucleotides

Achieving efficient nonenzymatic replication of RNA is an important step toward the synthesis of self-replicating protocells that may mimic early forms of life. Despite recent progress, the nonenzymatic copying of templates containing mixed sequences remains slow and inefficient. Here we demonstrate that activating nucleotides with 2-aminoimidazole results in superior reaction kinetics and improved yields of primer extension reaction products. This new leaving group significantly accelerates monomer addition as well as trimer-assisted RNA primer extension, allowing efficient copying of a variety of short RNA templates with mixed sequences.

Unusual Base-Pairing Interactions in Monomer-Template Complexes

Many high-resolution crystal structures have contributed to our understanding of the reaction pathway for catalysis by DNA and RNA polymerases, but the structural basis of nonenzymatic template-directed RNA replication has not been studied in comparable detail. Here we present crystallographic studies of the binding of ribonucleotide monomers to RNA primer-template complexes, with the goal of improving our understanding of the mechanism of nonenzymatic RNA copying, and of catalysis by polymerases. To explore how activated ribonucleotides recognize and bind to RNA templates, we synthesized an unreactive phosphonate-linked pyrazole analogue of guanosine 5'-phosphoro-2-methylimidazolide (2-MeImpG), a highly activated nucleotide that has been used extensively to study nonenzymatic primer extension. We cocrystallized this analogue with structurally rigidified RNA primer-template complexes carrying single or multiple monomer binding sites, and obtained high-resolution X-ray structures of these complexes. In addition to Watson-Crick base pairing, we repeatedly observed noncanonical guanine:cytidine base pairs in our crystal structures. In most structures, the phosphate and leaving group moieties of the monomers were highly disordered, while in others the distance from O3' of the primer to the phosphorus of the incoming monomer was too great to allow for reaction. We suggest that these effects significantly influence the rate and fidelity of nonenzymatic RNA replication, and that even primitive ribozyme polymerases could enhance RNA replication by enforcing Watson-Crick base pairing between monomers and primer-template complexes, and by bringing the reactive functional groups into closer proximity.

Synthesis of activated 3'-amino-3'-deoxy-2-thio-thymidine, a superior substrate for the nonenzymatic copying of nucleic acid templates

We present a scalable synthesis of 3'-amino-3'-deoxy-2-thio-thymidine-5'-phosphoro-2-methylimidazolide, an activated monomer that can copy adenosine residues in nucleic acid templates rapidly without a polymerase. The sulfur atom substitution enhances the rate of template copying by 5-fold compared with the 3'-amino-3'-deoxy-T monomer, while the 3'-amino monomers exhibit a 2- to 30-fold enhancement compared with their ribonucleotide counterparts.

Effect of terminal 3′-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension

Displacing the hydroxyl nucleophile at the 3′-end of a primer by a single methylene group drastically decreases the rate of primer extension, illustrating the importance of the precise position of the hydroxyl nucleophile.

Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling

Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s(2)U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s(2)U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s(2)U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s(2)U:A and s(2)U:U pairs and their native counterparts. These results indicate that s(2)U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s(2)U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s(2)U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s(2)U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using (1)H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying.

Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self-consistent density-functional tight-binding semiempirical models are evaluated against high-level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling "modified divide-and-conquer" model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions.

Uncovering the thermodynamics of monomer binding for RNA replication

The nonenzymatic replication of primordial RNA is thought to have been a critical step in the origin of life. However, despite decades of effort, the poor rate and fidelity of model template copying reactions have thus far prevented an experimental demonstration of nonenzymatic RNA replication. The overall rate and fidelity of template copying depend, in part, on the affinity of free ribonucleotides to the RNA primer-template complex. We have now used (1)H NMR spectroscopy to directly measure the thermodynamic association constants, Kas, of the standard ribonucleotide monophosphates (rNMPs) to native RNA primer-template complexes. The binding affinities of rNMPs to duplexes with a complementary single-nucleotide overhang follow the order C > G > A > U. Notably, these monomers bind more strongly to RNA primer-template complexes than to the analogous DNA complexes. The relative binding affinities of the rNMPs for complementary RNA primer-template complexes are in good quantitative agreement with the predictions of a nearest-neighbor analysis. With respect to G:U wobble base-pairing, we find that the binding of rGMP to a primer-template complex with a 5'-U overhang is approximately 10-fold weaker than to the complementary 5'-C overhang. We also find that the binding of rGMP is only about 2-fold weaker than the binding of rAMP to 5'-U, consistent with the poor fidelity observed in the nonenzymatic copying of U residues in RNA templates. The accurate Ka measurements for ribonucleotides obtained in this study will be useful for designing higher fidelity, more effective RNA replication systems.

Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension

The nonenzymatic replication of RNA oligonucleotides is thought to have played a key role in the origin of life prior to the evolution of ribozyme-catalyzed RNA replication. Although the copying of oligo-C templates by 2-methylimidazole-activated G monomers can be quite efficient, the copying of mixed sequence templates, especially those containing A and U, is particularly slow and error-prone. The greater thermodynamic stability of the 2-thio-U(s²U):A base pair, relative to the canonical U:A base pair, suggests that replacing U with s²U might enhance the rate and fidelity of the nonenzymatic copying of RNA templates. Here we report that this single atom substitution in the activated monomer improves both the kinetics and the fidelity of nonenzymatic primer extension on mixed-sequence RNA templates. In addition, the mean lengths of primer extension products obtained with s²U is greater than those obtained with U, augmenting the potential for nonenzymatic replication of heritable function-rich sequences. We suggest that noncanonical nucleotides such as s²U may have played a role during the infancy of the RNA world by facilitating the nonenzymatic replication of genomic RNA oligonucleotides.

Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

Neglect of diatomic differential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models commonly employed in combined quantum mechanical/molecular mechanical simulations fail to adequately describe the deoxyribose and ribose sugar ring puckers. This failure limits the application of these methods to RNA and DNA systems. In this work, we provide benchmark ab initio gas-phase two-dimensional potential energy scans of the RNA and DNA sugar puckering. The benchmark calculations are compared with semiempirical models. Pucker corrections are introduced into the semiempirical models via B-spline interpolation of the potential energy difference surface relative to the benchmark data. The corrected semiempirical models are shown to well reproduce the ab initio puckering profiles. Furthermore, we demonstrate that the uncorrected semiempirical models do not usually produce a transition state between the A-form and B-form sugar puckers, but the ab initio transition state is reproduced when the B-spline correction is used.

The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids

The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2'-endo and C3'-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2'-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3'-endo state. However, at a 2'-5' linkage, the minimum shifts to the C2'-endo conformation. The free energy of the C3'-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3'-endo to C2'-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2'-5' linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations.

Escalation of polymerization in a thermal gradient

For the emergence of early life, the formation of biopolymers such as RNA is essential. However, the addition of nucleotide monomers to existing oligonucleotides requires millimolar concentrations. Even in such optimistic settings, no polymerization of RNA longer than about 20 bases could be demonstrated. How then could self-replicating ribozymes appear, for which recent experiments suggest a minimal length of 200 nt? Here, we demonstrate a mechanism to bridge this gap: the escalated polymerization of nucleotides by a spatially confined thermal gradient. The gradient accumulates monomers by thermophoresis and convection while retaining longer polymers exponentially better. Polymerization and accumulation become mutually self-enhancing and result in a hyperexponential escalation of polymer length. We describe this escalation theoretically under the conservative assumption of reversible polymerization. Taking into account the separately measured thermophoretic properties of RNA, we extrapolate the results for primordial RNA polymerization inside a temperature gradient in pores or fissures of rocks. With a dilute, nanomolar concentration of monomers the model predicts that a pore length of 5 cm and a temperature difference of 10 K suffice to polymerize 200-mers of RNA in micromolar concentrations. The probability to generate these long RNAs is raised by a factor of >10(600) compared with polymerization in a physical equilibrium. We experimentally validate the theory with the reversible polymerization of DNA blocks in a laser-driven thermal trap. The results confirm that a thermal gradient can significantly enlarge the available sequence space for the emergence of catalytically active polymers.

Nucleotide-based copying of nucleic acid sequences without enzymes

Chemical primer extension is the enzyme-free incorporation of nucleotides at the end of an oligonucleotide, directed by a template. The reaction mimics the copying of sequences during replication but relies on recognition and reactivity of nucleic acids alone. Copying is low-yielding, particularly for long RNA. Hydrolysis of active esters and inhibition through hydrolysis products have been identified as factors that prevent high yields, and approaches to overcoming them have culminated in successful template-directed solid-phase syntheses for RNA and phosphoramidate DNA.

Synthesis of N3'-P5'-linked phosphoramidate DNA by nonenzymatic template-directed primer extension

A fast and accurate pathway for nonenzymatic RNA replication would simplify models for the emergence of the RNA world from the prebiotic chemistry of the early earth. However, numerous difficulties stand in the way of an experimental demonstration of effective nonenzymatic RNA replication. To gain insight into the necessary properties of potentially self-replicating informational polymers, we have studied several model systems based on amino–sugar nucleotides. Here we describe the synthesis of N3′–P5′-linked phosphoramidate DNA (3′-NP-DNA) by the template-directed polymerization of activated 3′-amino-2′,3′-dideoxyribonucleotides. 3′-NP-DNA is an interesting model because of its very RNA-like A-type duplex conformation and because activated 3′-amino-2′,3′-dideoxyribonucleotides are much more reactive than the corresponding activated ribonucleotides. In contrast to our previous studies with 2′-amino-2′,3′-dideoxyribonucleotides (for which G and C but not A and T exhibit efficient template copying), we have found that all four canonical 3′-amino-2′,3′-dideoxyribonucleotides (G, C, A, and T) polymerize efficiently on RNA templates. RNA templates are generally superior to DNA templates, and oligo-ribo-T templates are superior to oligo-ribo-U templates, which are the least efficient of the RNA homopolymer templates. We have also found that activation of 3′-aminonucleotides with 2-methylimidazole results in a ca. 10-fold higher polymerization rate relative to activation with imidazole, an observation that parallels earlier findings with ribonucleotides. We discuss the implications of our experiments for the possibility of self-replication in the 3′-NP-DNA and RNA systems.

Synthesis and structural studies of S-type/N-type-locked/frozen nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2'-5' linked oligonucleotides

2'-endo locked or frozen (S-type)/3'-endo locked or frozen (N-type) nucleoside analogues were synthesized. Conformational analysis based on (3)J(HH) and NOE measurements is presented which is further confirmed by X-ray crystal structural studies. 2'-5'isoDNA oligonucleotides (ON) were synthesized using these modified nucleoside analogues and UV-T(m) studies of the resultant 2'-5'isoDNA : RNA duplexes reflect the site- and sequence-dependent effects and confirm that the S-type sugar conformations were preferred over the N-type sugar geometry in such duplexes.

The XNA world: progress towards replication and evolution of synthetic genetic polymers

Life's diversity is built on the wide range of properties and functions that can be encoded in natural biopolymers such as polypeptides and nucleic acids. However, despite their versatility, the range of chemical functionalities is limited, particularly in the case of nucleic acids. Chemical modification of nucleic acids can greatly increase their functional diversity but access to the full phenotypic potential of such polymers requires a system of replication. Here we review progress in the chemical and enzymatic synthesis, replication and evolution of unnatural nucleic acid polymers, which promises to enable the exploration of a vast sequence space not accessible to nature and deliver ligands, catalysts and materials based on this new class of biopolymers.