Phototriggered DNA phosphoramidate ligation in a tandem 5'-amine deprotection/3'-imidazole activated phosphate coupling reaction.

We report the preparation and use of an N-methyl picolinium carbamate protecting group for applications in a phototriggered nonenzymatic DNA phosphoramidate ligation reaction. Selective 5'-amino protection of a modified 13-mer oligonucleotide is achieved in aqueous solution by reaction with an N-methyl-4-picolinium carbonyl imidazole triflate protecting group precursor. Deprotection is carried out by photoinduced electron transfer from Ru(bpy)(3)(2+) using visible light photolysis and ascorbic acid as a sacrificial electron donor. Phototriggered 5'- amino oligonucleotide deprotection is used to initiate a nonenzymatic ligation of the 13-mer to an imidazole activated 3'-phospho-hairpin template to generate a ligated product with a phosphoramidate linkage. We demonstrate that this methodology offers a simple way to exert control over reaction initiation and rates in nonenzymatic DNA ligation for potential applications in the study of model protocellular systems and prebiotic nucleic acid synthesis.

Interactions between catalysts and amphiphilic structures and their implications for a protocell model.

One of the essential elements of any cell, including primitive ancestors, is a structural component that protects and confines the metabolism and genes while allowing access to essential nutrients. For the targeted protocell model, bilayers of decanoic acid, a single-chain fatty acid amphiphile, are used as the container. These bilayers interact with a ruthenium-nucleobase complex, the metabolic complex, to convert amphiphile precursors into more amphiphiles. These interactions are dependent on non-covalent bonding. The initial rate of conversion of an oily precursor molecule into fatty acid was examined as a function of these interactions. It is shown that the precursor molecule associates strongly with decanoic acid structures. This results in a high dependence of conversion rates on the interaction of the catalyst with the self-assembled structures. The observed rate logically increases when a tight interaction between catalyst complex and container exists. A strong association between the metabolic complex and the container was achieved by bonding a sufficiently long hydrocarbon tail to the complex. Surprisingly, the rate enhancement was nearly as strong when the ruthenium and nucleobase elements of the complex were each given their own hydrocarbon tail and existed as separate molecules, as when the two elements were covalently bonded to each other and the resulting molecule was given a hydrocarbon tail. These results provide insights into the possibilities and constraints of such a reaction system in relation to building the ultimate protocell.

Coarse graining and scaling in dissipative particle dynamics.

Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent the applicability of the method to the whole mesoscopic range. This article aims to re-establish DPD as a truly mesoscopic method by analyzing the problems reported by other authors and by presenting a scaling scheme that allows one to apply DPD simulations directly to any desired length scale.

Nucleobase mediated, photocatalytic vesicle formation from an ester precursor.

We report the use of photoinduced electron transfer to drive reductive cleavage of an ester to produce bilayer-forming molecules; specifically, visible photolysis in a mixture of a decanoic acid ester precursor, hydrogen donor molecules, and a ruthenium-based photocatalyst that employs a linked nucleobase (8-oxo-guanine) as an electron donor generates decanoic acid. The overall transformation of the ester precursor to yield vesicles represents the use of an external energy source to convert nonstructure forming molecules into amphiphiles that spontaneously assemble into vesicles. The core of our chemical reaction system uses an 8-oxo-G-Ru photocatalyst, a derivative of [tris(2,2'-bipyridine)-Ru(II)](2+).

Eutectic phase in water-ice: a self-assembled environment conducive to metal-catalyzed non-enzymatic RNA polymerization.

Information and catalytic polymers play an essential role in contemporary cellular life, and their emergence must have been crucial during the complex processes that led to the assembly of the first living systems. Polymerization reactions producing these molecules would have had to occur in aqueous medium, which is known to disfavor such reactions. Thus, it was proposed early on that these polymerizations had to be supported by particular environments, such as mineral surfaces and eutectic phases in water-ice, which would have led to the concentration of the monomers out of the bulk aqueous medium and their condensation. This review presents the work conducted to understand how the eutectic phases in water-ice might have promoted RNA polymerization, thereby presumably contributing to the emergence of the ancient information and catalytic system envisioned by the 'RNA-World' hypothesis.

Bridging coarse-grained models by jump-in-sample simulations.

We present an efficient method to construct coarse-grained (CG) models from models of finer resolution. The method estimates the free energies in a generated sample of the CG conformational space and then fits the entire effective potential surface in the high-dimensional CG conformational space. A jump-in-sample algorithm that uses a random jumping walk in the CG sample is used to iteratively estimate the free energies. We test the method in a tetrahedral molecular fluid where we construct the intermolecular effective potential and evaluate the CG molecular model. Our algorithm for calculating the free energy involves an improved Wang-Landau (WL) algorithm, which not only works more efficiently than the standard WL algorithm, but also can work in high-dimensional spaces.

Life cycle of a minimal protocell--a dissipative particle dynamics study.

Cross-reactions and other systematic difficulties generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key issues as we represent and analyze in simulation a full implementation of a minimal protocell. Using a 3D dissipative particle dynamics simulation method, we are able to address the coupled diffusion, self-assembly, and chemical reaction processes required to model a full life cycle of a protocell composed of coupled genetic, metabolic, and container subsystems. Utilizing this minimal structural and functional representation of the constituent molecules, their interactions, and their reactions, we identify and explore the nature of the many linked processes for the full protocellular system. Obviously the simplicity of this simulation method combined with the inherent system complexity prevents us from expecting quantitative simulation predictions from these investigations. However, we report important findings on systemic processes, some previously predicted and some newly discovered, as we couple the protocellular self-assembly processes and chemical reactions.

Generic Darwinian selection in catalytic protocell assemblies.

To satisfy the minimal requirements for life, an information carrying molecular structure must be able to convert resources into building blocks and also be able to adapt to or modify its environment to enhance its own proliferation. Furthermore, new copies of itself must have variable fitness such that evolution is possible. In practical terms, a minimal protocell should be characterized by a strong coupling between its metabolism and genetic subsystem, which is made possible by the container. There is still no general agreement on how such a complex system might have been naturally selected for in a prebiotic environment. However, the historical details are not important for our investigations as they are related to assembling and evolution of protocells in the laboratory. Here, we study three different minimal protocell models of increasing complexity, all of them incorporating the coupling between a 'genetic template', a container and, eventually, a toy metabolism. We show that for any local growth law associated with template self-replication, the overall temporal evolution of all protocell's components follows an exponential growth (efficient or uninhibited autocatalysis). Thus, such a system attains exponential growth through coordinated catalytic growth of its component subsystems, independent of the replication efficiency of the involved subsystems. As exponential growth implies the survival of the fittest in a competitive environment, these results suggest that protocell assemblies could be efficient vehicles in terms of evolving through Darwinian selection.

Emergence of protocellular growth laws.

Template-directed replication is known to obey a parabolic growth law due to product inhibition (Sievers & Von Kiedrowski 1994 Nature 369, 221; Lee et al. 1996 Nature 382, 525; Varga & Szathmáry 1997 Bull. Math. Biol. 59, 1145). We investigate a template-directed replication with a coupled template catalysed lipid aggregate production as a model of a minimal protocell and show analytically that the autocatalytic template-container feedback ensures balanced exponential replication kinetics; both the genes and the container grow exponentially with the same exponent. The parabolic gene replication does not limit the protocellular growth, and a detailed stoichiometric control of the individual protocell components is not necessary to ensure a balanced gene-container growth as conjectured by various authors (Gánti 2004 Chemoton theory). Our analysis also suggests that the exponential growth of most modern biological systems emerges from the inherent spatial quality of the container replication process as we show analytically how the internal gene and metabolic kinetics determine the cell population's generation time and not the growth law (Burdett & Kirkwood 1983 J. Theor. Biol. 103, 11-20; Novak et al. 1998 Biophys. Chem. 72, 185-200; Tyson et al. 2003 Curr. Opin. Cell Biol. 15, 221-231). Previous extensive replication reaction kinetic studies have mainly focused on template replication and have not included a coupling to metabolic container dynamics (Stadler et al. 2000 Bull. Math. Biol. 62, 1061-1086; Stadler & Stadler 2003 Adv. Comp. Syst. 6, 47). The reported results extend these investigations. Finally, the coordinated exponential gene-container growth law stemming from catalysis is an encouraging circumstance for the many experimental groups currently engaged in assembling self-replicating minimal artificial cells (Szostak 2001 et al. Nature 409, 387-390; Pohorille & Deamer 2002 Trends Biotech. 20 123-128; Rasmussen et al. 2004 Science 303, 963-965; Szathma ry 2005 Nature 433, 469-470; Luisi et al. 2006 Naturwissenschaften 93, 1-13).

Hyperdynamics for entropic systems: time-space compression and pair correlation function approximation.

We develop a generalized hyperdynamics method that is able to simulate slow dynamics in atomistic general (both energy- and entropy-dominated) systems. We show that a few functionals of the pair correlation function, involving two-body entropy, form a low-dimensional collective space, which is a good approximation that is able to distinguish stable and transitional conformations. A bias potential, which raises the energy in stable regions, is constructed on the fly. We examine the slow nucleation processes of a Lennard-Jones gas and show that our method can generate correct long-time dynamics without prior knowledge.