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.

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.

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.

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.

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.

Question 9: prospects for the construction of artificial cells or protocells.

The construction of artificial cells or protocells that are a simplified version of contemporary cells will have implications for both the understanding of the origins of cellular Life and the design of "cell-like" chemical factories. In this short communication, we discuss the progress and remaining issues related to the construction of protocells from metabolic products. We further outline the de novo design of a simple chemical system that mimics the functional properties of a living cell without being composed of molecules of biological origin, thereby addressing issues related to Life's origins.

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.

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.

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.