Self-programmable, self-assembling two-dimensional genetic matter

Fundamental constraints to the logic of living systems

It has been argued that the historical nature of evolution makes it a highly path-dependent process. Under this view, the outcome of evolutionary dynamics could have resulted in organisms with different forms and functions. At the same time, there is ample evidence that convergence and constraints strongly limit the domain of the potential design principles that evolution can achieve. Are these limitations relevant in shaping the fabric of the possible? Here, we argue that fundamental constraints are associated with the logic of living matter. We illustrate this idea by considering the thermodynamic properties of living systems, the linear nature of molecular information, the cellular nature of the building blocks of life, multicellularity and development, the threshold nature of computations in cognitive systems and the discrete nature of the architecture of ecosystems. In all these examples, we present available evidence and suggest potential avenues towards a well-defined theoretical formulation.

Two-dimensional adaptive membranes with programmable water and ionic channels

Membranes are ubiquitous in nature with primary functions that include adaptive filtering and selective transport of chemical/molecular species. Being critical to cellular functions, they are also fundamental in many areas of science and technology. Of particular importance are the adaptive and programmable membranes that can change their permeability or selectivity depending on the environment. Here, we explore implementation of such biological functions in artificial membranes and demonstrate two-dimensional self-assembled heterostructures of graphene oxide and polyamine macromolecules, forming a network of ionic channels that exhibit regulated permeability of water and monovalent ions. This permeability can be tuned by a change of pH or the presence of certain ions. Unlike traditional membranes, the regulation mechanism reported here relies on specific interactions between the membranes' internal components and ions. This allows fabrication of membranes with programmable, predetermined permeability and selectivity, governed by the choice of components, their conformation and their charging state.

Real-space evidence of Watson-Crick and Hoogsteen adenine-uracil base pairs on Au(111)

From the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, we show the real-space evidence of the formation of Watson-Crick and Hoogsteen adenine-uracil base pairs on an Au(111) surface with the employment of base derivatives, and further investigate the relative stability of the two types of adenine-uracil base pairs.

Interaction of Nucleic Acid Bases with the Au(111) Surface

The fate of an individual DNA molecule when it is deposited on a hard inorganic surface in a "dry" environment is unknown, while it is a crucial determinant for nanotechnology applications of nucleic acids. In the absence of experimental approaches that are able to unravel the three-dimensional atomic structure of the target system, here we tackle the first step toward a computational solution of the problem. By using first-principles quantum mechanical calculations of the four nucleobases on the Au(111) surface, we present results for the geometries, energetics, and electronic structure, in view of developing a force field that will enable classical simulations of DNA on Au(111) to investigate the structural modifications of the duplex in these non-native conditions. We fully characterize each system at the individual level. We find that van der Waals interactions are crucial for a correct description of the geometry and energetics. However, the mechanism of adsorption is well beyond pure dispersion interactions. Indeed, we find charge sharing between the substrate and the adsorbate, the formation of hybrid orbitals, and even bonding orbitals. Yet, this molecule-surface association is qualitatively distinct from the thiol adsorption mechanism: we discuss such differences and also the relation to the adsorption mechanism of pure aromatic molecules.

Steering supramolecular patterns by nucleobase-terminated molecules

Supramolecular patterns formed by adsorption from a liquid of nucleobase-terminated molecular rods on a graphite surface were investigated by scanning tunneling microscopy.

Recognition ability of DNA for carbon nanotubes correlates with their binding affinity

The ability to sort mixtures of carbon nanotubes (CNTs) based on chirality has recently been demonstrated using special short DNA sequences that recognize certain matching CNTs of specific chirality. In this work, we report on a study of the relationship between recognition sequences and the strength of their binding to the recognized CNT. We have chosen the (6,5) CNT and its corresponding DNA recognition sequences for investigation in this study. Binding strength is quantified by studying the kinetics of DNA replacement by a surfactant, which is monitored by following shifts in the absorption spectrum. We find that recognition ability correlates strongly with binding strength thus measured; addition or subtraction of just one base from the recognition sequence can enhance the kinetics of DNA displacement some 20-fold. The surfactant displaces DNA in two steps: a rapid first stage lasting less than a few seconds, followed by progressive removal lasting tens of minutes. The kinetics of the second stage is analyzed to extract activation energies. Fluorescence studies support the finding that the DNA sequence that recognizes the (6,5)-CNT forms a more stable hybrid than its close relatives.

Emergence of self-reproduction in cooperative chemical evolution of prebiological molecules

The paper presents a model of coevolution of short peptides (P) and short oligonucleotides (N) at an early stage of chemical evolution leading to the origin of life. The model describes polymerization of both P and N types of molecules on mineral surfaces in aqueous solution at moderate temperatures. It is assumed that amino acid and nucleotide monomers were available in a prebiotic milieu, that periodic variation in environmental conditions between dry/warm and wet/cool took place and that energy sources were available for the polymerization. An artificial chemistry approach in combination with agent-based modeling was used to explore chemical evolution from an initially random mixture of monomers. It was assumed that the oligonucleotides could serve as templates for self-replication and for translation of peptide compositional sequences, and that certain peptides could serve as weak catalysts. Important features of the model are the short lengths of the peptide and oligonucleotide molecules that prevent an error catastrophe caused by copying errors and a finite diffusion rate of the molecules on a mineral surface that prevents excessive development of parasitism. The result of the simulation was the emergence of self-replicating molecular systems consisting of peptide catalysts and oligonucleotide templates. In addition, a smaller but significant number of molecules with alternative compositions also survived due to imprecise reproduction and translation of templates providing variability for further evolution. In a more general context, the model describes not only peptide-oligonucleotide molecular systems, but any molecular system containing two types of polymer molecules: one of which serves as templates and the other as catalysts.The presented coevolutionary system suggests a possible direction towards finding the origin of molecular functionality in a prebiotic environment.

A van der Waals density functional study of adenine on graphene: single-molecular adsorption and overlayer binding

The adsorption of an adenine molecule on graphene is studied using a first-principles van der Waals functional, vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401). The cohesive energy of an ordered adenine overlayer is also estimated. For the adsorption of a single molecule, we determine the optimal binding configuration and adsorption energy by translating and rotating the molecule. The adsorption energy for a single molecule of adenine is found to be 711 meV, which is close to the calculated adsorption energy of the similarly sized naphthalene. On the basis of the single-molecular binding configuration, we estimate the cohesive energy of a two-dimensional ordered overlayer. We find a significantly stronger binding energy for the ordered overlayer than for single-molecule adsorption.

Influence of tunable external stimuli on the self-assembly of guanosine supramolecular nanostructures studied by atomic force microscope

The self-assembly of guanosine (G) molecules on solid surfaces is investigated by tapping-mode atomic force microscopy (AFM) upon controlling and introducing external factors (stimuli) to the G stock solution such as incubation time, presence/absence of metal cations, and mechanical shaking. Surprisingly, at different stages of incubation time at room temperature and in the absence of any metal cations in the G stock solution, which are known to be one of the governing factors in forming G-nanostructures, two assembly pathways resulting into two distinct supramolecular nanostructures were revealed. Astonishingly, by introducing a mechanical shaking of the tube containing the G stock solution, one-dimensional (1D) wires of G molecules are observed by AFM, and very interestingly, novel "branched" supramolecular nanostructures are formed. We have also observed that the later branched G nanostructures can grow further into a two-dimensional (2D) thin film by increasing the incubation time of the G stock solution at room temperature after it is exposed to the external mechanical stimuli. The self-assembled nanostructures of G molecules are changed significantly by tuning the assembly conditions, which show that it is indeed possible to grow complex 2D nanostructures from simple nucleoside molecules.

Two-dimensional self-assembly and complementary base-pairing between amphiphile nucleotides on graphite

2D supramolecular structures on HOPG by self-assembly of physisorbed amphiphile nucleotides have been successfully imaged by high resolution STM. The organization of the systems depends on the nature of nucleic bases. In the case of the thymidine derivative a head-to-tail self-assembly is observed, whereas the amphiphile adenosine affords head-to-head nanostructures. The co-adsorption of complementary A+T amphiphile molecules induces the formation of a third head-to-head 2D supramolecular structure stabilized via base pairing. Molecular modelling calculations including the graphite surface provide models for all the 2D supramolecular systems observed.

Steps towards the formation of a protocell: the possible role of short peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.

Spontaneous self-association of adenine and uracil in polycrystals from low temperature FTIR spectra in the range below 1000 cm(-1)

FTIR spectra of solid samples of co-crystallized adenine and uracil were measured at 10K in the range below 1000cm(-1). New bands ascribable to the N3H (uracil) and NH(2) (adenine) out of plane vibrations, which disappear upon D-exchange, were revealed in comparison with the spectra of pure polycrystalline adenine and uracil obtained in the same conditions. The observed changes relate to the same groups that establish the H-bonds in base pairs of naturally occurring nucleic acids, despite the presence of an extra proton donor NH-group in both molecules. The well-established empirical correlation between the out of plane NH vibrational frequencies and H-bond energies was successfully applied for estimation of the latter in the mixed crystal.

Attracted by long-range electron correlation: adenine on graphite

The adsorption of adenine on graphite is analyzed from first-principles calculations as a model case for the interaction between organic molecules and chemically inert surfaces. Within density-functional theory we find no chemical bonding due to ionic or covalent interactions, only a very weak attraction at distances beyond the equilibrium position due to the lowering of the kinetic energy of the valence electrons. Electron exchange and correlation effects are much more important for the stabilization of the adsystem. They are modeled by the local density or generalized gradient approximation supplemented by the London dispersion formula for the van der Waals interaction.

Coulombic amino group-metal bonding: adsorption of adenine on Cu110

The interaction between molecular amino groups and metal surfaces is analyzed from first-principles calculations using the adsorption of adenine on Cu110 as a model case. The amino group nitrogens are found to adsorb on top of the surface copper atoms. However, the bonding clearly cannot be explained in terms of covalent interactions. Instead, we find it to be largely determined by mutual polarization and Coulomb interaction between substrate and adsorbate.

Early assembly of cellular life

Popular hypotheses that attempt to explain the origin of prebiotic molecules and cellular life capable of growth and division are not always agreed upon. In this manuscript, information on early bacterial life on Earth is examined using information from several disciplines. For example, knowledge can be integrated from physics, thermodynamics, planetary sciences, geology, biogeochemistry, lipid chemistry, primordial cell structures, cell and molecular biology, microbiology, metabolism and genetics. The origin of life also required a combination of elements, compounds and environmental physical-chemical conditions that allowed cells to assemble in less than a billion years. This may have been widespread in the subsurface of the early Earth located at microscopic physical domains.

Primordial coding of amino acids by adsorbed purine bases

Scanning tunneling microscopy and chromatography experiments exploring the potential templating properties of nucleic acid bases adsorbed to the surface of crystalline graphite, revealed that the interactions of amino acids with the bare crystal surface are significantly modulated by the prior adsorption of adenine and hypoxanthine. These bases are the coding elements of a putative purine-only genetic alphabet and the observed effects are different for each of the bases. Such mapping between bases and amino acids provides a coding mechanism. These observations demonstrate that a simple pre-RNA amino acid discrimination mechanism could have existed on the prebiotic Earth providing critical functionality for the origin of life.

Life before RNA

The hypothesis that life originated and evolved from linear informational molecules capable of facilitating their own catalytic replication is deeply entrenched. However, widespread acceptance of this paradigm seems oblivious to a lack of direct experimental support. Here, we outline the fundamental objections to the de novo appearance of linear, self-replicating polymers and examine an alternative hypothesis of template-directed coding of peptide catalysts by adsorbed purine bases. The bases (which encode biological information in modern nucleic acids) spontaneously self-organize into two-dimensional molecular solids adsorbed to the uncharged surfaces of crystalline minerals; their molecular arrangement is specified by hydrogen bonding rules between adjacent molecules and can possess the aperiodic complexity to encode putative protobiological information. The persistence of such information through self-reproduction, together with the capacity of adsorbed bases to exhibit enantiomorphism and effect amino acid discrimination, would seem to provide the necessary machinery for a primitive genetic coding mechanism.

Modulation of adenosine 5'-monophosphate adsorption onto aqueous resident pyrite: potential mechanisms for prebiotic reactions

The adsorption of adenosine 5'-monophosphate (5'-AMP) onto pyrite (FeS2) and its modulation by acetate, an organic precursor of complex metabolic pathways, was studied in aqueous media that simulate primitive environments. 5'-AMP adsorption requires divalent cations, indicating that a cationic bridge mediates its attachment to negatively charged sites of the mineral surface. The isotherm of 5'-AMP adsorption exhibits a strong cooperative effect at low nucleotide concentrations in acetate-rich medium, whereas high levels of adsorption were only found at high nucleotide concentrations in a model of primitive seawater (acetate free). The modulating role of acetate is also evidenced in the presence of high dipolar moment molecules: dimethyl sulfoxide (Me2SO) and dimethyl formamide (DMF) strongly inhibit 5'-AMP adsorption in acetate-rich media, whereas no effect of DMF was found in artificial seawater. The observation that exogenous divalent cations are not needed for acetate attachment onto FeS2 reveals that organic acids can interact with the Fe2+ atoms in the mineral surface. All considered, the results show that complex and flexible ironsulfide/biomonomers interactions can be modulated by molecules that accumulate in the interface layer.

Origins of life: a route to nanotechnology

The origins of life and nanotechnology are two seemingly disparate areas of scientific investigation. However, the fundamental questions of life's beginnings and the applied construction of a Drexlerian nanotechnology both share a similar problem; how did and how can self-reproducing molecular machines originate? Here we draw attention to the coincidence between nanotechnology and origins research with particular attention paid to the spontaneous adsorption and scanning tunneling microscopy investigation of purine and pyrimidine bases self-organized into monolayers, adsorbed to the surfaces of crystalline solids. These molecules which encode biological information in nucleic acids, can form supramolecular architectures exhibiting enantiomorphism with the complexity to store and encode putative protobiological information. We conclude that the application of nanotechnology to the investigation of life's origins, and vice versa, could provide a viable route to an evolution-driven synthetic life.

Differential adsorption of nucleic acid bases: Relevance to the origin of life

The adsorption of organic molecules onto the surfaces of inorganic solids has long been considered a process relevant to the origin of life. We have determined the equilibrium adsorption isotherms for the nucleic acid purine and pyrimidine bases dissolved in water on the surface of crystalline graphite. The markedly different adsorption behavior of the bases describes an elutropic series: guanine > adenine > hypoxanthine > thymine > cytosine > uracil. We propose that such differential properties were relevant to the prebiotic chemistry of the bases and may have influenced the composition of the primordial genetic architecture.

Effect of temperature on the adsorption of adenine

Equilibrium adsorption isotherms for the purine base adenine on the surface of graphite crystals have been obtained at 30, 40, 50, and 60 degrees C by frontal analysis using water as a mobile phase. These data were fitted to the Langmuir isotherm model and interpreted in terms of the well-characterized adsorbate monolayer structure. A van't Hoff plot was used to estimate the adsorption enthalpy, -delta H degree which we determined to be 20 kJ mol-1. The susceptibility of nucleic acid bases to aqueous-phase hydrolysis may have been a limiting feature for their inclusion in the primordial genetic architecture; our results suggest that the effects of temperature and the presence of inorganic solids must also be included when assessing the prebiotic availability of adenine.