Self-programmable,Self-assembling Two-dimensional Genetic Matter

Putative two-dimensional coding systems can beconstructed from aqueous solutions of purine andpyrimidine nucleic acid bases evaporated at moderatetemperatures on the surfaces of inorganic solids. Theresultant structures are monolayers which are formedspontaneously by molecular self-assembly and they havebeen observed with molecular resolution by scanningtunnelling microscopy (STM). When formed fromsolutions of a single base, the monolayers of adenineand uracil have crystalline characteristics and theSTM images can be interpreted in terms of thegeometrical placement of planar arranged moleculesthat interact laterally by intermolecular hydrogenbonding. When formed from solutions containing amixture of adenine and uracil, the monolayers haveaperiodic structures. Small crystalline domainswithin these monolayers can be interpreted in terms ofthe single phase configurations of the molecules andthe remaining aperiodic structures can presumably beinterpreted, geometrically, in terms of the 21theoretically possible adenine-adenine, uracil-uraciland adenine-uracil hydrogen bonding interactions. Wepropose that combinatorial arrangements of planararranged purine and pyrimidine bases could provide thenecessary complexity to act as a primitive geneticmechanism and may have relevance to the origin of life.     

Problems,successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual–Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual–Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future.     

Scanning tunneling microscopy with applications to biological surfaces

Each major advance in the field of microscopy has eventually been translated into major advances in the biological and medical sciences. The scanning tunneling microscope (STM) offers exciting new ways of imaging biological surfaces with resolution to the sub-molecular scale. Rigid, conductive surfaces can readily be imaged with the STM with atomic resolution. Unfortunately, few biological surfaces are sufficiently conductive or rigid enough to be examined directly with the STM. At present, non-conductive surfaces can be examined in two ways: 1) Sufficiently thin molecular layers attached to conductive substrates so that tunneling can occur through the molecules; or 2) coating or replicating non-conductive surfaces with metal layers so as to make them conductive, then imaging with the STM. We present images of biological and organic molecules obtained with these techniques that demonstrate the possibilities and limitations of each. Future advances leading to atomic resolution STM of biological surfaces depend on significant progress in the art and science of making biomaterials compatible with the restrictions of the instrument.     

Direct observation of microtubules with the scanning tunneling microscope

To observe surface topography of microtubules, we have applied scanning tunneling microscopy (STM), which can image metal and semiconductive surfaces with atomic resolution. Isolated microtubules fixed in 0.1% glutaraldehyde in reassembly buffer containing 0.8 M glycerol were imaged in air on a graphite substrate. The presence of microtubules in solution was verified by electron microscopy. At atmospheric pressure and room temperature, STM probing of both freeze-dried and hydrated microtubules reveals structures approximately 25 nm in width, consisting of longitudinal filaments about 4 nm in width. These structures match electron microscopy images of microtubules and their component protofilaments. Microtubules imaged by STM frequently appear buckled and semiflattened. Top-view shaded scans show what appear to be individual tubulin subunits within protofilaments. We believe these results represent the first direct STM observation of protein assemblies in which components can be identified. Although the microtubule image resolution described here is no better than that presently obtainable by other techniques (e.g., electron microscopy with freeze-drying, shadowing, and/or negative staining), it is significant that suitably prepared biomolecules may be sufficiently conductive and stable for STM imaging, which is ultimately capable of atomic resolution. Further development of STM technology, computer-enhanced image processing, and elucidation of optimal STM sample preparation indicate that STM and related applications will offer unique opportunities for the study of biomolecular surfaces.     

Self-assembly processes in the prebiotic environment

An important question guiding research on the origin of life concerns the environmental conditions where molecular systems with the properties of life first appeared on the early Earth. An appropriate site would require liquid water, a source of organic compounds, a source of energy to drive polymerization reactions and a process by which the compounds were sufficiently concentrated to undergo physical and chemical interactions. One such site is a geothermal setting, in which organic compounds interact with mineral surfaces to promote self-assembly and polymerization reactions. Here, we report an initial study of two geothermal sites where mixtures of representative organic solutes (amino acids, nucleobases, a fatty acid and glycerol) and phosphate were mixed with high-temperature water in clay-lined pools. Most of the added organics and phosphate were removed from solution with half-times measured in minutes to a few hours. Analysis of the clay, primarily smectite and kaolin, showed that the organics were adsorbed to the mineral surfaces at the acidic pH of the pools, but could subsequently be released in basic solutions. These results help to constrain the range of possible environments for the origin of life. A site conducive to self-assembly of organic solutes would be an aqueous environment relatively low in ionic solutes, at an intermediate temperature range and neutral pH ranges, in which cyclic concentration of the solutes can occur by transient dry intervals.     

On the chemistry and evolution of the pioneer organism

The theory of a chemo-autotrophic origin of life in a volcanic Iron-Sulfur World postulates the emergence of a pioneer organism within a flow of volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure, iron, cobalt, nickel, and other transition-metal centers with sulfido, carbonyl, cyano, and other ligands are catalytically active, and promote the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer organism is reproductive by an autocatalytic feedback effect, whereby some organic products serve as ligands for activating the catalytic metal centres whence they arise. This unitary structure-function relationship of the pioneer organism constitutes the 'Anlage' for two major strands of evolution: enzymatization and cellularization, whereby the upward evolution of life by increase of molecular complexity is grounded ultimately in the transition metal-catalyzed, synthetic redox chemistry of the pioneer organism.     

Scanning tunneling microscopic images show a laminated structure for glycogen molecules

Scanning tunneling microscopy (STM) has been used to examine glycogen molecules. Individual molecules were approximately ellipsoidal with dimensions in the 20- to 60-nm range. Images of the glycogen molecular surfaces have a laminar appearance. The layered features seen on the surfaces of the molecules suggest that glycogen may grow from one edge as a laminar structure to form an ellipsoid rather than originating at a central point with radial growth of the oligosaccharide chains to form a sphere. The results of these studies indicate that STM can be used to determine details of polysaccharide structures.     

早期地球的环境变化和生命的化学进化

生命起源是当代最大的科学疑谜之一,也是历来人类普遍关注的一个焦点。在地球上最早的生物出现之前,有机物经历了漫长而复杂的化学进化过程,称为生命的化学进化。地球上生命的化学进化与非生物部分的早期演化过程,是密切地相互关联、相互作用并相互制约的。文章着重阐述与生命的化学关系最为密切的冥古宙和太古宙的地球演化历史,指出这两个阶段所形成的还原性原始大气和古海洋条件在生命的化学进行中起了极其重要的作用,并且从宇宙形成、太阳系演化和地球环境早期演化的角度,探讨地球生命的化学进化历程;以地球形成初期发生了一系列复杂的有机化学反应过程,由无机分子生成生物小分子,再进一步生成生物大分子,直至最后产生原始细胞。此外,文章评述当前国际上最流行的生命化学进化学说,对早期地球的化学进化是发生在地球表面的原始海洋、粘土矿物、火山喷发等,或是来源于地球之外的宇宙空间进行了综合的阐述。     

High-resolution topography of the S-layer sheath of the archaebacterium Methanospirillum hungatei provided by scanning tunneling microscopy.

The inner and outer surfaces of the sheath of Methanospirillum hungatei GP1 have been imaged for the first time by using a bimorph scanning tunneling microscope (STM) on platinum-coated or uncoated specimens to a nominal resolution in height of ca. 0.4. nm. Unlike more usual types of microscopy (e.g., transmission electron microscopy), STM provided high-resolution topography of the surfaces, giving good depth detail which confirmed the sheath to be a paracrystalline structure possessing minute pores and therefore impervious to solutes possessing a hydrated radius of greater than 0.3 nm. STM also confirmed that the sheath consisted of a series of stacked hoops approximately 2.5 nm wide which were the remnants of the sheath after treatment with 2% (wt/vol) sodium dodecyl sulfate-2% (vol/vol) beta-mercaptoethanol (pH 9.0). No topographical infrastructure could be seen on the sides of the hoops. This research required the development of a new long-range STM capable of detecting small particles such as bacteria on graphite surfaces as well as a new "hopping" STM mode which did not deform the poorly conducting bacterial surface during high-resolution topographical analysis.     

Role of amphiphilic compounds in the evolution of membrane structure on the early earth

A variety of amphiphilic compounds have the capacity to self-assemble into membranous structures in the form of bilayers. The earliest cellular organisms must have incorporated such compounds into boundary membranes, and this review discusses amphiphilic components of the prebiotic environment which would be candidates. One possible source is organic material carried to the earth's surface by meteoritic infall. To test this, we have extracted and analysed non-polar substances from the Murchison carbonaceous chondrite, and found that at least some of the components can produce boundary structures which resemble membranes. This observation suggests that membranous boundary structures were present on the early earth, and available to participate in the origin and evolution of the first cellular forms of life.     

Interfacial electrochemical electron transfer in biology - towards the level of the single molecule

Physical electrochemistry has undergone a remarkable evolution over the last few decades, integrating advanced techniques and theory from solid state and surface physics. Single-crystal electrode surfaces have been a core notion, opening for scanning tunnelling microscopy directly in aqueous electrolyte (in situ STM). Interfacial electrochemistry of metalloproteins is presently going through a similar transition. Electrochemical surfaces with thiol-based promoter molecular monolayers (SAMs) as biomolecular electrochemical environments and the biomolecules themselves have been mapped with unprecedented resolution, opening a new area of single-molecule bioelectrochemistry. We consider first in situ STM of small redox molecules, followed by in situ STM of thiol-based SAMs as molecular views of bioelectrochemical environments. We then address electron transfer metalloproteins, and multi-centre metalloenzymes including applied single-biomolecular perspectives based on metalloprotein/metallic nanoparticle hybrids.     

Controversies on the origin of life.

Different viewpoints, many with deep philosophical and historical roots, have shaped the scientific study of the origin of life. Some of these argue that primeval life was based on simple anaerobic microorganisms able to use a wide inventory of abiotic organic materials (i.e. a heterotrophic origin), whereas others invoke a more sophisticated organization, one that thrived on simple inorganic molecules (i.e. an autotrophic origin). While many scientists assume that life started as a self-replicative molecule, the first gene, a primitive self-catalytic metabolic network has also been proposed as a starting point. Even the emergence of the cell itself is a contentious issue: did boundaries and compartments appear early or late during life's origin? Starting with a recent definition of life, based on concepts of autonomy and open-ended evolution, it is proposed here that, firstly, organic molecules self-organized in a primordial metabolism located inside protocells. The flow of matter and energy across those early molecular systems allowed the generation of more ordered states, forming the cradle of the first genetic records. Thus, the origin of life was a process initiated within ecologically interconnected autonomous compartments that evolved into cells with hereditary and true Darwinian evolutionary capabilities. In other words, the individual existence of life preceded its historical-collective dimension.     

From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya

The theory of a chemoautotrophic origin of life in a volcanic iron-sulphur world postulates a pioneer organism at sites of reducing volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure iron, cobalt, nickel and other transition metal centres with sulphido, carbonyl and other ligands were catalytically active and promoted the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer metabolism was reproductive by an autocatalytic feedback mechanism. Some organic products served as ligands for activating catalytic metal centres whence they arose. The unitary structure-function relationship of the pioneer organism later gave rise to two major strands of evolution: cellularization and emergence of the genetic machinery. This early phase of evolution ended with segregation of the domains Bacteria, Archaea and Eukarya from a rapidly evolving population of pre-cells. Thus, life started with an initial, direct, deterministic chemical mechanism of evolution giving rise to a later, indirect, stochastic, genetic mechanism of evolution and the upward evolution of life by increase of complexity is grounded ultimately in the synthetic redox chemistry of the pioneer organism.     

Atomic-resolution STM structure of DNA and localization of the retinoic acid binding site

Single-molecule imaging by scanning tunnelling microscopy (STM) yields the atomic-resolution (0.6A) structure of individual B-type DNA molecules. The strong correlation between these STM structures and those predicted from the known base sequence indicates that sequencing of single DNA molecules using STM may be feasible. There is excellent agreement between the STM and X-ray structures, but subtle differences exist due to radial distortions. We show that the interactions of other molecules with DNA, their binding configurations, and the structure of these complexes can be studied at the single-molecule level. The anti-cancer drug retinoic acid (RA) binds selectively to the minor groove of DNA with up to 6 RA molecules per DNA turn and with the plane of the RA molecule approximately parallel to the DNA symmetry axis. Similar studies for other drug molecules will be valuable in the a priori evaluation of the effectiveness of anti-cancer drugs.     

A Model for the Origin of Life through Rearrangements among Prebiotic Phosphodiester Polymers

This model proposes that the origin of life on Earth occurred as a result of a process of alteration of the chemical composition of prebiotic macromolecules. The stability of organic compounds assembled into polymers generally exceeded the stability of the same compounds as free monomers. This difference in stability stimulated accumulation of prebiotic macromolecules. The prebiotic circulation of matter included constant formation and decomposition of polymers. Spontaneous chemical reactions between macromolecules with phosphodiester backbones resulted in a non-Darwinian selection for chemical stability, while formation of strong structures provided an advantage in the struggle for stability. Intermolecular structures between nucleotide-containing polymers were further stabilized by occasional acquisition of complementary nucleotides. Less stable macromolecules provided the source of nucleotides. This process resulted first in the enrichment of nucleotide content in prebiotic polymers, and subsequently in the accumulation of complementary oligonucleotides. Finally, the role of complementary copy molecules changed from the stabilization of the original templates to the de novo production of template-like molecules. I associate this stage with the origin of life in the form of cell-free molecular colonies. Original life acquired ready-to-use substrates from constantly forming prebiotic polymers. Metabolism started to develop when life began to consume more substrates than the prebiotic cycling produced. The developing utilization of non-polymeric compounds stimulated the formation of the first membrane-enveloped cells that held small soluble molecules. Cells “digested” the nucleotide-containing prebiotic macromolecules to nucleotide monomers and switched the mode of replication to the polymerization of nucleotide triphosphates.     

Layered Double Hydroxide Minerals as Possible Prebiotic Information Storage and Transfer Compounds

One of the fundamental difficulties when considering the origin of life on Earth is the identification of an emergent system that not only replicated, but also had the capacity to undergo discrete mutation in such a way that following generations might inherit and pass on the mutation. We speculate that the layered double hydroxide (LDH) minerals are plausible candidates for a proto-RNA molecule. We describe a hypothetical LDH-like system which, when intercalated with certain anions, forms crystals with a high degree of internal order giving rise to novel information storage structures in which replication fidelity is maintained, a concept we use to propose an explanation for interstratification in terephthalate LDHs. The external surfaces of these hypothetical crystals provide active sites whose structure and chemistry is dictated by the internal information content of the LDH. Depending on the LDH polytype, the opposing external surfaces of a crystal may give rise to reactive sites that are either complementary or mirror images of each other, and so may be chiral. We also examine similarities between these proposed “proto-RNA” structures and the DNA that encodes the hereditary information in life today, concluding with a hypothetical scenario wherein these proto-RNA molecules predated the putative RNA-world.     

The organic codes. The basic mechanism of macroevolution.

The origin of the genetic code coincided with the origin of life, while the human codes of cultural evolution emerged almost four billion years later. Modern biology does not recognize any other organic code in nature, and is bound therefore to conclude that the whole of cellular evolution consisted of informational changes. Semantic transformations, natural conventions and biological meaning are things that officially do not exist in the organic world, and play no part in our reconstruction of development and evolution. And yet the properties of organic codes are beginning to emerge in various biological processes. Here it is shown that splicing, signal transduction and pattern formation can be accounted for precisely by the existence of organic codes. It is also shown that those processes were instrumental in bringing about major changes in the history of life, and it is concluded that every main step of macroevolution corresponded to the origin of a new organic code.     

An Experimental Framework for Generating Evolvable Chemical Systems in the Laboratory

Most experimental work on the origin of life has focused on either characterizing the chemical synthesis of particular biochemicals and their precursors or on designing simple chemical systems that manifest life-like properties such as self-propagation or adaptive evolution. Here we propose a new class of experiments, analogous to artificial ecosystem selection, where we select for spontaneously forming self-propagating chemical assemblages in the lab and then seek evidence of a response to that selection as a key indicator that life-like chemical systems have arisen. Since surfaces and surface metabolism likely played an important role in the origin of life, a key experimental challenge is to find conditions that foster nucleation and spread of chemical consortia on surfaces. We propose high-throughput screening of a diverse set of conditions in order to identify combinations of “food,” energy sources, and mineral surfaces that foster the emergence of surface-associated chemical consortia that are capable of adaptive evolution. Identification of such systems would greatly advance our understanding of the emergence of self-propagating entities and the onset of adaptive evolution during the origin of life.     

Origins of life: A comparison of theories and application to Mars

The field of study that deals with the origins of life does not have a consensus for a theory of life's origin. An analysis of the range of theories offered shows that they share some common features that may be reliable predictors when considering the possible origins of life on another planet. The fundamental datum dealing with the origins of life is that life appeared early in the history of the Earth, probably before 3.5 Ga and possibly before 3.8 Ga. What might be called the standard theory (the Oparin-Haldane theory) posits the production of organic molecules on the early Earth followed by chemical reactions that produced increased organic complexity leading eventually to organic life capable of reproduction, mutation, and selection using organic material as nutrients. A distinct class of other theories (panspermia theories) suggests that life was carried to Earth from elsewhere — these theories receive some support from recent work on planetary impact processes. Other alternatives to the standard model suggest that life arose as an inorganic (clay) form and/or that the initial energy source was not organic material but chemical energy or sunlight. We find that the entire range of current theories suggests that liquid water is the quintessential environmental criterion for both the origin and sustenance of life. It is therefore of interest that during the time that life appeared on Earth we have evidence for liquid water present on the surface of Mars.     

The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.