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The thermophilic enzyme, Thermus aquaticus (Taq) DNA polymerase, is an essential tool in molecular biology because of its ability to synthesis DNA in vitro and its inherent thermal stability. Taq DNA polymerase is widely used in the polymerase chain reaction (PCR), an essential technique in a broad range of different fields from academic research to clinical diagnostics. The use of PCR-based tests in diagnostic testing is ever increasing; however, many of the samples being tested contain substances that inhibit PCR and prevent target amplification. Many attempts have been made to engineer polymerases not only to increase resistance to overcome the problem of inhibition, but also to enhance other characteristics such as fidelity, processivity and thermostability. Heparin, found in blood samples, and phytate, found in faecal samples, are two examples from a number of known PCR inhibitors. The mode of action of most PCR inhibitors is not well understood, but inhibition is thought to occur by enzyme binding or through the chelation of Mg2+ ions essential for PCR. In this project, a system of directed evolution by compartmentalised self-replication (CSR) was established and successfully employed to screen a mutant library for Taq DNA polymerase variants with enhanced resistance to the inhibitors heparin and phytate. CSR is a recently-established high-throughput method for the creation of novel polymerases, based on a feedback loop whereby polymerase variants replicate their own encoding gene. A mutant library of 106 variants was produced by random mutagenesis error-prone PCR, in which only the polymerase domain of Taq was mutagenised. Firstly, the CSR system was established and tested by performing a screen in the presence of heparin to select for heparin-resistant variants. Characterisation of selected variants revealed that a single round of CSR had produced a Taq variant (P550S, T588S) with a 4-fold increase in heparin resistance. The IC50 was increased from 0.012U/ml heparin to 0.050U/ml heparin. The study with heparin was followed by a phytate screen, in which two rounds of CSR were performed with an initial round of error-prone PCR followed by re-diversification (recombination) of the mutant library using the staggered extension process (StEP). The two rounds of CSR yielded a Taq variant with a 2-fold increase in phytate-resistance compared to the wild-type, with IC50 increased from 360μM phytate to 700μM phytate. The best phytate mutant (P685S, M761V, A814T) was further characterised and it was found that the catalytic activity, thermostability and fidelity of the mutant were comparable to the wildtype enzyme. The position of resistance-conferring mutations of the novel Taq variants evolved in this study provided some evidence for the inhibitors’ predicted modes of action in the case 2 of both phytate and heparin. As phytate’s mode of action is poorly understood, further investigations were performed to elucidate its role in PCR inhibition. A thorough investigation into the importance of relative phytate and Mg2+ levels on PCR was conducted and revealed for the first time convincing evidence that the primary mode of phytatemediated PCR inhibition is by chelation. Further work led to the successful crystallisation of Taq in the presence of phytate, although subsequent X-ray diffraction data to 2.5Å did not reveal phytate bound within the enzyme structure. Site-directed mutagenesis studies were used to probe cross-over between heparin and phytate-conferring mutations. Thus, in addition to providing valuable information for novel Taq variants with a potential application in fecal-based PCR diagnostic tests, this project has begun to provide insight into the fundamental aspects of the mode of action of phytate as a polymerase and PCR inhibitor.

In this work, we seek to expand synthetic in vitro biological systems by using water-in-oil emulsions to provide an environment conducive to directed evolution. We approach this primarily by utilizing a model transcription system, the T7 RNA polymerase and promoter, which is orthogonal to both bacterial and eukaryotic transcription systems and is highly functional in vitro. First, we develop a method to identify functional promoter sequences completely in vitro. This method is tested using the T7 RNA polymerase-promoter model system. We then configure the T7 transcription system as an ‘autogene’ and investigate how this positive feedback circuit (whereby a T7 promoter expresses a T7 RNA polymerase gene) functions across various in vitro platforms, including while compartmentalized. The T7 autogene can be envisioned as a self-replicating system when compartmentalized, and its use for directed evolution is examined. Finally, we look towards future uses for these in vitro systems. One interesting application is to expand the utilization of unnatural base pairs within the context of a synthetic system. We investigate the ability of T7 RNA polymerase to recognize and utilize unnatural base pairs within the T7 promoter, complementing existing work on the utilization of unnatural base pairs for in vitro replication and transcription with an investigation of more complex protein-dependent regulatory function. We envision this work as a foundation for future in vitro synthetic biology efforts. / text

All known living cells contain a complex set of molecular machinery to support their growth and replication. However, the earliest cells must have been much simpler, consisting of a compartment and a genetic material to allow for Darwinian evolution. To study these intermediates, plausible model `protocells' must be synthesized in the laboratory since no fossils remain. Recent work has shown that fatty acids can self-assemble into vesicles that are able to grow and divide through simple mechanisms. However, a self-replicating protocell genome has not yet been developed. Here we discuss studies of systems that allow for the copying of nucleic acid templates without enzymes and how they could be developed into a genetic material.

Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability to multi-stability and chaotic dynamics. Nevertheless, there are some general principles that govern their overall behavior. We focus on the question to what extent the dynamics of replication can explain the accumulation of genetic information that eventually leads to the emergence of the first cell and hence the origin of life as we know it. A large class of ligation-based replication systems, which includes the experimentally available model systems for template directed self-replication, is of particular interest because its dynamics bridges the gap between the survival of a single fittest species to the global coexistence of everthing. In this intermediate regime the selection is weak enough to allow the coexistence of genetically unrelated replicators and strong enough to limit the accumulation of disfunctional mutants.

Issues of control and causation are central to the Quantum Theory of Computation. Yet there is no place for them in fundamental laws of Physics when expressed in the prevailing conception, i.e., in terms of initial conditions and laws of motion. This thesis aims at arguing that Constructor Theory, recently proposed by David Deutsch to generalise the quantum theory of computation, is a candidate to provide a theory of control and causation within Physics. To this end, I shall present a physical theory of information that is formulated solely in constructor-theoretic terms, i.e., in terms of which transformations of physical systems are possible and which are impossible. This theory solves the circularity at the foundations of existing information theory; it provides a unifying relation between classical and quantum information, revealing the single property underlying the most distinctive phenomena associated with the latter: the unpredictability of the outcomes of some deterministic processes, the lack of distinguishability of some states, the irreducible perturbation caused by measurement and the existence of locally inaccessible information in composite systems (entanglement). This thesis also aims to investigate the restrictions that quantum theory imposes on copying-like tasks. To this end, I will propose a unifying, picture-independent formulation of the no-cloning theorem. I will also discuss a protocol to accomplish the closely related task of transferring perfectly a quantum state along a spin chain, in the presence of systematic errors. Furthermore, I will address the problem of whether self-replication (as it occurs in living organisms) is compatible with Quantum Mechanics. Some physicists, notably Wigner, have argued that this logic is in fact forbidden by Quantum Mechanics, thus claiming that the latter is not a universal theory. I shall prove that those claims are invalid and that the logic of self-replication is, of course, compatible with Quantum Mechanics.

In the last twenty years, chemists have devised numerous synthetic chemical systems in which self-replication operates, demonstrating that molecules can replicate themselves without the aid of enzymes and that self-replication is not a prerogative of nucleic acids only. However, the coupling of replication to other recognition-mediated events and its exploitation in the amplification of large supramolecular assemblies, such as mechanically interlocked molecules, have remained unexplored areas. Among mechanically interlocked molecules, rotaxanes represent particularly attractive targets because of their application as molecular switches. This thesis describes how the recognition-mediated synthesis of a rotaxane can be combined to the amplification of its structure by replication. Kinetic models for the integration of self-replication with the formation of a rotaxane are presented. The logical steps required to convert these models into molecular structures through consideration of the design criteria highlighted by the models are discussed and executed. The macrocyclic component is an essential part of a rotaxane. The synthesis of several novel macrocycles is presented. Their ability to bind guests in their cavities through hydrogen bonds was probed. The best macrocycle/guest pairs were integrated in the formation of rotaxanes. Further investigations on the stoppering reaction and on the various recognition processes involved in the system lead ultimately to the construction of self-replicating rotaxanes.

This thesis explores the question of why life can not be revived when death occurs due to lack of resources. For example, why can't something as simple as E.coli be revived after its death? The hypothesis is that death is not defined by the end of metabolism itself, but rather a continued metabolism which in turn destructs the entity itself. Consequently, a virus should not be capable of ”dying” due to its lack of metabolism. To study self replication, a recent mathematical model utilising Gillespie's algorithm and differential equations has been explored. Using this model, real systems such as the Formose reaction can be modeled. Furthermore, an analytical analysis has been carried out in order to study what impact a side reaction will have on a self replicating system's total growth rate. The result of the analysis states that the growth rate of a self replicating system peaks when all the reactions have the same reaction rate, and declines as the reaction rate of a side reaction increases. In conclusion, a self replicating system that either contains a side reaction or is coupled with another self replicating system can suffer an irreversible death. The reason for this is the metabolism that occurs when the resources have been depleted. At this point, other reactions not belonging to the main metabolism can destroy the self replication. This argument strengthens the hypothesis that a virus does not die in the same way as a living cell, as it does not have a metabolism of its own.

We present simulation results of a minimal life-like, artificial, molecular aggregate (i.e. protocell) that has been proposed by Steen Rasussen and coworkers and is currently pursued both experimentally and computationally in interdisciplinary international research projects. We develop a space-time continuous physically motivated simulation framework based on the method of dissipative particle dynamics (DPD) which we incrementally extend (most notably by chemical reactions) to cope with the needs of our model. The applicability of the method over the entire length scale of interest is reintroduced, by rejecting a concern that DPD introduces a freezing artifact for any model above the atomistic scale. This is achieved by deriving an alternative scaling procedure for interaction parameters in the model. We perform system-level simulations of the design which attempt to account for theoretical, and experimental knowledge, as well as results from other computational models. This allows us to address key issues of the replicating subsystems container, genome, and metabolism both individually and in mutual coupling. We analyze each step in the life-cycle of the molecular aggregate, and a finnal integrated simulation of the entire life-cycle is prepared. Our simulations confirm most assumptions of the theoretical designs, but also exhibit unanticipated system-level dynamics. These findings are used to revise the original design of the Los Alamos minimal protocell over the course of the analysis. The results support the hypothesis that self-replication and probably other life-like features can be achieved in systems of formerly unanticipated simplicity if these systems exploit physicochemical principles that are immanent to their physical scale.