Chemical synthetic biology

ABSTRACT Although both the most popular form of synthetic biology (SB) and chemical synthetic biology (CSB) share the biotechnologically useful aim of making new forms of life, SB does so by using genetic manipulation of extant microorganism, while CSB utilises classic chemical procedures in order to obtain biological structures which are non-existent in nature. The main query concerning CSB is the philosophical question: why did nature do this, and not that? The idea then is to synthesise alternative structures in order to understand why nature operated in such a particular way. We briefly present here some various examples of CSB, including those cases of nucleic acids synthesised with pyranose instead of ribose, and proteins with a reduced alphabet of amino acids; also we report the developing research on the "never born proteins" (NBP) and "never born RNA " (NBRNA), up to the minimal cell project, where the issue is the preparation of semi-synthetic cells that can perform the basic functions of biological cells. Keywords: synthetic biology, origin of life, PNA, random proteins, never born proteins, random RNA, never born RNA, determinism, contingency, minimal cell 1. Introduction The new and fashionable term synthetic biology (SB) is used mostly to indicate a field that is aimed at synthesising biological structures or life forms in the laboratory which do not exist in nature; this is based on the engineering principles of standardisation, modularisation and characterisation, coupled to systematic design. The accepted definition is that "synthetic biology aims to design and engineer biologically based parts, novel devices and systems--as well as redesigning existing, natural biological systems". Interesting examples of these techniques can be found in recent reviews (1,2). Synthetic biology engages various branches of life science such as biochemistry, molecular and cell biology, structural biology, protein engineering and design, chemical biology, each one contributing to the development of this new field. One branch of SB is chemical synthetic biology (CSB) which is not based on genetic manipulation but emphasises instead a chemical approach, aiming at the synthesis of molecular structures and/or multi-molecular organised biological systems which do not exist in nature (3-5). These man-made, in nature non-existing, biological molecular or supra-molecular structures can be obtained either by chemical or biochemical synthesis. While SB is more focussed on bioengineering-genetic aspects, CSB is more oriented towards basic science which has to do with the questions: "why nature did this and not that?"; why ribose in nucleic acids and not glucose?; why proteins with 20 amino acids and not with 10 or 15?; etc. It focuses on the philosophical "why this, not that" learning process. The beauty of CSB is the possibility of answering these questions, or at least, of trying to tackle them with experimental laboratory means: just making "that" and comparing it with "this", that is with what we have in nature. In this way, we may discover--this is the hope--why nature went into one avenue and discarded the others. In this kind of SB, chemistry more than genetic manipulation is the main tool and for this the term "chemical synthetic biology" has been coined (3,5-7). In order to give a broad range of examples of CSB experiments, this review will cover a series of various approaches to CSB, ranging from the bio-polymers (nucleic acids and proteins) to complex systems (e.g. minimal ribosomes and living cells). The review, partially following the organisation of our recent publication on this topic (3), is divided into the three sections: nucleic acids, peptides/proteins and complex systems. The limitations of SB in general will be discussed in the Conclusion. 2. Nucleic acids The first interesting example of CSB we present is the work of Albert Eschenmoser and co-workers at the ETH Zurich on synthetic DNA which has pyranose instead of the natural furanose sugar in its main chain (8) (Figure 1). …