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Conclusion

We have seen that a large palette of approaches is available to the protein engineer ranging from biological chemistry, molecular modeling and structural biology to microbiology through molecular biology and biochemistry. Success in protein design may well rely on highly interdisciplinary expertise in these various fields.

From all the studies we have presented, we can draw some conclusions. Firstly, it is clear that a highly successful approach is to start from a natural protein in order to have the benefit of its foldability and stability. Practically, to achieve a drastic change in the properties of a protein, the use of predictive and combinatorial approaches in parallel happened to be very efficient. The key points are to choose a starting protein adapted to the targeted properties in terms of architecture, folding and stability, and also to have powerful screening or selection tools to identify clones of interest among the wide diversity of the generated variants. The natural repertoire of twenty amino acids of the genetic code is generally sufficient for the engineering of proteins with new functions (binding, folding, solubility and catalytic activity). The extension of the genetic code towards non-natural amino acids should prove useful for the engineering of protein conjugates defined at the atomic level. Secondly, a lesson from combinatorial approaches is that foldability of a polypeptide chain is a characteristic that can be quite easily determined in a library with minimal rational design. But, it is striking to see that even without any design, a library of fully random polypeptide chains can contain some foldable and functional proteins at a frequency accessible to our tools of selection. Thirdly, recent works using in silico approaches to predict and design protein structures have now reached some landmarks and it is realistic to think that in the near future this approach will become more important for the design of new proteins.

The advancements in protein design during the last fifteen years can be realized in a citation by Rainer Jaenicke [79]: ''When and whether the time is approaching when new and even useful proteins will be de novo designed, synthesized, and technologically applied is a question of enthusiasm and belief.'' Ab initio design of proteins has been mostly limited to small proteins with simple folds, whilst the design of proteins endowed with new or improved functions has generally resulted from screening or selection strategies. Major challenges in protein design continue for the 21st century. The identification of mutations that are associated with new or improved functions and that cannot be interpreted given their sequence-structure-function relationships is certainly an issue of importance. Prediction of protein functions from their primary sequences still remains a challenge and advancements in this area should also facilitate the design of proteins.

Acknowledgments

We thank Dr. F. Bahrami and Dr. J.F. Satchell for critical reading of the manuscript. The Pymol software was used to draw the figures representing protein structures.

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Nucleic Acid Foldamers: Design, Engineering and Selection of Programmable Biomaterials with Recognition, Catalytic and Self-assembly Properties1

Arkadiusz Chworos and Luc Jaeger 10.1

Introduction

The remarkable complexity of living organisms essentially relies on proteins, RNA and DNA, that carry out most of the major cellular functions necessary for life. These biopolymers rely on two basic self-assembly processes: the spontaneous folding of one polymer chain into a stable, well-defined three-dimensional (3-D) structure, and the assembly of multiple subunits into well-defined modular supramolecular architectures. Key characteristics are (i) sequence heterogeneity, (ii) hierarchical organization of conformation (secondary structure versus tertiary structure), (iii) modular components, (iv) stereochemically specific and selective interactions and (v) cooperativity of folding. Proteins and nucleic acids are thus perfect prototypes of functional, biological foldamers.

In the past 15 years, the development of in vitro selection and evolution techniques and progress in the rational design of nucleic acids has led to an incredible new world of novel functional nucleic acids capable of exquisite recognition, and having catalytic and responsive properties. Despite the fact that these artificial molecules are typically of greater size than synthetic foldamers, such as those described in Chapters 1-5, and that they have not been described as such in the literature, they can be seen as nucleic acid foldamers.

In the course of this chapter, nucleic acid foldamers are defined as non-natural nucleic acid polymers able to fold into well-defined 3-D shapes with recognition, catalytic and/or assembly properties. By non-natural or artificial nucleic acids, we want to express (i) that they are the product of combinatorial or/and rational synthetic and supramolecular design and (ii) that, besides RNA and DNA, they can be based on analogs that mimic nucleic acid.

This chapter focuses on DNA and RNA foldamers rather than nucleic acid bio-mimetics and analogs. It aims to provide the reader with a broad outline of the various concepts behind the nanoconstruction of functional nucleic acid based

1) A list of abbreviations appears at the end of this chapter.

materials. First we give an overview of the structural and functional properties of RNA and DNA foldamers. Then we emphasize how nucleic acid sequences can be synthesized, engineered and controlled to sculpt new 3-D molecular architectures with catalytic, responsive and supramolecular properties. After a description of the various self-assembly strategies used to direct the assembly of foldamers into nanostructures of increasing complexity, we finally address how RNA and DNA foldamers can potentially lead to the development of novel biomaterials for electronics or biomedical applications.

By exemplifying our present ability to program linear polymer sequences to fold and self-assemble into defined 3-D shapes, nucleic acid foldamers offer a great source of inspiration to the supramolecular chemist [1, 2]. It is our hope that they will pave the way to the creation of useful complex materials based on novel fully synthetic biomimetic foldamers that will be chemically more robust, cheaper and easier to obtain than nucleic acids.

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