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Algorithmic applications of XPCR

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Abstract

An emerging trend in DNA computing consists of the algorithmic analysis of new molecular biology technologies, and in general of more effective tools to tackle computational biology problems. An algorithmic understanding of the interaction between DNA molecules becomes the focus of some research which was initially addressed to solve mathematical problems by processing data within biomolecules. In this paper a novel mechanism of DNA recombination is discussed, that turned out to be a good implementation key to develop new procedures for DNA manipulation (Franco et al., DNA extraction by cross pairing PCR, 2005; Franco et al., DNA recombination by XPCR, 2006; Manca and Franco, Math Biosci 211:282–298, 2008). It is called XPCR as it is a variant of the polymerase chain reaction (PCR), which was a revolution in molecular biology as a technique for cyclic amplification of DNA segments. A few DNA algorithms are proposed, that were experimentally proven in different contexts, such as, mutagenesis (Franco, Biomolecular computing—combinatorial algorithms and laboratory experiments, 2006), multiple concatenation, gene driven DNA extraction (Franco et al., DNA extraction by cross pairing PCR, 2005), and generation of DNA libraries (Franco et al., DNA recombination by XPCR, 2006), and some related ongoing work is outlined.

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Acknowledgements

The experimental research reported in this paper was funded by the Italian National Research Project FIRB 2003, RBA01PHZS. The experiments were performed at the laboratories of the Department of General Pathology at University of Verona, and the authors wish to thank Cinzia Giagulli and Carlo Laudanna for their technical support. They are also grateful for very helpful comments and suggestions of anonymous referees. The first author is thankful for the interesting discussions with Susannah Gal and Tony Macula (from SUNY Binghamton University, USA) about experimental and combinatorial analyses of XPCR protocol.

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  1. Department of Computer Science, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy

    Giuditta Franco & Vincenzo Manca

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  1. Giuditta Franco
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  2. Vincenzo Manca
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Correspondence to Giuditta Franco.

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Franco, G., Manca, V. Algorithmic applications of XPCR. Nat Comput 10, 805–819 (2011). https://doi.org/10.1007/s11047-010-9199-8

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