Algorithmic applications of XPCR
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 etal., DNA extraction by cross pairing PCR, 2005; Franco etal., DNA recombination by XPCR, 2006; Manca and Franco, Math Biosci 211:282298, 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 computingcombinatorial algorithms and laboratory experiments, 2006), multiple concatenation, gene driven DNA extraction (Franco etal., DNA extraction by cross pairing PCR, 2005), and generation of DNA libraries (Franco etal., DNA recombination by XPCR, 2006), and some related ongoing work is outlined.
pcr algorithmic analysis dna recombination dna extraction dna mutagenesis splicing