Computing by polymerase chain reaction

Abstract

A mathematical notation is introduced to represent, at a symbolic level, different mechanisms of DNA recombination, and a 'PCR lemma' is proven by analytically describing the combinatorial properties of the polymerase chain reaction process. This approach led to the discovery of novel techniques, based on a form of PCR which we called cross pairing PCR (briefly XPCR). They were mathematically analyzed and already experimentally proven in different contexts, such as DNA extraction and recombination. Thus, a mathematical analysis of standard methodologies may highlight novel mechanisms of DNA recombination and this can provide new technologies for DNA manipulation.

Informational laws of genome structures

“…In recent years, many studies have approached the investigation of DNA strings and genomes by means of algorithms, information theory and formal languages 11 12 13 14 15 16 17 18 19 20 21 22 , and methods were developed for investigating whole genome structures. In particular, dictionaries of words occurring in genomes, distributions defined over genomes, and concepts related to word occurrences and frequencies have been very useful and seem to characterize important genomic features relevant in biological contexts 23 24 25 26 27 28 29 30 .…”

From biopolymer duplication to membrane duplication and beyond

“…Of course, some enzymatic activity, similar to that one of polymerases, is necessary for completing such a kind of concatenation duplication. The general idea is very simple and inspired by the computational ability of polymerase enzymes [12] (see Fig. 8).…”

A Marvelous Accident: The Birth of Life

“…Marco is a well-known Italian novelist and an expert of Italian Literature (Dante, Petrarca). I am a mathematician-computer scientist, studying mathematical models of biological phenomena (especially, computational genomics) [2][3][4][5][6][7][8]. The topic of the book is the origin of life, with the intent of explaining the basic mechanisms and questions to the interested layman.…”