Template-guided DNA recombination

The family of stichotrichous ciliates have received a great deal of study due to the presence of scrambled genes in their genomes. The mechanism by which these genes are descrambled is of interest both as a biological process and as a model of natural computation. Several formal models of this process have been proposed, the most recent of which involves the recombination of DNA strands based on template guides. We generalize this template-guided DNA recombination model proposed by Prescott, Ehrenfeucht and Rozenberg to an operation on strings and languages. We then proceed to investigate the properties of this operation with the intention of viewing ciliate gene descrambling as a computational process.

[1]  Erik Winfree,et al.  Evolution as Computation , 2002, Natural Computing Series.

[2]  Gheorghe Paun,et al.  Regular Extended H Systems are Computationally Universal , 1996, J. Autom. Lang. Comb..

[3]  Arto Salomaa,et al.  Formal languages , 1973, Computer science classics.

[4]  David I. Lewin,et al.  DNA computing , 2002, Comput. Sci. Eng..

[5]  D M Prescott,et al.  The unusual organization and processing of genomic DNA in hypotrichous ciliates. , 1992, Trends in genetics : TIG.

[6]  Seymour Ginsburg,et al.  Algebraic and Automata Theoretic Properties of Formal Languages , 1975 .

[7]  Jean Berstel,et al.  Transductions and context-free languages , 1979, Teubner Studienbücher : Informatik.

[8]  David M. Prescott,et al.  Genome gymnastics: unique modes of dna evolution and processing in ciliates , 2000, Nature Reviews Genetics.

[9]  A Ehrenfeucht,et al.  Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates. , 2003, Journal of theoretical biology.

[10]  Andrzej Ehrenfeucht,et al.  Computational Aspects of Gene (Un)Scrambling in Ciliates , 2002 .

[11]  L F Landweber,et al.  The evolution of cellular computing: nature's solution to a computational problem. , 1999, Bio Systems.

[12]  Ion Petre,et al.  Patterns of Micronuclear Genes in ciliates , 2001, DNA.

[13]  L F Landweber.  The evolution of cellular computing. , 1999, The Biological bulletin.

[14]  Dennis Pixton,et al.  Splicing in abstract families of languages , 2000, Theor. Comput. Sci..

[15]  Lila Kari,et al.  Computational power of gene rearrangement , 1999, DNA Based Computers.

[16]  Andrzej Ehrenfeucht,et al.  Molecular operations for DNA processing in hypotrichous ciliates , 2001 .

[17]  D M Prescott,et al.  Cutting, splicing, reordering, and elimination of DNA sequences in hypotrichous ciliates , 1992, BioEssays : news and reviews in molecular, cellular and developmental biology.