Colloque

Advanced computational techniques for triplex-DNA engineering

Anthony Kusalik

Membre a labase

Anthony Kusalik

Résumé du colloque

Biological data, such as DNA sequences, can be effectively analyzed for structure and patterns using techniques such as computational grammars. One type of grammar that is expressive, flexible, and readily implemented is definite clause grammars (DCGs). High-level computational paradigms such as constraint logic programming (CLP) allow the effective modelling of problems from the natural sciences involving rules and constraints, and efficient solution of those problems. Both DCGs and CLP are supported by most modern logic programming (LP) systems. Triplex DNA is a naturally occuring conformation where a nucleotide sequence binds to a purine-rich strand of a conventional DNA duplex. Tailored oligonucleotides can be created and used to form triplex complexes with specific DNA sequences. Ideally, transcription of selected genes can be inhibited. Triplex DNA has many useful applications including the study of physiological pathways and control of gene-linked diseases. Calmodulin is a regulator of calcium-dependent signalling in eucaryotic cells. Higher eucaryotes, including humans, have three calmodulin (CaM) genes which are differentially regulated, yet encode identical proteins. The regulation of expression and function of each of the CaM genes is an area of active research. One possible approach is to use custom-designed triplex-DNA forming oligonucleotides to inhibit the transcription of individual CaM genes. At the U of S we are using advanced computational techniques to design such oligonucleotides. The identification of triplex-forming regions in each of the three CaM genes is performed using DCGs. CLP is used to design the oligonucleotides, including representing and reasoning with various (currently imprecise) biological rules for ranking the triplex forming regions (the targets) and candidate oligonucleotides (the probes). This talk will describe triplex DNA, DCGs and CLP, the grammar rules used to identify triplex-forming regions, rules used to rank candidate targets and probes, how imprecision in biological " rules " was handled, results to date for the three CaM genes, and other applications for the technology.