Entwicklung eines integrierten Softwarepaketes zur Unterstützung des Designs und der Synthese artifizieller Gene in einer Hochdurchsatz-Umgebung

David Raab
2004
Synthetic genes, several thousend basepairs long double stranded DNA fragments built from oligonucleotides, have become a valuable tool in many areas of molecular biology and medicine. Nevertheless, the high potential of this technology is used only to a small extent till now. The main reason is, that despite huge progress the production of a synthetic gene is still tedious and expensive for the single scientist. Moreover, the possibilities of rational sequence design are hardly used due to a
more » ... dly used due to a lack in suitable software. Nevertheless, the idea is near to significantly reduce synthesis costs and time by automation of the synthesis process. To approach this goal, an integrated software package was developed in the course of this thesis, which supports the high-throughput synthesis of artificial genes, starting with the design, proceeding with the planning of the synthesis and finally ending with the quality control. At the heart of the GeneOptimizer Software is a user-friendly sequence editor, which supports all usual editing functions and represents a sketchboard for the sequence design. To fit the (coding) sequence optimally to the experimental requirements and the chosen expression system, often multiple criteria, like adaption of codon usage and GC-content, exclusion of certain DNA-motives and repetitions, avoidance of stable secondary structures have to be taken into consideration. Due to the degeneration of the genetic code even a very small protein can be coded by a huge number of different DNA-sequences. To find a sequence, which fits optimally to the above mentioned criteria, an algorithm was developed, which relies upon a so called �sliding combination window�. Within this several codons long window all possible combinations of synonymous codons are generated and every combination is evaluated together with the already optimized upstream sequence by a scoring function with user defined parameters. The first codon of the optimal combination is chosen and the combination window is moved in 3� direction by one [...]
doi:10.5283/epub.10234 fatcat:7m4seo54qzh4jmdzgdyzvm3qpi