Probe Design For Peptide Nucleic Acids Chip Based On Suffix Array

Abstract:With the completion of the Human Genome Project and some biological genome sequencing, the microarray technology develops more and more rapidly. Now, DNA microarray has become an essential medical genetic diagnostic tool for its high-throughput, miniaturization and automation. The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality. With the deepening of the research of bioinformatics techniques and methods, there are some effective ways which have been provided for probe design. Several DNA probe design soft wares are available to perform this work, and each software orients to different target sequences, exhibiting different advantages and limitations. As a kind of DNA analogue, PNA has shown its importance in the microarray field. However, existing methods can not satisfy the accurate design of PNA probe and traditional nucleic acid probe. A method for PNA probe design is proposed in this article, which is based on the differences of physical and chemical properties between the PNA molecules and the nucleic acid molecules. And three basic standards used to screen for traditional nucleic acid probe, including specificity, sensitivity and melting temperature (Tm), also have been referenced, and the main contents are arranged as follows:This article focused on the specificity detecting of the probes, which uses suffix array and a method for multiple sequence alignment based on fast Fourier transform (MAFFT) to detect and cover the tandem repeats. Some probe selection criteria are also developed based on the characteristics of PNA probes. For example, the specific formula for melting temperature calculation is applied for PNA probes, and in order to overcome the self-aggregation of PNA probes, the number of purine is limited. Based on all these algorithms, sets of qualified probes have been accessed.Microsoft Visual Studio2010and C#was chosen as the programming environment. Combining with the proposed suffix array and MAFFT algorithm, a friendly Graphical User Interface was designed. User can adjust the parameters to fit the needs of probe design, exam screening results and save the resulted file for further query and analysis. The human FRDA gene promoter region and exon1sequence are used as target sequences in the simulation experiment. A set of qualified probes have been listed by running the program. Some of the qualified probes have been analyzed by manually and proved the reliability of the program.