Pseudoknot Prediction And Identification Of Schistosoma Japonicum

RNA is a kind of very important biomacromolecule that plays huge roles in the organisms. The function of RNA is not decided by the sequence but of the structure. The types of RNA structure include hairpin, loop, pseudoknot, and so on. Pseudoknot is a kind of stable RNA molecular as well as represent a kind of second level structure of RNA. The types of pseudoknot contain 14 different kinds. The research of RNA structure has became a important research field of computational biology.Based on the different structure, RNA shows different functions, so that they play a variety of diverse roles in biological processes. These roles include forming the catalytic core of various ribozymes, self-splicing introns, and telomerase. Additionally, pseudoknots play critical roles in altering gene expression by inducing ribosomal frameshifting in many viruses.The most common function of pseudoknot is to stimulate ribosomal frameshifting. The pseudoknot structure likely causes the ribosome to pause on the slippery sequence, so the ribosome slips back one nucleotide and subsequently continues translation in the -1 reading frame.The formation of pseudoknot can also influence the stability of the RNA molecule. It is believed that we can get more knowledge of RNAs' structure and function by learning pseudoknot.We have developed a bioinformatics procedure to use these pseudoknot prediction softwares to pick the the candidate sequences with pseudoknot from the 8452 sequences in the Schistosoma japonicum database. The primary screening results were used to construct database. Using with RNA frameshift site analysis and other ways to analyse the characteristic of the sequence, we finaly select 26 candidate seuqences. After screening the S. japonicum proteomics database, we found 7 pepetide fragments matching to the 26 candidate gene encoding proteins, one of them is matching the encoding protein after frameshift expression. We try to use molecular cloning and protein expression, as well as western blot, to test and verify the pseudoknot and gene frameshift expression. Though the evidence of frameshift expression in vitro haven't got, the eukaryotes experimental testing methods have already explored, which supply a base for the following experimental frameshift verification of preudoknot and investigation of the characterilazation and significance of preudoknot.