ABSTRACT
We developed a novel method for constructing nearly random peptide library. Genomic DNAs extracted from tissue or cells of large genome species were digested with frequent cutter to produce short DNA fragments. These short fragments can be considered nearly random. Nearly random peptide libraries can be constructed by cloning the short fragments into appropriate expression vectors and transformation into host cells. Genomic DNA from one species can be digested with different restriction enzymes and ligated to different reading frames to produce several different libraries. In this study, we digested tobacco genomic DNA with two enzymes and cloned into three different reading frames to make totally six nearly random peptide libraries.
Subject(s)
DNA, Plant , Genetics , Genome, Plant , Genetics , Peptide Library , Nicotiana , GeneticsABSTRACT
<p><b>OBJECTIVE</b>To deduce all potential ligands undiscovered experimentally by searching all the proteins containing same C-termini, which can bind a certain PDZ domain.</p><p><b>METHODS</b>We developed a JAVA program for searching short exact sequence matches at C-terminus. According to the known C-termini, which PDZ domains recognized experimentally, Swissprot database has been searched by this program for all potential ligands.</p><p><b>RESULTS</b>Some PDZ domains may have more potential ligand proteins, which are undiscovered yet experimentally. These bioinformatic results also provide clues for studying functions of hypothetical proteins and PDZ domains' protein interactions in many different organisms.</p><p><b>CONCLUSION</b>The results may provide useful clues for discovering potential functions of hypothetical proteins and new functions of known proteins.</p>