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Example sentences for: zas-c
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MAST is a program designed to search biological sequence databases for sequences that contain one or more of a group of known motifs [ 34 ] . Of a total of 923,310 sequences analyzed, only a total of 15 hits were obtained: 5 hits for KRC/ZAS-N (Figure 13) and 10hits for KRC/ZAS-C (Figure 14).
After cloning and DNA sequencing, the KRC-selected sequence datasets were analyzed by the computer program Multiple Expectation Maximum for Motif Elicitation (MEME version 3.0) to generate sets of position specific scoring matrices (PSSMs) or motifs [ 30 ] . When the program was set to identify wider sequences (= 9 nucleotides) the PSSMs were homologous to Sb [ 29 ] , the κB motif [ 31 ] , and the canonical heptamer and nonamer elements of the RSS [ 32 ] . However, shortening the width of the motifs to 5 nucleotides, the target length for the C 2 H 2 zinc finger pairs of the tramtrack [ 33 ] , the ZAS-N dataset yielded two motifs, "GGTAT" and "T(T/C)TT(T/G)G" and the ZAS-C dataset yielded a single motif, "TGTGG".
Although previous results of protein titration experiments suggested that KRC/ZAS-C binds DNA in a cooperative manner for a given oligonucleotide, the presence of multiple binding sites might not be favored over a single site in our site selection assay which used a degenerate pool of oligonucleotides and limited rounds of amplification.
We used site selection amplification binding assays to select specific DNA targets recognized by KRC fusion proteins containing ZAS-N or ZAS-C from an initial oligonucleotide pool containing degenerate 25-mers.
The fusion proteins KRC/ZAS-N and KRC/ZAS-C were produced in E. coli and purified by affinity chromatography as described previously [ 24 28 ] . The regions of KRC used to generate KRC/ZAS-N and KRC/ZAS-C are schematically shown in Fig.
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