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The C427Z/C638Z/C669Z (NBD1/linker) and C1070Z/C1121Z/C1223Z (NBD2) mutant blocks were generated by site-saturation mutagenesis using oligonucleotides that contained a fully degenerate codon at each Cys position (NNN, where N represents an equal mixture of A, T, G and C nucleotides), as outlined in Figure 2 (Supplementary Table S1 at http://www.bioscirep.org/bsr/034/bsr034e116add.htm).htm
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A pair of custom oligonucleotides that contained a unique 19-nt sequence derived from the chicken Jagged2 mRNAs were designed using the RNAi Design Tool (http://www.oligoengine.com).com
We have generated double-stranded oligonucleotides that contain no damage, each single 8-oxodG or the MDS.
For the Oct3/4-binding motifs of Tcl1, we used an s1 oligonucleotide that contains an AAAGGCAT motif and an s2 oligonucleotide that contains an ATGTAGAT motif (Figure 5E).
This problem was eliminated by using a hairpin-containing self-templating oligonucleotide that contains a suicide cassette, a recognition site for a nicking enzyme, and recircularizing and monomerizing the tandem repeated complements by nicking the suicide cassette [7].
In the present study, the same positions were randomized by parsimonious mutagenesis [ 11] using oligonucleotides, which contained 79% of the nucleotide that is present in H10-03-6 and 7% of the respective three other ones.
In control reactions, we used oligonucleotides that instead of C, 5 hmC or 5 mC, contained the products of their deamination: U, 5 hmU or T, respectively.
Since the A1 sequence (GTAAACA) is only one of four possible sequences derived from the computationally-identified FOXP3 consensus site (G/A T/c AAACA) [30], we repeated the EMSA assays using A' (A1-A1) oligonucleotide probes that contained all the possible combinations of these preferred nucleotides: AT, AC, GT and GC (Figure 3A).
Ugni Blanc using oligonucleotide microarrays containing 3,200 elements [ 19].
Global transcription profiles were determined using oligonucleotide microarrays containing 31,770 mouse transcripts.
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