Table 1.
Oligomer | Size (bases) | Sequence |
---|---|---|
MeP-half-site (top strand) | 27 | 5′ ACTTGGATCCATAACTTCGTATAA(mp)TGT 3′ |
P-half-site (top strand) | 27 | 5′ ACTTGGATCCATAACTTCGTATAATGT 3′ |
P- or MeP-half-site (bottom strand); hydrolysis assays | 30 | 5′ CATACATTATACGAAGTTATGGATCCAAGT 3′ |
P- or MeP-half-site (bottom strand); strand joining assays | 39 | 5′ TGTATGTTTCATACATTATACGAAGTTATGGATCC AAGT 3′ |
Template oligo used to synthesize the 54-mer strand (top and bottom) of the short MeP-full-site by Klenow polymerase fill-in reaction | 45 | 5′ ACTTGGATCCATAACTTCGTATAATGTACATTATAC GAAGTTAT(ddC) 3′ |
Template oligo used to synthesize the 70-mer strand (top and bottom) of the long MeP-full-site by Klenow polymerase fill-in reaction | 61 | 5′ GCATGCATGCATGCATACTTGGATCCATAACTTCGT ATAATGTACATTATACGAAGTTAT(ddC) 3′ |
47-mer used to generate a 74-mer strand (top and bottom) of a long MeP-full-site by ligation to the 27-mer shown in row1 | 47 | 5′ ACATTATACGAAGTTATGGATCCAAGTATGCATGCA TGCATGCATGC 3′ |
splint oligo used in the ligation to generate the 74-mer strand of the long MeP-full-site | 44 | 5′ GATCCATAACTTCGTATAATGTACATTATACGAAGT TATGGATC 3′ |
The string of nucleotides shown in bold represents the Cre binding element. The scissile phosphate or methylphosphonate is indicated by ‘p’ or ‘mp’, respectively. The template oligos employed in the Klenow polymerase reactions contained a 3′-terminal dideoxy-C (ddC).