Here is a list of restriction enzymes that could be used for the ARRF technique. Whether a particular enzyme cuts rarely enough to be suitable depends on the genome size and GC content of your organism; most of the six-cutters listed here will cut too frequently to be useful for the ARRF technique in most plants and animals. Six-cutters would be useful for prokaryotes and those eukaryotes with small genomes, and those six-cutters with all GCs in their restriction sites may be useful for eukaryotes with normal-sized genomes that are AT-rich.
Enzymes that leave 5' overhangs are listed first, because you can buy a single (expensive) labeled oligo and pair it with a variety of (inexpensive) unlabeled oligos to create adapters to match 5' overhangs. I have attempted to list all of the commercially available six-cutters, seven-cutters and eight-cutters that leave 5' overhangs. Enzymes that leave 3' overhangs require a different labeled oligo for each overhang, so I have listed only eight-cutters and the six-cutters that leave the same overhangs. For more information about these enzymes, including where to buy them, see REBASE.
Enzymes that are grouped together leave the same cohesive end. When more than one name is shown for a restriction sequence, more than one isoschizomer is commercially available.
AscI GG^CGCG_CC (eight-cutter) BsePI, BssHII G^CGCG_C (all GC) MluI A^CGCG_T NotI, CciNI GC^GGCC_GC (eight-cutter) EagI, XmaIII C^GGCC_G (all GC) PspOMI G^GGCC_C (all GC) SgrAI CR^CCGG_YG (seven-cutter) AgeI A^CCGG_T BspEI T^CCGG_A NgoMIV G^CCGG_C (all GC) XmaI C^CCGG_G (all GC) BbvCI CC^TCA_GC (seven-cutter) AvrII C^CTAG_G NheI G^CTAG_C SpeI A^CTAG_T XbaI T^CTAG_A AclI AA^CG_TT AsuII, BstBI TT^CG_AA ClaI AT^CG_AT NarI GG^CG_CC (all GC) BspHI T^CATG_A BspLU11I, PciI A^CATG_T NcoI C^CATG_G BamHI G^GATC_C BclI T^GATC_A BglII A^GATC_T Acc65I G^GTAC_C BsiWI C^GTAC_G Bsp1407I, BsrGI T^GTAC_A EcoRI G^AATT_C MfeI C^AATT_G AseI, VspI AT^TA_AT NdeI CA^TA_TG SalI G^TCGA_C XhoI C^TCGA_G ApaLI G^TGCA_C Ppu10I A^TGCA_T BssSI C^ACGA_G HindIII A^AGCT_T KasI G^GCGC_C (all GC) AflII C^TTAA_G
PacI TTA_AT^TAA (eight-cutter) AsiSI, SgfI GCG_AT^CGC (eight-cutter) PvuI CG_AT^CG SbfI, Sse8387I, SdaI CC_TGCA^GG (eight-cutter) NsiI A_TGCA^T PstI C_TGCA^G FseI GG_CCGG^CC (eight-cutter)
These enzymes, if used with an adapter that matched just one of the possible cohesive ends, might be used as seven-cutters, nine-cutters, or even an eleven-cutter (SfiI). I haven't tried this yet, though.
BlpI GC^TNA_GC BstEII G^GTNAC_C Bsu36I CC^TNA_GG RsrII CG^GWC_CG SanDI GG^GWC_CC SexAI A^CCWGG_T AlwNI CAG_NNN^CTG BglI GCCN_NNN^NGGC DraIII CAC_NNN^GTG PflMI CCAN_NNN^NTGG SfiI GGCCN_NNN^NGGCC
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This page was last revised July 23, 2002. Its URL is http://udel.edu/~mcdonald/enzymes.html