Re: Where are the missing fragments of a restriction enzyme reaction?

I ran a restriction enzyme analysis on the pUC18 sequence in MacVector^TM, and only found 4 Taq I sites:

Sequence Range: 1 to 2686


Digest with TaqI:

Fragment  Left      Cut by                    Cut by   Right
  Size    Overhang  Enzyme      From : To     Enzyme   Overhang

   1444    [+ 1]    TaqI         1019:2462    TaqI      [+ 1]
    754    [+ 1]    TaqI          265:1018    TaqI      [+ 1]
    458    [+ 1]    TaqI         2463:234     TaqI      [+ 1]
     30    [+ 1]    TaqI          235:264     TaqI      [+ 1]

Assuming you're performing a partial digestion, you should actually see up to 15 bands, depending on the relative concentrations of enzyme and substrate and the reation time. That is, you should see 4 digestion fragments, 8 partial digestion fragments and the linearized, supercoiled, and nicked-circular forms of the plasmid:

Fragment                  
  Size           From : To  

   2686           linearized
  
   2654            265:234
   2226            235:2462
   2197            265:2462
   1931           1019:264
   1901           1019:234
   1444           1019:2462   
   1240           2463:1018
    783            235:1018
    754            265:1018   
    487           2463:264
    458           2463:234    
     30            235:264  

Nicked and supercoiled plasmids run faster than linearized plasmids, but their mobilities also depend on the concentration of ethidium bromide in the gel, so it is hard to predict their mobilities exactly. Some of these fragments are similar enough in size that they may appear as doublets on your gel, depending on your agarose concentration and the distance you run the fragments on the gel.