Help constructing a restriction map of a linear fragment of DNA?

Question

[bryden.daniel]

I've been trying for hours with not much luck.

This is my attempt to so far....

DNA Sizes of Fragments (bp) 

uncut DNA 900 

DNA cut with EcoRI 500, 350, 50 

DNA cut with HindIII 600, 300 

DNA cut with BamHI 400, 300, 200

DNA cut with EcoRI + HindIII 350, 300, 200, 50 

DNA cut with EcoRI + BamHI 300, 250, 200, 100, 50 

DNA cut with HindIII + BamHI 300, 200, 100

[Anima Mundi]

Hello, I just gave you some hints on that here. In my opinion, you should try to explain with more detail what you need and what you already tried to do, without expecting people to just do your homework. I think the suggestions provided for the other question should guide you to a solution of your problem. Also, to my eyes it is not clear whether your main difficulty lies in the conceptual resolution of the problem or rather in the final rendering of the map.

[bryden.daniel]

Hi, I don't expect anyone to just do it as I would not gain anything from that. I've attempted to complete it and the problem lies in the final rendering of the map.

Answer 1

[skbrimer]

Have you tried using ApE (A plasmid Editor) from the University Of Utah by M. Wayne Davis. I think it would work for what you are wanting to do. http://biologylabs.utah.edu/jorgensen/wayned/ape/

Answer 2

[Anima Mundi]

Ok, in order to produce a graphical map I would proceed as follows. Open a Python shell and input print 'N'*900. This would yield a 900 bp-long sequence, equal in size to your undigested DNA, copy this sequence and paste it into SnapGene (or any equivalent program). For each restriction site you previously located, you can either generate a misc_feature to annotate it in the map, or alternatively you can substitute those Ns in the cutting position with the actual restriction site of the pertinent enzyme (e.g. G^GATCC for BamHI, the ^ marking the position you identified); if you then display restriction enzyme sites with the appropriate option, you obtain your restriction map. You can also annotate restriction fragments for each of the digestion reactions you showed above. Hope this helps!