Formerly of the Centre for Studies in Science and Mathematics Education
The following set of instructions assumes that you have downloaded the two files: uncut and master and copied them onto a disc. The files are all plain text files ending with the suffix '.doc'. Please configure your Web browser to download files with this suffix as word processor documents. The following instructions were written for use with Microsoft Word; other word processors can be used in a similar way.
A third file - simulate - is a copy of these instructions which can be modified to suit other word processors or different teaching needs.
You are presented with a word processor file showing the entire Lambda genome. This enables you to simulate theoretically the same restrictions which you are carrying out practically with The Lambda DNA protocol.
(The other file on the disc, master.doc is the entire Lambda DNA sequence and serves as a back-up copy of the genome. It is best not to load this so that there is no danger of altering it.)
The Lambda base sequence may be cut at various points with restriction enzymes. As we have seen each enzyme cuts within a particular base sequence; e.g., EcoRI cuts between the A and the G in the six base sequence GAATTC and nowhere else. This is usually shown as G | AATTC. Other restriction sites are BamHI - G | GATCC and HindIII - A | AGCTT. You can use this word processor file of the Lambda base sequence to find the restriction sites of these three enzymes - and indeed any other enzymes for which you know the 'recognition' sequence. You can then 'cut the genome' and count the number of fragments and the lengths of each of these fragments. These can later be compared with the results of your gel electrophoresis runs from The Lambda DNA protocol.
This cuts the base sequence at all the EcoRI restriction sites and puts a paragraph break (^p) at each point where the sequence has been cut. It also converts the recognition sequence of six bases to upper case letters so that you can see them more easily.
EcoRI - restriction site G | AATTC
You should now have the number of fragments you noted in answer to the second question above and shown on the EcoRI bar. You should also have the fragment lengths expressed as the number of bases.
BamHI - restriction site G | GATCC
HindIII - restriction site A | AGCTT