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DNA Strider Manual: Bio312 2000
Bonnie K. Baxter, Lewis & Clark College
Step 1: Opening a DNA strider file and exploring the "enz" options:
First, double-click on the DNA Strider folder icon.
This icon should be either on your computer's desktop or (in Green Lab) in a "Bio312" folder on the desktop.
Within this folder, you should see a folder labeled "Bio312 sequences." (If you don't, use the command-F command in the finder to have Sherlock find this folder for you.) Double click.
You'll see a list of DNA sequences that I've compiled and provided for your use. Included are sequences of both pCITE vectors (2a and 4a), as well as sequences with names such as "LTV1-pCITE2 PCR." This latter sequence is the sequence of the PCR product that should be created by amplifying LTV1 with the LTV1-pCITE-dir and LTV1-pCITE2-rev primer pair. There should be one PCR product sequence file for each group.
Double click on your pCITE vector sequence file. DNA Strider should start up and open this file, giving you a screen that looks something like this:
Across the top of the window is a series of descriptions. DNA indicates that this is a DNA file, and not a protein sequence file. 3800 bp is the length of the sequence. The beginning and ending sequences are shown next. Circular means that this sequence is circular as opposed to linear.
The main box in this window contains the DNA sequence itself, with numbers around the outside of the box to help you orient yourself. The bottom box contains room for a text "comment"--any description that you'd like to provide to remind yourself (and others) what this particular sequence represents.
The "enz" menu bar option provides a series of commands that allow you to analyze this sequence for the presence of restriction enzyme sites. Go to the menu bar and select this item.
Explore each of these options in turn to see what it does. There are many useful tools here. One that you may not recognize is "silent map." A "silent" restriction site is a restriction site that is not present in the wild-type sequence, but could be created by a "silent" mutation--a mutation that does not change the encoded amino acid sequence. This kind of map can be useful for researchers who want to be able to use restriction enzymes for cloning a gene fragment but find that the sites they need do not exist.
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