Purpose: to use a database to design specific PCR primers to amplify a region of DNA.
Go to Biology Workbench and log in.
Select Session Tools and then New Session.
Name the New Session Deer Bone
Next select Nucleic Tools and then Ndjinn (this is a search engine for DNA and protein sequences)
In the search window enter the following three ascession numbers separated by "or"
When the three sequences appear, select Import Sequences
These three sequences will now be imported into your Deer Bone folder.
What region of DNA do these sequences correspond to? From which species?
Click on the boxes next to each sequence file and then select CLUSTALW
This program will
align the three sequences.
Yourassignment is to use this aligned sequence to design PCR primers which will amplify all three DNAs.
The Tm of the primers should be >50C. Also design the primers such that the PCR products from the two different species will be different sizes. This will allow for rapid identification of the species.
To check the Tm of
primers use the program on the page PRIMER
DESIGN in BioWeb.
To be turned in for credit:
qTurn in a printout of the aligned sequences with the location of the two primers indicated.
qWhat sized PCR product will you generate in each species?