Searching BLAST with short DNA sequences
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You have a rat DNA library, and you have been given four potential primer sequences (assume all are sense primers) from a rat sequence XM_006251609. You want to search the DNA databases to see if you get any hits other than to your rat sequence of interest.
Hint: Make sure you search all the databases (i.e. 'Nucleotide collection (nr/nt)') and do no restrict your search to human genomic and transcript. Remember - these primers are designed for a rat sequence, and the accession number is XM_006251609.... Also, if you were doing this in the lab, you would also check that the melting temperatures (Tm) of the primers were suitable, that they didn't form primer-dimer pairs, and that they didn't form hairpin loops.
The sequences are:
  1. Sequence 1: GTATGATCGCTTTAAGCTCAGTA
  2. Sequence 2: ATTTGGATTAGTCCATTTCTGTC
  3. Sequence 3: AGGGGTGAGCCCTTGGTGGCCG
  4. Sequence 4: TACTGCGTCAGCTTGCTCCACACCCC
  1. Run a BLAST search at: http://www.ncbi.nlm.nih.gov/blast/ for EACH sequence (i.e. four blast searches).
  2. Complete the quiz below.
1) Could Sequence 1 be used as a primer?
One answer only.
   Yes
   No
   Don't know
2) Could Sequence 2 be used as a primer?
One answer only.
   Yes
   No
   Don't know
3) Could Sequence 3 be used as a primer?
One answer only.
   Yes
   No
   Don't know
4) Could Sequence 4: be used as a primer?
One answer only.
   Yes
   No
   Don't know
We have now completed a series of BLAST searches using short DNA and protein sequences, and you have:
  1. carried out the searches
  2. analysed the results and identified a protein that could produce the small peptide
  3. assessed the suitability of 4 potential DNA primer sequences for a PCR reaction
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