Fun with DNA worksheet

DNA structure

Write the complementary sequence to the following polynucleotides.

• 5’ TCAGAACGTAGTAGACACAAGTGACAGATACACAGTAGACAGATTTAGAAA
3’

2. 5’ AAGAGAGGATTACCATAGTAGTATAAACCCAGTGATAGATAGAGGATGAG 3’

3. 3’ ATGACCCACAGTAGGATTTGAGAAGGAGATTTGATAGAGTGATGAGGA 5’

Using Chargaff’s Rules, complete the following questions. For each question, we are referring to
double stranded DNA.

• If a piece of DNA contains 20% A, how much T (i.e., %) does it contain? How much G
does it contain? What is ratio of purines to pyrimidines?

• If a piece of DNA contains 30% G/C content, how much A does it have?
Primer design

For each of the following a) write the complementary sequence, b) design two primers 15 base
pairs in length, c) write both primers according the conventional method.

• 5’
TCTCATACTACTACTACTACAGGATCTATCGATCTAGCGACGATCTGACGACGC
AGGCT 3’

• 5’
AAGACTACAGGCAGAATCATCTAGCGCAGCAGCAGACGCATAATACTGCGAGC
TACTGG 3’

• 5’
AGGCTTAGGAGCGCAGTATTAAGAGACTCTCGAGCGCGCGCTATCGGACGATA
CTGACG 3’
For the primers that you designed in the following questions, how could you change the
specificity/stringency of the primer by modifying the primer? How could you change the
stringency by not changing the primer but by changing the way in which PCR was done?

Melting Temperature

For the following primers, calculate the melting temperature. Indicate whether it would make a
good primer for PCR (keep in mind that Tm is very close to annealing temperature).

• 5’ TGAGCATTACACCACA 3’

• 5’ ACCAGACAGAGAGTGAGGC 3’

• 5’ AAAAATTATATATTATT 3’

• 5’ CCGCGCGGGCGGGAGAGGCG 3’

If you wanted to increase the melting temperature of primer 3, how could you do that? If you
wanted to decrease the melting temperature of primer 4, how could you do that?

Transcription

Write out the RNA strand that would be transcribed from the DNA strand. Remember always
start at the +1 site (bolded nucleotide). The -10 consensus sequence is indicated in italics.

• 5 ‘ TATAATAGCGCACAGAGTGAATCGAGCGACTACATGACGACTACGAC 3’

2. 3’ GAGAAGAGCAAATCGCGTTCGCAGCAGCACGGAGCTCTCTAATAT 5’
Translation

Using the codon table on page 410 of your book (Figure 15.10), write out the amino acid
sequence for each of the following mRNAs. Remember to start translating at the right codon in
order to get the correct sequence. Is there a stop codon present in each mRNA?

• 5’ CUAUGUCGUACAUCAUCUGGGUACUACAUCAUUGA 3’

• 5’ GGACACAACGCAGAAAUGGGACGACGAUAGAGUAGUUAA 3’

• 3’
GAUGCGCGCGUAGCUGUCUUAUCUCAUUCUAUCAUCUAUCUAGUAUUUAU
5’

th
For sequence 1, delete the 9 nucleotide from the 5’ end and re-translate the sequence. What
does this do to the polypeptide? Does it contain a stop codon?

DNA replication

Draw out a replication fork and draw all of the enzymes involved in the DNA replication.
Indicate which strand is the leading and lagging strand. Indicate is synthesis is continuous or
discontinuous. Indicate DNA orientation and label as many parts as you can.