Number Question Marks
1. If a linear piece of DNA has 2 recognition sites, how many bands would you
expect to see on a gel after digestion with a restriction enzyme that
recognizes each site?
1
2. If a circular piece of DNA has 2 recognition sites, how many bands would you
expect to see on a gel after digestion with a restriction enzyme that
recognizes each site?
1
3. If a liner DNA molecule is digested exactly in the middle, how many
fragments would you expect to see on a gel? Explain your answer.
2
4. When electrophoresed on an agarose gel, will the largest DNA fragment be
closest to or farthest form the loading well? Explain your answer.
1
5. How does voltage influence the speed of migration of bands on an agarose
gel – if you increase the voltage applied to a gel, will larger fragments
migrate proportionally faster or slower than small fragments? Explain your
answer.
2
6. If you wanted to resolve small DNA molecules (e.g. 100 – 1000 bp in length),
would you use a higher agarose percent gel or a lower agarose percent gel?
Why?
2
7. If you wanted to resolve larger DNA molecules (e.g. 5000 – 50000 bp in
length), would you use a higher agarose percent gel or a lower agarose
percent gel? Why?
2
8. How would you resolve two fragments of similar size as 2 separate bands? 1
9. How does the number of restriction sites for each digest relate to the
number of fragments produced in the digest?
1
10. Add up the lengths of the fragments in each digest and verify that the total
length matches that of the uncut lambda DNA.
1
11. Using NEB cutter, generate an EcoRI digest of linear lambda DNA. View the
gel using 0.7% agarose, 1.4% agarose and 2% agarose. You can change the
agarose % by changing the gel type in the “view gel” window. How and why
does the number and position of bands change as you increase the agarose
percentage?
2
12. Consider Figure 1. Does the experimental gel look like the virtual gel(s)
generated by NEB cutter? If not, why not?
1
13. Count the number of bands in each lane of the experimental gel in Figure 1.
How does the number of bands you counted compare to the number of
bands generated in the corresponding NEB cutter digests? What could be a
possible explanation for the deviation seen between the experimental digest
and the in silico digest?
1
5
J. References ( /3)
• The list of references should only include works that are cited in the text and that have been
published or accepted for publication
• Reference list entries should be alphabetized by the last names of the first author of each
work.
• Journal article
1. Gamelin FX, Baquet G, Berthoin S, Thevenet D, Nourry C, Nottin S, Bosquet L (2009)
Effect of high intensity intermittent training on heart rate variability in prepubescent
children. Eur J Appl Physiol 105:731-738. doi: 10.1007/s00421-008-0955-8
• Article by DOI (digital object identifier)
1. Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production. J
Mol Med. doi:10.1007/s001090000086
• Book
1. South J, Blass B (2001) The future of modern genomics. Blackwell, London
• Book chapter
1. Brown B, Aaron M (2001) The politics of nature. In: Smith J (ed) The rise of modern
genomics, 3rd edn. Wiley, New York, pp 230-257
• Online document
1. Cartwright J (2007) Big stars have weather too. IOP Publishing PhysicsWeb.
http://physicsweb.org/articles/news/11/6/16/1. Accessed 26 June 2007
• Dissertation
1. Trent JW (1975) Experimental acute renal failure. Dissertation, University of California
• Always use the standard abbreviation of a journal’s name according to the ISSN List of Title
Word Abbreviations, see ISSN Website