Rajavel-Problem Set 1 #3 and #4 (page 2 of 2) 3. Suppose you have a circular bacterial genome of 7200 bp (total length) with a linking number of 540, and adopt a conformation of 10.6 bp/turn of the helix, calculate the writhe component and indicate the topology of such a molecule? The linking number (Lk) of a closed circular DNA can be solved into two components- the twists (Tw) and writhes or supercoiling (Wr) with the following equation (Watson et al., 2014): Lk = Tw + Wr 540 = (7200/10.6) + (Wr) 540 = (679) + (Wr) -139 = Wr There are 139 negative supercoils (that’s 139 360º right-handed turns of the DNA duplexes you look down the supercoiling) over the 7200bp length of the circular genome. This writhe value is energetically favorable. 4. Suppose you have discovered a novel phage and you are interested in the characterization of this phage for further research use. You have performed a base composition of this phage and the results are as follows: A is 23%; T is 36%; G is 21%; C is 20%. Based on this information, what can you conclude about the DNA structure of your novel phage? Justify your response According to Chargaff’s rule, DNA from all organisms should have a 1:1 ratio (base pair rule) where the sum of pyrimidine nucleotides equals that of purine nucleotides (Watson et al., 2014). For example, A _ T and G _ C; A _ G _C _ T for duplex DNA. In the scenario, the percentage of A (23%) does not equal that of T (36%), nor does that of G (21%) equal that of C (20%). Thus, this lack of equality between purine and pyrimidine nucleotides shows that the interested DNA is single-stranded, not double-stranded. Lastly, this DNA could be double-stranded when only replicating in the host cell. REFERENCES: Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R, Harrison SC. (2014). Molecular Biology of the Gene. New York: Cold Spring Laboratory Press (pp 11-12, 24-26, 93-95). US National Library of Medicine (NLM): Genetics Home Reference. (2010). Hereditary hypophosphatemic rickets. Retrieved on 31 JAN 2014 from http://ghr.nlm.nih.gov/condition/hereditary-hypophosphatemic-rickets University of Vermont (UVM). (2012). Education. Inheritance. Inheritance Patterns. Retrieved on 31 JAN 2014 from