7. For each of the circular DNAs described below, indicate a location (1, 2, or

Question

7. For each of the circular DNAs described below, indicate a location (1, 2, or 3) that the DNA would migrate on an agarose gel. Detcrgcnt can inactivate and remove nucloosome protcins. Hint. Nucleosome assembly in the absence of topoisomerase I can introduce negative supercoiling to DNA. You should justify your answers to get a full credit (12 pt) A. Relaxed circular DNA B. Initiate nucleosome assembly without tonoisomerase I1 and then treat the sample with detergent before running the products on an agarose ge C. Add topoisomerase II to the previous reaction in B but prevent additional nuclcosomc assembly. Add detergant before running the products on an agarosc gel. D. Add topoisomerase II to the reaction described in B and allow additional nucleosome assembly. Add detergent before running the products on an agarose gel . The figure shown bclow is about the effect of salt and GC contenn on Tm of DNA double helix. Answer whether each of following statement is true T or fabe( information that can be inferred from results in the figure. If the answer is F, please justify your answer (15 pt) based on A. Increasing heat can denature DNA molecules B. The higher the content of A:T hase pairs, the higher the melting temperature (Tm) C. Increasing salt concentration of the solution make t difficult to denature the double-stranded DNA. D. UV light absorption of single-stranded DNA is lower than that of double-stranded DNA E. Adding urea in the solution with DNA will increase Tm. Urea can disrupt non-covalent

Explanation / Answer

8) a. True. High heat/ temperature disrupts the hydrogen bonds, the strands are no longer held together i.e., double helix is denatured.

b. False. dsDNA with a high GC content has a higher Tm than DNA with a lower GC cntent or with higher AT content. It is due to higher number of hydrogen bonds (A:T has two hydrogen bonds and G:C has three hydrogen bonds) and high hydrophobic and vander waals forces.

c) False. The lower the ionic strength , lower will be the melting temperature and hence difficlt to seperate the strands. DNA is negatively charge, so on increasing ionic strength(high negative charge), charges will not be shielded leading to electrostatic repulsion and hence can easily seperate the strands

d) True. UV absorption is used to dtermine the concentration of nucleic acids in solution. Absorption at 260nm is proportional to nucleic acid concentration.

e) False. Urea addition lowers melting temperature, it forms hydrogen bond with bases and restricts the formation of hydrogen bonds between complementary bases, lowers melting temperature and denatures DNA strand

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