DO ALL PARTS TO THIS QUESTION: DO NOT SKIP OVER C. Every answer has skipped part
ID: 179327 • Letter: D
Question
DO ALL PARTS TO THIS QUESTION: DO NOT SKIP OVER C. Every answer has skipped part C so far and it is frustrating.
In a recent publication, gold nanoparticles conjugated to DNA(self-hybridized) exposed to Radio Frequency (RF) energy resulted in the dehybridization of the DNA as shown in the figures below:
A. Describe the potential structure of the hybridized and dehybridized DNA.
B. Describe how the A260 reading could change under RF.
C. Propose a mathematic equation to model the dehybridization seen in the figure.
0.24 0.23 0.22 0.21 0,20 0.19 On OM AA gTA Time (min)Explanation / Answer
When nucleic acids from different sources are involved in renaturation, the reaction is called hybridisation. The principle of hybridization reaction is to expose two single stranded nucleic acid preparations to each other and then to measure the amount of double stranded structure that forms. The two preparations of single stranded DNA are mixed together in solution. The hybridization reaction can be followed by monitoring the optical density (UV light - 260 nm is strongly absorbed by denatured DNA than by DNA itself. This is called hypochromatic effect). As hybridisation increases, the temperature of UV wavelength falls.
Renaturation of DNA depends on random collision of the complementary strands and it follows second order kinetics. The rate of reaction is governed by the equation
dC / dt = -kC2
where C is the concentration of DNA that is single stranded at time t, and k is a reassociation rate constant. By integrating this equation between the limits of the initial concentration of DNA, Co at time t = 0, and the concentration C that remains single stranded after time t, we can describe the progress of the reaction as
C / Co = 1 / 1+k. Cot
This equation shows that the parameter controlling the reassociation reactin is the product of DNA concentration (Co) and time of incubation (t), usually described as Cot. A useful parameter can be derived by considering the conditions when the reaction is half complete at time t1/2. Then
C / Co = 1/2 = 1 / 1+ k.Cot1/2
so that
Cot1/2 = 1/k
The value required for half-reassociation is called Cot1/2. Since it is the product of the concentration and time required to proceed half way, a greater Cot means a slower reaction. The reassociation of DNA can be described by Cot1/2. It is given in nucleotide-moles x seconds/liter. It can also be described in the form of its reciprocal rate constant k ( in units of liter - nucleotides - moles-1second -1).
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