Melting point and thermodynamics of DNA
- Dashboard
- Melting point and thermodynamics of DNA
Most Recent Score Report
| Questions Correct | Questions Answered | Time Spent | Status | Attempt Date | |
|---|---|---|---|---|---|
| -- | -- | -- | -- | -- |
Previous Score Reports
| Questions Correct | Questions Answered | Time Spent | Status | Attempt Date | |
|---|---|---|---|---|---|
| -- | -- | -- | -- | -- |
Melting point and thermodynamics of DNA
Array
(
[passage] => WP_Post Object
(
[ID] => 560242
[post_author] => 12815
[post_date] => 2025-01-14 05:57:37
[post_date_gmt] => 2025-01-14 10:57:37
[post_content] => Practice Passage (Question 1-5)
*This passage is the property of Khan Academy and has been reformatted into an AAMC-style interface in their entirety by MedLife Mastery. MedLife Mastery does not endorse and is not an affiliate of Khan Academy.
The melting temperature of DNA refers to the temperature at which 50% of DNA in a sample has denatured from double-stranded DNA (dsDNA) to single-stranded DNA (ssDNA). Sensitive measurement of the melting curve of a sample of DNA can be used to detect single nucleotide differences between two DNA samples. This technique is possible because guanine-cytosine (GC) pairs contribute greater stability to dsDNA than adenosine-thymine (AT) pairs. Figure 1 shows three samples of DNA with different percentages of GC content.
Figure 1 - DNA melting curves for three strands of DNA with different levels of GC content. The y-axis indicates the fraction of DNA molecules that are single-stranded.
To better understand the nature of DNA melting, researchers characterized how different structural elements of dsDNA affect its stability and therefore its melting temperature. They suspected that the two main contributors to dsDNA stability would be hydrogen bonding between base pairs and pi-stacking, a non-covalent interaction that occurs only between the aromatic portions of bases. They were able to isolate the free energy contributions of individual structural elements by making chemical alterations that effectively eliminated the free energy contributions of all other structural elements. Table 1 shows the free energy contributions of the different structural elements they investigated. They also observed how DNA stability was affected by salt concentration, pH, and the presence of DNA intercalators, aromatic compounds that can be toxic or mutagenic due to their ability to insert between DNA bases. Table 2 shows how each of these factors changes the free energy (∆G) of dsDNA formation, represented by ∆∆G.
Table 1 - Free energy (∆G) contributions of individual non-covalent interactions to the thermodynamic stability of dsDNA. Experiments were performed in cellular conditions (T = 37 °C).
Table 2 - Changes to free energy (∆∆G) of dsDNA formation in various conditions. Experiments were performed in cellular conditions (T = 37 °C).
Data adapted from: Yakovchuk, P., Protozanova, E., & Frank-Kamenetskii, M. D. (2006). Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Research, 34 (2) 564-574 . doi:10.1093/nar/gkj454
[post_title] => Melting point and thermodynamics of DNA
[post_excerpt] =>
[post_status] => publish
[comment_status] => closed
[ping_status] => closed
[post_password] =>
[post_name] => melting-point-and-thermodynamics-of-dna
[to_ping] =>
[pinged] =>
[post_modified] => 2025-01-14 05:58:51
[post_modified_gmt] => 2025-01-14 10:58:51
[post_content_filtered] =>
[post_parent] => 0
[guid] => https://medlifemastery.com/?post_type=passage&p=560242
[menu_order] => 0
[post_type] => passage
[post_mime_type] =>
[comment_count] => 0
[filter] => raw
)
[questions] => Array
(
[0] => Array
(
[quiz_unique_key] => 578908434
[question] => Which compound is most likely to represent the structure of Intercalator A?
[value] => Array
(
[answer] => 1
[description] => Reason for the Correct Answer:
The passage states that intercalators of dsDNA are aromatic, allowing them to insert between nucleotide bases. The question is really asking which compound is aromatic.
For a cyclic compound to be aromatic, it must satisfy the criteria of Huckel’s rule. One criterion is that the compound has 4n+2 delocalized, conjugated pi electrons (in this case, the double-bonds).
Another criterion of Huckel’s rule is that the compound must be planar. We can eliminate the following answer because a monocyclic ring of this size is not stable in a planar conformation; the angle of the C-C bonds would create too much ring strain.
The only compound that satisfies all criteria to be an aromatic compound is shown below.
)
[answers] => Array
(
[0] => Array
(
[each_answer] => A.
)
[1] => Array
(
[each_answer] => B.
)
[2] => Array
(
[each_answer] => C.
)
[3] => Array
(
[each_answer] => D.
)
)
)
[1] => Array
(
[quiz_unique_key] => 3873426850
[question] => Suppose the net change in enthalpy (∆H) of the two H-bonds of the AT base pair forming is -1.2 kJ. What is the net change in entropy (∆S) of the same process, assuming cellular conditions?
[value] => Array
(
[answer] => 1
[description] => Reason for the Correct Answer:
Based on the data table in the passage, the free energy contribution, ∆G, of the two AT hydrogen bonds is 2.1 kJ/mol.
We can find the entropy using the equation ∆G= ∆H – T∆S.
In “cellular conditions,” the temperature is assumed to be 37 °C. Don’t forget! You have to convert to Kelvin (37 + 273 = 310) to match the units of entropy, J/(mol*K).
Plugging known values into the equation, we get (2.1 kJ/mol) = – (1.2 kJ/mol) – (310 K)*∆S.
Solving for ∆S and converting units, we get:
∆S = (- 1.2 kJ/mol – 2.1 kJ/mol) / 310 K
∆S = -(3.3 kJ/mol) / (310 K) * (1000 J / 1 kJ)
Since we are not allowed a calculator on the MCAT, we need to approximate:
-(1/100) * 1000 = -10. The closest answer is -10.6 J/(mol*K).
Double check that this makes sense. The positive ∆G value tells us that the overall contribution of the two AT base pair H-bonds is destabilizing. The question tells us ∆H is negative and therefore stabilizes dsDNA. The entropy must be destabilizing and negative. So the negative value for entropy does make sense.
)
[answers] => Array
(
[0] => Array
(
[each_answer] => A.-10.6 J/(mol*K)
)
[1] => Array
(
[each_answer] => B.2.9 J/(mol*K)
)
[2] => Array
(
[each_answer] => C.-2.9 J/(mol*K)
)
[3] => Array
(
[each_answer] => D.10.6 J/(mol*K)
)
)
)
[2] => Array
(
[quiz_unique_key] => 83407773
[question] => Consider the sample of DNA whose melting curve is shown by the solid line in Figure 1. How would adding a significant concentration of MgCl2 to the sample affect the melting curve?
[value] => Array
(
[answer] => 3
[description] => Reason for the Correct Answer:
Table 2 shows that a concentration of 100 mM MgCl2 decreases ∆G of dsDNA formation by 2.1 kJ/mol.
A decrease in ∆G of dsDNA formation means dsDNA becomes more stable.
Greater stability of dsDNA will increase the melting temperature of dsDNA.
Adding a significant concentration of MgCl2 to the sample will shift the DNA melting curve to the right.
)
[answers] => Array
(
[0] => Array
(
[each_answer] => A.It would shift the melting curve left.
)
[1] => Array
(
[each_answer] => B.It would not change the position of the melting curve.
)
[2] => Array
(
[each_answer] => C.It would shift the melting curve right.
)
[3] => Array
(
[each_answer] => D.We do not have enough information to predict the effect.
)
)
)
[3] => Array
(
[quiz_unique_key] => 2377279144
[question] => Changing the pH of a sample from 7 to 11 would have what effect on the melting temperature of a sample of DNA?
[value] => Array
(
[answer] => 4
[description] => Reason for the Correct Answer:
Notice that in Table 2, the researchers tested the effect of using a 1.0*10^-3 NaOH M solution. Assuming a starting pH of 7, this would change the pH to 11, so we can base our answer on the measured ∆∆G of 2.0 kJ/mol.
A positive ∆∆G indicates that dsDNA became less stable.
If dsDNA is less stable, it will have a lower melting point.
If dsDNA is less stable, ssDNA must be more stable.
Changing the pH from 7 to 11 in a sample of DNA would decrease the melting point by stabilizing ssDNA
)
[answers] => Array
(
[0] => Array
(
[each_answer] => A.It would increase the melting point by stabilizing dsDNA.
)
[1] => Array
(
[each_answer] => B.It would increase the melting point by stabilizing ssDNA.
)
[2] => Array
(
[each_answer] => C.It would decrease the melting point by stabilizing dsDNA.
)
[3] => Array
(
[each_answer] => D.It would decrease the melting point by stabilizing ssDNA
)
)
)
[4] => Array
(
[quiz_unique_key] => 2261298308
[question] => Salts increase the melting temperature of DNA due to the presence of positive ions in solution. Which is the most likely mechanism by which this stabilization occurs?
[value] => Array
(
[answer] => 4
[description] => Reason for the Correct Answer:
DNA is comprised of three different structural elements: nitrogenous bases that are paired through hydrogen bonds, a pentose sugar (ribose), and a phosphate backbone.
The question tells us that it is the positive ions of salts that cause the melting temperature of DNA to increase.
Intercalation can only occur with aromatic compounds.
Positive ions can localize between two negative charges and reduce the repulsion between them.
The phosphate groups are negatively charged and positive ions can sit between them, reducing repulsion and allowing for strengthened pi-stacking. The mechanism by which the stabilization occurs is interaction with phosphate groups.
)
[answers] => Array
(
[0] => Array
(
[each_answer] => A.Adding to pi-stacking by intercalation
)
[1] => Array
(
[each_answer] => B.Interaction with deoxyribose
)
[2] => Array
(
[each_answer] => C.Stronger ionic bonds replace weaker hydrogen bonds
)
[3] => Array
(
[each_answer] => D.Interaction with phosphate groups
)
)
)
)
[total_question] => 5
[correct_answers] => Array
(
[560242|1] => A
[560242|2] => A
[560242|3] => C
[560242|4] => D
[560242|5] => D
)
[hide_display_feedback_settings] =>
[hide_solutions] =>
)
