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Ch. 20 - Recombinant DNA Technology
All textbooksKlug 12th EditionCh. 20 - Recombinant DNA TechnologyProblem 30
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Chapter 19, Problem 30

A widely used method for calculating the annealing temperature for a primer used in PCR is 5 degrees below the melting temperature, Tₘ(°C), which is computed by the equation 81.5+0.41×(%GC)−(675/N), where %GC is the percentage of GC nucleotides in the oligonucleotide and N is the length of the oligonucleotide. Notice from the formula that both the GC content and the length of the oligonucleotide are variables. Assuming you have the following oligonucleotide as a primer,

5′-TTGAAAATATTTCCCATTGCC-3′

compute the annealing temperature for PCR. What is the relationship between  and %GC? Why? (Note: In reality, this computation provides only a starting point for empirical determination of the most useful annealing temperature.) <>

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Melting Temperature (Tₘ)

The melting temperature (Tₘ) of a DNA oligonucleotide is the temperature at which half of the DNA strands are in the double-helix state and half are in the 'melted' single-strand state. It is influenced by the nucleotide composition, particularly the percentage of guanine (G) and cytosine (C) bases, which form three hydrogen bonds compared to the two formed by adenine (A) and thymine (T). A higher GC content typically results in a higher Tₘ due to the increased stability of the double helix.
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GC Content

GC content refers to the percentage of guanine (G) and cytosine (C) nucleotides in a DNA sequence. It is a critical factor in determining the stability and melting temperature of DNA strands, as GC pairs form stronger bonds than AT pairs. The formula provided in the question incorporates GC content to calculate Tₘ, highlighting its importance in PCR primer design, where optimal annealing temperatures are crucial for successful amplification.
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Annealing Temperature in PCR

The annealing temperature in PCR is the temperature at which primers bind to the target DNA sequence. It is typically set a few degrees below the Tₘ of the primers to ensure specific binding while minimizing non-specific interactions. The relationship between Tₘ and %GC is significant because higher GC content generally leads to a higher Tₘ, thus influencing the optimal annealing temperature for effective primer hybridization during the PCR process.
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Textbook Question

As you will learn later in the text (Special Topics Chapter 1— CRISPR-Cas and Genome Editing), the CRISPR-Cas system has great potential but also raises many ethical issues about its potential applications because theoretically it can be used to edit any gene in the genome. What do you think are some of the concerns about the use of CRISPR-Cas on humans? Should CRISPR-Cas applications be limited for use on only certain human genes but not others? Explain your answers.

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Textbook Question

The gel presented here shows the pattern of bands of fragments produced with several restriction enzymes. The enzymes used are identified above the lanes of the gel, and six possible restriction maps are shown in the column to the right.

One of the six restriction maps shown is consistent with the pattern of bands shown in the gel.

From your analysis of the pattern of bands on the gel, select the correct restriction map and explain your reasoning. <>.

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Textbook Question

The gel presented here shows the pattern of bands of fragments produced with several restriction enzymes. The enzymes used are identified above the lanes of the gel, and six possible restriction maps are shown in the column to the right.

One of the six restriction maps shown is consistent with the pattern of bands shown in the gel.

The highlighted bands (magenta) in the gel hybridized with a probe for the gene pep during a Southern blot. Where in the gel is the pep gene located? 

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Textbook Question

Most of the techniques described in this chapter (blotting, cloning, PCR, etc.) are dependent on hybridization (annealing) between different populations of nucleic acids. Length of the strands, temperature, and percentage of GC nucleotides weigh considerably on hybridization. Two other components commonly used in hybridization protocols are monovalent ions and formamide. A formula that takes monovalent Na⁺ ions ((M[Na⁺]) and formamide concentrations into consideration to compute a Tₘ (temperature of melting) is as follows:

Tₘ=81.5+16.6(log M[Na+])+0.41(%GC)−0.72(%formamide)


For the following concentrations of Na⁺ and formamide, calculate the Tₘ. Assume 45% GC content.
    [Na⁺]     % Formamide
   0.825             20
   0.825             40
   0.165             20
   0.165             40

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Textbook Question

Most of the techniques described in this chapter (blotting, cloning, PCR, etc.) are dependent on hybridization (annealing) between different populations of nucleic acids. Length of the strands, temperature, and percentage of GC nucleotides weigh considerably on hybridization. Two other components commonly used in hybridization protocols are monovalent ions and formamide. A formula that takes monovalent Na⁺ ions ((M[Na⁺]) and formamide concentrations into consideration to compute a Tₘ (temperature of melting) is as follows:

Tₘ=81.5+16.6(log M[Na+])+0.41(%GC)−0.72(%formamide)

Given that formamide competes for hydrogen bond locations on nucleic acid bases and monovalent cations are attracted to the negative charges on nucleic acids, explain why the Tₘ varies as described in part (a).

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Textbook Question

In humans, congenital heart disease is a common birth defect that affects approximately 1 out of 125 live births. Using reverse transcription PCR (RT-PCR) Samir Zaidi and colleagues [(2013) Nature 498:220.223] determined that approximately 10 percent of the cases resulted from point mutations, often involving histone function. To capture products of gene expression in developing hearts, they used oligo(dT) in their reverse transcription protocol.

How would such a high %T in a primer influence annealing temperature?

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