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Chapter 17: Problem 7

Restriction sites are palindromic; that is, they read the same in the \(5^{\prime}\) to \(3^{\prime}\) direction on each strand of DNA. What is the advantage of having restriction sites organized this way?

Short Answer

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Answer: The advantage of palindromic restriction sites is that they allow restriction enzymes to recognize and bind to target sites on both strands of the DNA molecule, ensuring complete cleavage of both strands. This produces compatible sticky or cohesive ends that can be ligated with other DNA fragments sharing the same restriction site, making it easier for scientists to manipulate and join different DNA fragments in molecular biology and genetic engineering applications.

Step by step solution

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1. Understanding restriction enzymes and their function

Restriction enzymes, also known as restriction endonucleases, are proteins that recognize and cut specific sequences of DNA called restriction sites. These enzymes play a crucial role in molecular biology, particularly for genetic engineering and recombinant DNA technology, as they enable scientists to manipulate and analyze DNA.
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2. Explaining the structure of DNA and the \(5^{\prime}\) to \(3^{\prime}\) orientation

DNA is a double-stranded molecule consisting of two complementary strands running in opposite directions. Each strand has a \(5^{\prime}\) end (where the phosphate group is attached to the 5th carbon of the sugar ring) and a \(3^{\prime}\) end (where the hydroxyl group is attached to the 3rd carbon of the sugar ring). The strands are antiparallel, meaning one runs in the \(5^{\prime}\) to \(3^{\prime}\) direction while the other runs in the \(3^{\prime}\) to \(5^{\prime}\) direction.
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3. Describing palindromic sequences in DNA

Palindromic sequences in DNA are sequences that read the same on both strands when read from the \(5^{\prime}\) to \(3^{\prime}\) direction. For example, if the \(5^{\prime}\) to \(3^{\prime}\) sequence in one strand is "GAATTC," the complementary strand will also read "GAATTC" in the \(5^{\prime}\) to \(3^{\prime}\) direction.
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4. The advantage of palindromic restriction sites

Having restriction sites organized as palindromic sequences offers a significant advantage. Since restriction enzymes only recognize and bind to specific sequences, having palindromic sites allows the enzyme to recognize the target site on both strands of the DNA. This ensures that the enzyme can cut through both strands of the DNA molecule. This cleavage produces compatible sticky or cohesive ends that can be ligated with other DNA fragments sharing the same restriction site, making it easier for scientists to manipulate and join different DNA fragments.

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Most popular questions from this chapter

What safety considerations must be taken before CRISPR-Cas is used to edit human embryos to cure disease?

Provide one example of a CRISPR-Cas application for biotechnology.

In this chapter we focused on how specific DNA sequences can be copied, identified, characterized, and sequenced. At the same time, we found many opportunities to consider the methods and reasoning underlying these techniques. From the explanations given in the chapter, what answers would you propose to the following fundamental questions? (a) In a recombinant DNA cloning experiment, how can we determine whether DNA fragments of interest have been incorporated into plasmids and, once host cells are transformed, which cells contain recombinant DNA? (b) What steps make PCR a chain reaction that can produce millions of copies of a specific DNA molecule in a matter of hours without using host cells? (c) How has DNA-sequencing technology evolved in response to the emerging needs of genome scientists? (d) How can gene knockouts, transgenic animals, and geneediting techniques be used to explore gene function?

One complication of making a transgenic animal is that the transgene might integrate at random into the coding region, or the regulatory region, of an endogenous gene. What might be the consequences of such random integrations? How might this complicate genetic analysis of the transgene?

What roles do restriction enzymes, vectors, and host cells play in recombinant DNA studies? What role does DNA ligase perform in a DNA cloning experiment? How does the action of DNA ligase differ from the function of restriction enzymes?
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