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Chapter 10: Problem 35

During gel electrophoresis, DNA molecules can easily be separated according to size because all DNA molecules have the same charge-to-mass ratio and the same shape (long rod). Would you expect RNA molecules to behave in the same manner as DNA during gel electrophoresis? Why or why not?

Short Answer

Expert verified
Answer: RNA molecules might not behave in the same manner as DNA during gel electrophoresis because they can have various secondary structures, resulting in different shapes and sizes that affect their migration in the gel matrix. Even though RNA and DNA have similar charge-to-mass ratios, the variation in RNA shape due to secondary structures might cause differences in their migration behavior during gel electrophoresis.

Step by step solution

01

Similarities between RNA and DNA

RNA and DNA are both nucleic acids, having a similar basic structure consisting of a sugar, a phosphate group, and a nitrogenous base. They have a similar charge and a similar charge-to-mass ratio.
02

Differences between RNA and DNA

DNA is double-stranded while RNA is usually single-stranded. DNA consists of deoxyribose sugar, while RNA contains ribose sugar. The nitrogenous bases in RNA include adenine, uracil, guanine, and cytosine, while DNA uses adenine, thymine, guanine, and cytosine.
03

Shape of RNA molecules

Unlike DNA, which has a consistent double helix structure, RNA molecules can form various secondary structures due to base-pairing interactions within the same molecule. These secondary structures can alter the shape and size of an RNA molecule.
04

Effect of shape and size on gel electrophoresis

During gel electrophoresis, molecules are separated based on their charge-to-mass ratio and shape. As RNA molecules can have different shapes and sizes due to their secondary structures, they can behave differently during gel electrophoresis compared to the more consistent shape of DNA molecules.
05

Conclusion

We would not expect RNA molecules to behave in the same manner as DNA during gel electrophoresis because RNA molecules can have various secondary structures, which can result in different shapes and sizes, affecting their migration in the gel matrix. Even though RNA and DNA have similar charge-to-mass ratios, the variation in RNA shape due to secondary structures might cause differences in their migration behavior during gel electrophoresis.

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Most popular questions from this chapter

What component of the nucleotide is responsible for the absorption of ultraviolet light? How is this technique important in the analysis of nucleic acids?

Newsdate: March \(1,2030 .\) A unique creature has been discovered during exploration of outer space. Recently, its genetic material has been isolated and analyzed. This material is similar in some ways to DNA in its chemical makeup. It contains in abundance the 4 -carbon sugar erythrose and a molar equivalent of phosphate groups. In addition, it contains six nitrogenous bases: adenine (A), guanine (G), thymine (T), cytosine (C), hypoxanthine (H), and xanthine (X). These bases exist in the following relative proportions: $$\mathrm{A}=\mathrm{T}=\mathrm{H} \text { and } \mathrm{C}=\mathrm{G}=\mathrm{x}$$ X-ray diffraction studies have established a regularity in the molecule and a constant diameter of about 30 A. Together, these data have suggested a model for the structure of this molecule. (a) Propose a general model of this molecule. Describe it briefly. (b) What base-pairing properties must exist for \(\mathrm{H}\) and for \(\mathrm{X}\) in the model? (c) Given the constant diameter of \(30 \AA\), do you think that either (i) both \(\mathrm{H}\) and \(\mathrm{X}\) are purines or both pyrimidines, or (ii) one is a purine and one is a pyrimidine?

Because of its rapid turnaround time, fluorescent in situ hybridization (FISH) is commonly used in hospitals and laboratories as an aneuploid screen of cells retrieved from amniocentesis and chorionic villus sampling (CVS). Chromosomes \(13,18,21, X,\) and \(Y(\text { see Chapter } 8)\) are typically screened for aneuploidy in this way. Explain how FISH might be accomplished using amniotic or CVS samples and why the above chromosomes have been chosen for screening.

List three main differences between DNA and RNA.

Electrophoresis is an extremely useful procedure when applied to analysis of nucleic acids as it can resolve molecules of different sizes with relative ease and accuracy. Large molecules migrate more slowly than small molecules in agarose gels. However, the fact that nucleic acids of the same length may exist in a variety of conformations can often complicate the interpretation of electrophoretic separations. For instance, when a single species of a bacterial plasmid is isolated from cells, the individual plasmids may exist in three forms (depending on the genotype of their host and conditions of isolation): superhelical/supercoiled (form I), nicked/open circle (form \(\mathrm{II}\) ), and linear (form III). Form I is compact and very tightly coiled, with both DNA strands continuous. Form II exists as a loose circle because one of the two DNA strands has been broken, thus releasing the supercoil. All three have the same mass, but each will migrate at a different rate through a gel. Based on your understanding of gel composition and DNA migration, predict the relative rates of migration of the various DNA structures mentioned above.
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