Suppose that you are given a short fragment of DNA to sequence. You clone the*fragment, isolate the cloned DNA fragments, and set up a series of four dideoxy reactions. You then separate the products of the reactions by gel electrophoresis and obtain the following banding pattern:
Draw a map of the EcoRI and SmaI restriction sites on this 14-kb piece of DNA, indicating the relative positions of the restriction sites and the distances between them.
23. Suppose that you want to sequence the following DNA fragment:
Fragment to be sequenced:
You first clone the fragment in bacterial cells to produce sufficient DNA for sequencing. You isolate the DNA from the bacterial cells and carry out the dideoxy sequencing method. You then separate the products of the polymerization reactions by gel electrophoresis. Draw the bands that should appear on the gel from the four sequencing reactions.
Write out the base sequence of the original fragment that you were given.
25. Microarrays can be used to determine the levels of gene expression. In one type of microarray, hybridization of the red (experimental) and green (control) cDNAs is proportional to the relative amounts of mRNA in the samples. Red indicates the overexpression of a gene and green indicates the underexpression of a gene in the experimental cells relative to the control cells, yellow indicates equal expression in experimental and control cells, and no color indicates no expression in either experimental or control cells.
In one experiment, mRNA from a strain of antibiotic-resistant bacteria (experimental cells) is converted into cDNA and labeled with red fluorescent nucleotides; mRNA from a nonresistant strain of the same bacteria (control cells) is converted into cDNA and labeled with green fluorescent nucleotides. The cDNAs from the resistant and nonresistant cells are mixed and hybridized to a chip containing spots of DNA from genes 1 through 25. The results are shown in the adjoining illustration. What conclusions can you make about which genes might be implicated in antibiotic resistance in these bacteria? How might this information be used to design new antibiotics that are less vulnerable to resistance?
*26. Genes for the following proteins are found in five different species whose genomes have been completely sequenced. On the basis of the presence-and-absence patterns of these proteins in the genomes of the five species, which proteins are most likely to be functionally related? (Hint: Create a table listing the presence or absence of each protein in the five species.)
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