E1. The location of the intron within the cDNA is shown below: cDNA: 5′-ATTGCATCCAGCGTATACTATCTCGGGCCCAATTAATGCCAGC GGCCAGACTATCACCCAACTCG...INTRON...GTTACCTACTAGTATATCCCATATACTAGCATATATTTTACCCATAATTTGTGTGTGGGTATACAGTATAATCATATA–3′You can figure this out by finding where the sequence of the genomic DNA begins to differ from the sequence of the cDNA. The genomic DNA has the normal splice sites that are described in Figure 12.21. Genomic DNA: 5′–ATTGCATCCAGCGTATACTATCTCGGGCCCAATTAATGCCAGCGGCCAGACTATCACCCAACTCGGCCCACCCCCCAGGTTTACACAGTCATACCATACATACAAAAATCGCAGTTACTTATCCCAAAAAAACCTAGATACCCCACATACTATTAACTCTTTCTTTCTAGTTACCTACTAGTATATCCCATATACTAGCATATATTTTACCCATAATTTGTGTGTGGGTATACAGTATAATCATATA–3′The splice donor and acceptor sites are underlined. The space indicates where the strands in the corresponding RNA would be cut. The branch site is also underlined. The large A is the adenine that participates in the transesterification reaction. E2. An R loop is a loop of DNA that occurs when RNA is hybridized to double-stranded DNA. While the RNA is hydrogen bonding to one of the DNA strands, the other strand does not have a partner to hydrogen bond with so it bubbles out as a loop. RNA is complementary to the template strand, so that is the strand it binds to.
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