A double-stranded fragment of viral DNA, one of whose strands is shown below, encodes two polypeptides called vir-1 and vir-2. AIDing this double stranded DNA fragment to an in vitro transcription and translation system yields peptides of 10 residues (vir-1) and 5 residues (vir-2).
(a) What are the nucleotide sequences of the open reading frames (start to stop codons, inclusively) within the mRNA transcripts coding for vir-1 and vir-2? Write them out and designate the 5′ and 3′-ends.
(b) What is the amino acid sequence of each polypeptide? Use one letter symbols to denote amino acids.
(c) In a mutant viral strain, the T at position 23 (counting from the left) on the DNA strand shown above has been replaced with G. Determine the amino acid sequences of the two peptides encoded by the mutant virus.
(d) What would be the sequences of the oligonucleotide primers (each 10 bp in length) required to amplify by polymerase chain reaction the DNA open reading frame (start to stop codons, inclusively) corresponding to the vir-1 polypeptide? Be sure to designate the 5′ and 3′ ends of the primers. HINT: you only want the vir-1 open reading frame amplified, not any flanking sequence.
(e) Draw the patterns of bands you would expect to see on the DNA sequencing gel below if you annealed the 10 residue primer 5′-CATATAGTTG-3′ to the above single-stranded wild-type DNA template and carried out a dideoxy sequencing experiment (Sanger sequencing). The primer contains a radioactive label at its 5′-end
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