Insert a random 9-mer containing at least one of each nucleobase in the following sequence: GCCUGUUGG-(N9)-CCAACAAU
(a) Calculate the molecular weight, percent GC content and molar absorptivity for the oligomer you designed.
(b) Provide a structural representation of your oligo using one letter nucleotide abbreviations. Show any intramolecular interactions you anticipate.
(c) Assume that fluorescein and tetramethylrhodamine were successfully bioconjugated to the 5â and 3â ends, respectively. Explain how the addition of a ssDNA oligo with a complementary base sequence to your 9-mer would confirm or refute your proposed structure. Use labelled illustrations to demonstrate this interaction i.e. show the hybrid and provide the sequence of the DNA strand.
(d) Suppose the hybrid was briefly subjected to N-cyclohexyl-3-aminopropanesulfonic acid (CAPS). What would this yield? Explain and demonstrate.
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