The document describes the process of polymerase chain reaction (PCR) using a figure showing a piece of double-stranded DNA with forward and reverse primers designed to anneal to the boundaries of a target sequence. During each PCR cycle, the DNA strands are separated, the primers anneal, and new DNA is synthesized using a heat-stable polymerase to selectively amplify only the target sequence.

1. 16. The figure (p. 155) shows a piece of double-stranded DNA containing a sequence of interest
to you. You have designed two primers-one forward and one reverse - that are complementary to
the double-stranded DNA: the primers are oligonucleotides that anneal to the boundaries of the
DNA sequence, as shown. (In practice, primers are usually 18-22 bases in length, but are shown
as 4 bases in length here for simplicity.) As shown in Figure 3.33, PCR proceeds in a series
Biomolecular Principles: Nucleic Acids of cycles. During each cycle, 1) the DNA strands are
separated (denatured), 2) the primers are annealed, and 3) DNA is synthesized using a heat-stable
polymerase. a. Explain why the primers are designed to bind at the 3 end of target sequence. b.
How many cycles does it take until DNA molecules are made that contain only the target
sequence (i.e. the blue sequence in the figure) and no adjacent "contaminating" DNA? c. Assume
that you have one copy of DNA at the start (before cycle 1). After 10 cycles, how many copies of
the target sequence are present? How many of these contain "contaminating" DNA? d. Assume
that you have 1000 copies of DNA at the start. How does the answer to c change? e. Write an
equation relating D, the number of copies of DNA, and X, the number of copies with
contamination, to the number of cycles, n.