I 10.17 Both DNA and RNA can form special secondary structures. (a) A hairpin, consisting of a region of paired bases (which forms the stem) and a region of unpaired bases between the complementary sequences (which form a loop at the end of the stem). (b) A stem with no loop. (c) Secondary structure, showing many hairpins, of an RNA component of a riboprotein, commonly referred to as the enzyme RNase P of E. coli. (d) A cruciform structure.

(b) Stem and form a hairpin (see Figure 10.17a). A hairpin consists of a region of paired bases (the stem) and sometimes includes intervening unpaired bases (the loop). When the complementary sequences are contiguous, the hairpin has a stem but no loop (see Figure 10.17b). Hairpins frequently control aspects of information transfer. RNA molecules may contain numerous hairpins, allowing them to fold up into complex structures (see Figure 10.17c).

In double-stranded DNA, sequences that are inverted replicas of each other are called inverted repeats. The following double-stranded sequence is an example of inverted repeats:

Notice that the sequences on the two strands are the same when read from 5' to 3' but, because the polarities of the two strands are opposite, their sequences are reversed from left to right. An inverted repeat that is complementary to itself, such as:

is also a palindrome, defined as a word or sentence that reads the same forward and backward, such as "rotator." Inverted repeats are palindromes because the sequences on the two strands are the same but in reverse orientation. When an inverted repeat forms a perfect palindrome, the double-stranded sequence reads the same forward and backward.

Another secondary structured, called a cruciform, can be made from an inverted repeat when a hairpin forms within each of the two single-stranded sequences. (see Figure 10.17d).


In DNA and RNA, base pairing between nucleotides on the same strand produces special secondary structures such as hairpins and cruciforms.

DNA Methylation

The primary structure of DNA can be modified in various ways. These modifications are important in the expression of the genetic material, as we will see in the chapters to come. One such modification is DNA methylation, in which methyl groups (-CH3) are added (by specific enzymes) to certain positions on the nucleotide bases.

In bacteria, adenine and cytosine are commonly methylated, whereas, in eukaryotes, cytosine is the most

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