Principles of Biochemistry, Volume 3 - A. Lehninger 1985

Molecular Mechanisms of Genetic Information Transmission
DNA: Structure of Chromosomes and Genes
Eukaryotic DNA contains a large number of palindromes

Eukaryotic DNA possesses another characteristic feature: it contains numerous (perhaps thousands of) palindromes. A palindrome (from the Greek "to run back") is a word or sentence that reads the same forwards and backwards. Here are two Examples¹:

Class="center">Able was I ere I saw Elba

Madam, in Eden I’m Adam.

In biochemical genetics, the term palindrome is used to denote regions of eukaryotic DNA that feature inverted repeats of nucleotide sequences with twofold rotational Symmetry, resembling the short sequences recognized by Restriction Endonucleases. An example of such a region is shown in Fig. 27-28.

Fig. 27-28. A. A palindrome, or inverted repeat, demonstrating rotational symmetry. The twofold axis of symmetry passes through the central point. B. A cruciform Structure that forms when the bases of the palindrome pair internally within each strand rather than between complementary strands. In native eukaryotic DNA, palindromes may consist of tens or even hundreds of bases.

¹ Since the English palindromes given above cannot be translated directly, we provide as examples two Russian palindromes composed by B. Goldstein, a researcher at the Institute of Biophysics of the USSR Academy of Sciences: Уж редко рукою окурок держу. Умер и мир ему.

Fig. 27-29. Intervening sequences (introns) in two eukaryotic genes. The Ovalbumin Gene contains six introns (shown in gray and labeled A–F) and is consequently divided into seven segments, or exons (indicated in red and numbered 1–7). The cytochrome b gene contains four introns (gray, A–D) and five exons (red, J–5). In both cases, introns make up the major portion of the gene's DNA. The numbers of Base Pairs comprising the introns of the cytochrome b gene are indicated.

Many palindromes are up to a thousand base pairs long. Shorter palindromes, much like restriction sequences, serve as specific regulatory signals. Longer palindromes are capable of forming cruciform structures through base pairing within each of the double-stranded loops (Fig. 27-28). The function of these long palindromes remains unknown.