up-down-and-sideways square carved into walls at Pompeii and other places:
S-A-T-O-R
A-R-E-P-O
T-E-N-E-T
O-P-E-R-A
R-O-T-A-S
At just two millennia old, however,
sator… rotas
* falls orders of magnitude short of the age of the truly ancient palindromes in DNA. DNA has even invented two kinds of palindromes. There’s the traditional, sex-at-noon-taxes type—GATTACATTAG. But because of A-T and C-G base pairing, DNA sports another, subtler type that reads forward down one strand and backward across the other. Consider the string CTAGCTAG, then imagine what bases must appear on the other strand, GATCGATC. They’re perfect palindromes.
Harmless as it seems, this second type of palindrome would send frissons of fear through any microbe. Long ago, many microbes evolved special proteins (called “restriction enzymes”) that can snip clean through DNA, like wire cutters. And for whatever reason, these enzymes can cut DNA only along stretches that are highly symmetrical, like palindromes. Cutting DNA has some useful purposes, like clearing out bases damaged by radiation or relieving tension in knotted DNA. But naughty microbes mostly used these proteins to play Hatfields versus McCoys and shred each other’s genetic material. As a result microbes have learned the hard way to avoid even modest palindromes.
Not that we higher creatures tolerate many palindromes,either. Consider CTAGCTAG and GATCGATC again. Notice that the beginning half of either palindromic segment could base-pair with the second half of itself: the first letter with the last (C… G), the second with the penult (T… A), and so on. But for these internal bonds to form, the DNA strand on one side would have to disengage from the other and buckle upward, leaving a bump. This structure, called a “hairpin,” can form along any DNA palindrome of decent length because of its inherent symmetry. As you might expect, hairpins can destroy DNA as surely as knots, and for the same reason—they derail cellular machinery.
Palindromes can arise in DNA in two ways. The shortish DNA palindromes that cause hairpins arose randomly, when A’s, C’s, G’s, and T’s just happened to arrange themselves symmetrically. Longer palindromes litter our chromosomes as well, and many of those—especially those that wreak havoc on the runt Y chromosome—probably arose through a specific two-step process. For various reasons, chromosomes sometimes accidentally duplicate chunks of DNA, then paste the second copy somewhere down the line. Chromosomes can also (sometimes after double-strand breaks) flip a chunk of DNA by 180 degrees and reattach it ass-backwards. In tandem, a duplication and inversion create a palindrome.
Most chromosomes, though, discourage long palindromes or at least discourage the inversions that create them. Inversions can break up or disable genes, leaving the chromosome ineffective. Inversions can also hurt a chromosome’s chances of crossing over—a huge loss. Crossing over (when twin chromosomes cross arms and exchange segments) allows chromosomes to swap genes and acquire better versions, or versions that work better together and make the chromosome more fit. Equally important, chromosomes take advantage of crossing over to perform quality-control checks: they can line up side by side, eyeball eachother up and down, and overwrite mutated genes with nonmutated genes. But a chromosome will cross over only with a partner that looks similar. If the partner looks suspiciously different, the chromosome fears picking up malignant DNA and refuses to swap. Inversions look dang suspicious, and in these circumstances, chromosomes with palindromes get shunned.
Y once displayed this intolerance for palindromes. Way back when, before mammals split from reptiles, X and Y were twin chromosomes and crossed over frequently. Then, 300 million years ago, a gene on Y mutated and became a master switch that causes testes to develop. (Before this, sex was probably
S-A-T-O-R
A-R-E-P-O
T-E-N-E-T
O-P-E-R-A
R-O-T-A-S
At just two millennia old, however,
sator… rotas
* falls orders of magnitude short of the age of the truly ancient palindromes in DNA. DNA has even invented two kinds of palindromes. There’s the traditional, sex-at-noon-taxes type—GATTACATTAG. But because of A-T and C-G base pairing, DNA sports another, subtler type that reads forward down one strand and backward across the other. Consider the string CTAGCTAG, then imagine what bases must appear on the other strand, GATCGATC. They’re perfect palindromes.
Harmless as it seems, this second type of palindrome would send frissons of fear through any microbe. Long ago, many microbes evolved special proteins (called “restriction enzymes”) that can snip clean through DNA, like wire cutters. And for whatever reason, these enzymes can cut DNA only along stretches that are highly symmetrical, like palindromes. Cutting DNA has some useful purposes, like clearing out bases damaged by radiation or relieving tension in knotted DNA. But naughty microbes mostly used these proteins to play Hatfields versus McCoys and shred each other’s genetic material. As a result microbes have learned the hard way to avoid even modest palindromes.
Not that we higher creatures tolerate many palindromes,either. Consider CTAGCTAG and GATCGATC again. Notice that the beginning half of either palindromic segment could base-pair with the second half of itself: the first letter with the last (C… G), the second with the penult (T… A), and so on. But for these internal bonds to form, the DNA strand on one side would have to disengage from the other and buckle upward, leaving a bump. This structure, called a “hairpin,” can form along any DNA palindrome of decent length because of its inherent symmetry. As you might expect, hairpins can destroy DNA as surely as knots, and for the same reason—they derail cellular machinery.
Palindromes can arise in DNA in two ways. The shortish DNA palindromes that cause hairpins arose randomly, when A’s, C’s, G’s, and T’s just happened to arrange themselves symmetrically. Longer palindromes litter our chromosomes as well, and many of those—especially those that wreak havoc on the runt Y chromosome—probably arose through a specific two-step process. For various reasons, chromosomes sometimes accidentally duplicate chunks of DNA, then paste the second copy somewhere down the line. Chromosomes can also (sometimes after double-strand breaks) flip a chunk of DNA by 180 degrees and reattach it ass-backwards. In tandem, a duplication and inversion create a palindrome.
Most chromosomes, though, discourage long palindromes or at least discourage the inversions that create them. Inversions can break up or disable genes, leaving the chromosome ineffective. Inversions can also hurt a chromosome’s chances of crossing over—a huge loss. Crossing over (when twin chromosomes cross arms and exchange segments) allows chromosomes to swap genes and acquire better versions, or versions that work better together and make the chromosome more fit. Equally important, chromosomes take advantage of crossing over to perform quality-control checks: they can line up side by side, eyeball eachother up and down, and overwrite mutated genes with nonmutated genes. But a chromosome will cross over only with a partner that looks similar. If the partner looks suspiciously different, the chromosome fears picking up malignant DNA and refuses to swap. Inversions look dang suspicious, and in these circumstances, chromosomes with palindromes get shunned.
Y once displayed this intolerance for palindromes. Way back when, before mammals split from reptiles, X and Y were twin chromosomes and crossed over frequently. Then, 300 million years ago, a gene on Y mutated and became a master switch that causes testes to develop. (Before this, sex was probably
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