Biophysicists Discover Four New Rules of DNA 'Grammar'
For 60 years, biologists have known of only two grammar-like rules that govern the language of DNA. Now they've found four more.
The Austrian biochemist, Erwin Chargaff, is famous for the two rules he discovered that now bear his name. At the time of this discovery, in 1950, the biggest problem in biology was understanding the structure of DNA. Chargaff's rules turned out to be an important clue in this puzzle.
Biologists had long known that DNA was built out of four molecules: adenine, guanine, thymine and cytosine. They assumed that these molecules occurred in equal quantity and dismissed any measurements that hinted otherwise as experimental errors.
Chargaff showed through careful measurement that this assumption was wrong. He found that the amount of adenine equalled that of thymine and the amount of guanine equalled that of cytosine but these were not equal to each other. The rough figures are: A=T=30% and G=C=20%.
Chargaff's first parity rule, as this is now called, was an important clue that James Watson and Francis Crick used to develop their base pair model for the double helix structure. Biologists now know that since A binds with T and G binds with C to form a double helix, this rule holds for all double stranded DNA.
Chargaff went on to discover that an approximate version of his rule also holds for most (but not all) single-stranded DNA. That's much more of a puzzle and biologists still aren't quite sure why it is true.
Chargaff's rules are important because they point to a kind of "grammar of biology", a set of hidden rules that govern the structure of DNA. This grammar ought to reveal itself as patterns in DNA that are invariant across all species.
But in the 60 years since Chargaff discovered his invariant patterns, no others have emerged. Until now.
Today, Michel Yamagishi at the Applied Bioinformatics Laboratory in Brazil and Roberto Herai at Unicamp in Sao Paulo, say they've discovered several new patterns that significantly broaden the grammar of DNA.
Their approach is straightforward. These guys use set theory to show that Chargaff's existing rules imply the existence of other, higher order patterns.
Read more here/Leia mais aqui: Technology Review
Chargaff's "Grammar of Biology": New Fractal-like Rules
(Submitted on 7 Dec 2011)
Chargaff once said that "I saw before me in dark contours the beginning of a grammar of Biology". In linguistics, "grammar" is the set of natural language rules, but we do not know for sure what Chargaff meant by "grammar" of Biology. Nevertheless, assuming the metaphor, Chargaff himself started a "grammar of Biology" discovering the so called Chargaff's rules. In this work, we further develop his grammar. Using new concepts, we were able to discovery new genomic rules that seem to be invariant across a large set of organisms, and show a fractal-like property, since no matter the scale, the same pattern is observed (self-similarity). We hope that these new invariant genomic rules may be used in different contexts since short read data bias detection to genome assembly quality assessment.
Comments: 17 pages
Subjects: Genomics (q-bio.GN); Computational Engineering, Finance, and Science (cs.CE); Discrete Mathematics (cs.DM)
Cite as: arXiv:1112.1528v1 [q-bio.GN]
From: Michel Yamagishi [view email]
[v1] Wed, 7 Dec 2011 11:37:36 GMT (689kb)
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