The figure illustrates the molecular shape of a region of nucleosomal DNA when wrapped around the histone core, with the narrow minor groove in dark grey. The red mesh shows a surface with negative electrostatic potential. The shape of narrow minor groove regions induces an enhanced negative electrostatic potential, which is read by histone arginines. Such interactions between the protein and DNA contribute to the stabilization of the nucleosome core particle.
Most of us carry a mental picture of DNA in its iconic form – the famous double helix unveiled by Francis Crick and James Watson. But researchers are beginning to develop a new picture of DNA that shows the molecule’s more dynamic side, which is capable of morphing into a large number of complex shapes. This shape-shifting ability permits proteins to attach and read the right region of DNA so genes can be turned on or off at the proper time.
The findings show that proteins are adept at reading nuances in the shape of the double helix. Those variations in shape transmit information about where proteins need to bind to make sure the right genes are activated or silenced during development.
“If you now realize that those nucleotides determine which proteins bind the DNA, and they do it in part through their effect on shape, you begin to understand how sensitive and subtle the DNA structure really is, and how this in turn affects how it's being read.”
Barry Honig
“The ideal double helix should not be viewed as a rigid entity but rather seen as a first approximation to a large set of more complex shapes that are recognized by proteins so as to bind to DNA in a sequence-specific fashion,” said Howard Hughes Medical Institute investigator Barry Honig at Columbia University.
Honig and his colleagues have discovered a new mechanism by which proteins recognize specific regions of DNA. Their research is reported in the October 29, 2009, issue of the journal Nature.
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