Not your standard black tie dinner party conversation, Jonathan, but I can talk about anything. Of course DNA structure and function are governed by the laws of physics, bonds must be obeyed, physical restraints respected, spatial integrity maintained. That's at the very heart of chromatin remodelling. Now, I had planned to write next about RNA, but this conversation reminded me that most amateur molecular biologists imagine that DNA is a linear molecule and everything happens along a long, flat line. That's not true. Firstly, you should all know that DNA is in fact double-stranded. Secondly, the bonds between the bases cause a torsion or twist, known as the helix. The entire double-stranded DNA helix is further wound around histones (ordered clumps of proteins), which adds another layer of constraint. And all of this is packed into the nucleus of the cell. Brilliant!
But here's the interesting bit. I have looked at the this very aspect of molecular modelling (biologist speak) or quantum physics (geek speak) using atomic force microscopy. This technique allows the researcher to obtain a topographical image of the DNA molecule undergoing re-modelling; I can see a region of DNA 'open' or 'close' varying only by a single base change in the sequence. This very simple variation in DNA sequence therefore changes the molecular stoichiometry, which affects DNA folding and the accessibility of the gene to factors which promote gene transcription (I promise we'll get to that in the next blog entry). Furthermore, these topographical changes can be predicted using folding software, which helps inform biologists about the type of experiments we should be doing to further elucidate the mysteries of the DNA molecule. Important, I think you'll agree?
And finally, I remember that a Professor I know has published a useful book, which I think I'll have another look at now. To be continued....