Unlocking the Secrets of DNA

ScienceDaily (Jan. 24, 2011) — Neutron scattering has been used to investigate the structure of fibre DNA during the melting transition. This is the range of temperatures over which the bonds between base pairs break, or denature, causing the two strands of DNA to separate.

Neutron scattering has been used to investigate the structure of fibre DNA during the melting transition. This is the range of temperatures over which the bonds between base pairs break, or denature, causing the two strands of DNA to separate. (Credit: Copyright Santiago Cuesta)

Neutron scattering gives information about the correlation between base pairs during denaturation, which is not possible using other techniques. This is used to measure the characteristic size of the denatured regions as the temperature is changed, and these sizes can be compared with those predicted by the theoretical model.

The Peyrard-Bishop-Dauxois (PBD) model predicted that fibre DNA denaturation due to temperature would happen in patches along the molecule, rather than 'unzipping' from one end to another. This experiment, the first to investigate the model, strongly supported the model's predications for the first part of the transition, as the molecule is heated. The experiment could only measure the first stage because when the strands become 50% denatured they are too floppy to remain ordered and the fibre structure is no longer stable -- the DNA sample literally falls to pieces.

"This is an important verification of the validity of model and the associated theory, so it can be applied with more confidence to predict the behaviour and properties of DNA," says Andrew Wildes, an instrument scientist at ILL. "This will help to understand biological processes such as gene transcription and cell reproduction, and is also a step toward technological applications such as using DNA as nanoscale tweezers or as computer components."

"There's been a lot of research producing good data -- eg nice melting curves -- about the transition point, but these couldn't tell us how it was happening. For example at 50% melted are half the DNA molecules totally denatured and the other half still firmly joined? Or are the strands of each molecule partially separated? Neutron scattering has enabled us to get structural information on the melting process to answer this kind of question," says Michel Peyrard Professor of Physics at Ecole Normale Supérieure de Lyon, and co-developer of the PBD model. "As well as implications for technological development it could also help biological applications, such as predicting where genes might be located on long stretches of DNA sequences."

The experiment follows from the pioneering work of Rosalind Franklin, who showed that x-ray scattering from DNA fibres would give structural information. Based on her work, James Watson and Francis Crick deduced the well-known double helix structure of DNA in 1953. DNA is a dynamic molecule that undergoes large structural changes during normal biological processes. For example, DNA inside the cell nucleus is usually 'bundled up' into chromosomes, but when the genetic information is being copied it must be unravelled and the strands separated to allow the code to be read.