Tuesday, September 21, 2010

DNA - melt it, stretch it, rip it, and unfold it

The first point of the DNA double-stranded helix which I shall talk about is the idea of "melting" it or making it fall apart into two strands. Sometimes referred to as another "helix-coil" transition, the degree of melting is a sigmoid curve, but the disorded state occurs at a high temperature (meaning that the sharp transition occurs past a definite melting point temperature). As melting occurs though, there are many things to consider.
1) A minor net change in free energy occurs as the basepair hydrogen bonds break and then reform between the bases and water.
2)The bases will stop being stacked neatly, causing the breaking of energetically favourable interactions (i.e. van der Waals). The energy coast however is slightly offset by gain of electrostatic repulsions.
3)Compression of counterion clouds released, leading to increased entropy. Single strands of DNA are also more flexible, to the backbone entropy also increases.
4) hydrophobic surfaces will become exposed to the water.

Now, for the fun we can have with DNA by applying forces.
1) Unzipping DNA - using a stretching apparatus, Heslot et al found that applying a force of 10-15pN could unsip the strands. Of course these days we also know that we can use helicase to do a similar job (though we need to also consider the provision of ATP, topoisomerase etc).

2) Overstretching - by applying a critical force (i.e. 65pN for lambda phage) we can force the DNA Duplex to go from being in the B-form (spiral staircase) and into a "ladder".

3) Unfolding - by increasing tension, we can cause proteins to undergo a change in structure. However, like a rubber band, when we release the tension, the protein returns to its original structure (though not quite in the same snapping motion)


  1. Your point three is somewhat simplified. For many proteins, stretching them out into a single chain would result in a permanently denatured protein. These proteins often require initial help to adopt their native form. There would, of course, be some proteins that readily adopt their native shape in solution.
    This distinction reminds me of the experiment with ribonuclease. When this protein was treated with urea is would denature. Once the urea was removed the protein would refold. This was due to the reformation of the disulfide bridges that had been broken by the urea.

  2. Yes, I realise that it does, but I was more giving summary to what Nelson has said. Of course we have to consider things like disulfide bonds, chaperones, binding molecules etc. but the general idea is that you can stretch out a protein and it will have the capability to return to its natural conformation once again. One of the most well-known examples of a protein which can refold to its correct conformation after being unfolded and denatured is ribonuclease, the experiment performed by Anfinsen, earning him the noble prize for chemistry in 1972. Ribonuclease contains 8 cysteins which are linked together through disulfide bonds.