Simulating DNA

It's no secret that one of the hottest areas of research in any scientific field these days is the study of DNA, the essential building block of all living entities. It is the precise make-up of our DNA that determines the color of our skin, the size of our rib cages, and whether or not we have those cute little dimples in our cheeks. Geneticists are making huge strides in putting DNA to use, as evidenced by the now-famous cloning projects that are the subjects of hot debate. Because of its role in determining our genetic code, it's understandable why DNA has garnered so much attention in the biochemistry area, but that is not the whole picture. It is well known that the function of a biological molecule is usually tied neatly to its particular chemical structure. As such, a detailed understanding of DNA on a molecular level promises to provide greater insight into this king of the biochemicals. As is true in most cases where a molecular- or atomic-level understanding is the goal, there is an important role in the DNA explosion to be played by computer simulation. We'll spend the next several weeks looking at some of the computational studies being conducted to gain a better understanding of DNA.

One good example comes to us from researchers in the Department of Chemical Physics at the Universidad Complutense de Madrid in Spain. These scientists have undertaken computational studies of the transition between two known forms of DNA. In the first form, dubbed B-DNA, the DNA molecule is not tightly wound. Because of this, the phosphates that connect the substituent nucleotides (DNA building blocks) are not extremely close to each other. In chemistry, when two like species are brought in close proximity to each other, an enormous repulsive energy can develop, making the structure very unstable. Since this is not the case here, B-DNA is generally more stable than Z-DNA, which is thinner, bringing its phosphates closer to each other.

The researchers working in this study decided to examine the energy pathway for conversion from one of the above forms of DNA to the other (specifically, B to Z). In the process, they evaluated several models often used in these types of simulations. By comparing the results of the various simulations to available experimental data, the scientists were able to determine which characteristics of the DNA system (DNA surrounded by counterions in a water medium) were the most crucial to be adequately represented in a model. In general, it seems that the phosphate groups must be represented by a fairly

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