Wednesday, September 14, 2016

Measuring Forces In the DNA

Measuring Forces in the DNA molecule 

   James Watson and Francis Crick proposed that DNA molecule is made up of strands which are twisted around each other in the form of a double helix. The double helix looks like a spiral staircase. The steps of this spiral ladder are composed of guanine/cytosine and thymine/adenine base pairs. Prof. Hendrik Deitz explains that double helices are stabilized by two types of interactions. First being hydrogen bonding and another being base pair stacking forces. Base pair stacking forces act between the stacked base pairs along the spiral axis. On the other hand, hydrogen bonding forces act perpendicular to the axis. Dietz explains that the extent to which these two forces contribute to the stability of DNA is not clear. Prof. Rief and prof. Zachrias developed an experimental setup in which very weak contact interactions between individual molecules becomes possible to measure.

   The measurement system involves microscopic beams and is designed hierarchically. At the tips of microscopic beams, one or more double helix structures running in parallel fashion are situated, and each end carries one base pair. Two microscopic beams are joined with a flexible polymer. The beams are connected to microscopic spheres on the other side which can be pulled separately by using optical laser tweezers. The base pairs on the end of one beam can intermingle with the base pairs on the end of other beam in solution. As a result, it is possible to measure the length of  a stacking bond between base pairs before they separate again, and the forces between base pairs.  The forces were in the range of piconewtons. Deitz explains that a newton is the weight of a bar of  a chocolate, and we have a thousandth of a billionth of that. Forces in the range of two piconewtons are enough to separate the bond formed by stacking forces. Moreover, the scientists noted that within just milliseconds, the bonds instinctively broke up and formed again. The extent to which base pairs are stacked on each other determine the strength and lifetime of these interactions.  

   The results of measurements could be helpful in better understanding of the fundamental aspects of biological processes such as DNA replication. Dietz uses DNA as programmable building material to build machines on the order of nanometers. He took inspiration from complex structures found in cells and among other stuff that serve as molecular "factories" to manufacture ATP in which energy is stored. At this time, lab is constructing a molecular rotational motor out of DNA. The components of  this motor is inter lockable and are held together through stacking forces. The ultimate goal is to control a directed rotation through thermal or chemical stimuli. To accomplish that, the timing of the movement of rotor in the stator is critical, and this task can be done easily because of new findings on the stacking forces. 

   I found this article interesting because it addresses the problem of measuring stacking forces between base pairs, and I got to learn the second type of interaction besides hydrogen bonding. This innovative knowledge will help to build specific molecular machines out of DNA. 

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