New Tool Developed for DNA Research

Luminescent markers are an essential tool for researchers working with DNA. However, the markers are troublesome; some tend to destroy the function and structure of DNA when inserted. Others emit so little light, that they can barely be detected in the hereditary material. Therefore, researchers have been asking for alternative markers. Now a Danish Ph.D. student has developed a tool that could solve both problems: a tool one might call a molecular gauge.

Ph.D. student Soren Preus from the department of chemistry at the University of Copenhagen (Denmark) in collaboration with researchers at Chalmers Technical University (Gothenburg, Sweden) investigated the properties of the two luminescent so-called DNA base analogues of the tricyclic cytosine (tC) family, tCO and tCnitro. They tried to determine whether they could measure the structure of DNA without disrupting it. The research showed that the function of DNA is unimpeded by the insertion of the molecular gauge. Moreover, one base analogue is very efficient at emitting light, and the other very good at receiving it. Therefore, because one can provoke transport of light energy between the two luminescent markers, they are usable for a measuring technique known as fluorescence resonance energy transfer (FRET).

In brief FRET, measurements are performed by forcing two luminescent markers to transfer light energy from one to the other, and then measuring the efficiency of the transfer. The two different markers are placed in the DNA helix. When they are subjected to a light pulse, one marker (tCO) emits part of the energy to the other (tCnitro). This energy transfer can be measured. Therefore, by calculating backwards it is possible obtain very exact information about the distance and angle that the two have relative to one another.

Knowing distance and angle of the markers allows for calculations of distance and angle of all the natural base pairs in the DNA structure. Thus, with this information the researcher can put together a picture showing every twist and turn of the structure. Because structure and function are closely related in DNA, the technique holds the potential to reveal new insights into the workings of DNA.

FRET measurements are not a new phenomenon. However, Mr. Preus has developed one of the base analogues tCnitro in collaboration with Swedish research institution Chalmers University of Technology. Mr. Preus has used the facilities of the Molecular Engineering Group at University of Copenhagen to analyze every aspect of the energy transfer between the two markers, because this allows future DNA researchers to translate measurements to structure.

Mr. Preus hopes that the new tool might find its use in characterizing the structural changes that take place when a protein binds to DNA or RNA as that could explain fundamental cellular mechanisms. Equally important is that the molecular gauge can be used to examine precisely how new drugs work and when they bind to DNA or RNA.

The results have been published in the January 21, 2010, issue of the Journal of Physical Chemistry and the March 9, 2009, issue of the Journal of the American Chemical Society.

Related Links:
University of Copenhagen
Chalmers Technical University