Improved base pairing for DNA

August 26, 2013, Nr. 63

New structure for the selective sequence detection

The highly specific evidence of genetic material is an important task for modern medicine, forensics and biology. However, some DNA sequences are difficult to prove because their core bases form weak base pairs. In particular the core base adenine ("A" in the genetic alphabet) only binds weakly to the complementary base thymine (T). Marco Minuth and Prof. Clemens Richert from the Institute of Organic Chemistry at the University of Stuttgart have now found a chemical substitute for thymine that responds to a stronger and more selective base pairing with adenine and report about this in the leading trade journal “Applied Chemistry”*). This helps in suppressing unwanted base combinations in the double helix more effectively and makes it easier to avoid misinterpretations in genetic analyses.

One could assume that in the course of evolution nature has exhaustively optimised the base pairing between two DNA strands. Yet the truth is that the DNA in the cell has to meet different requirements than in diagnostic tests. In this respect it is necessary in the cell for the double helix to be particularly easy to open in certain areas so that the genetic information can be read from this point onwards. This is the case, for example, directly before the start codon of a gene (i.e. the sequence section directly before a reading section), where both strands have to be separated before one of the two strands can be read enzymatically. Weak base pairs are therefore an advantage here.
In diagnostic tests that do without enzymes in contrast, the separation of the strands takes place chemically or through heating up. The following evidence becomes difficult if only weak duplexes with special strands can be formed in the sequence section to be proven. That is the reason why many “false negative” readings occur, particularly on modern DNA "Chips", on which many different sequences are to be proven simultaneously.
Prof. Richert’s group from the University of Stuttgart has now found a structure that not only forms the two hydrogen bonds with the core base adenine that is hard to bind, known from the base pairs described by Watson und Crick, but also responds to additional molecular contacts. The structure of adenine is in addition “picked up” by a substitute derived from acetylene (a technical gas). This makes the base pairing stronger and more specific. “It’s a little bit like extending the barb of a key in order to achieve a higher level of specificity in recognising a lock“, is how the Stuttgart chemists explained it. “This makes it possible to suppress false base combinations in the double helix more effectively.“
The new substitute for thymine is a so-called "C-Nucleoside”, that has a particularly fixed bond between core base and sugar. Developing a synthesis for this substance turned out to be a real challenge that required in total over ten years of research. After the first short special DNA strands were able to be manufactured, the measurements showed that the improved base pair formed when bonding to DNA target strands as well as when bonding to RNA target strands. This gives the new core base, which the researchers call "E" (from ethynylpyridine), the potential to enter many diagnostic and forensic tests.

*Marco Minuth and Clemens Richert: "A Nucleobase Analogue that Pairs Strongly with Adenine", Applied Chemistry (2013), DOI: 10.1002/ange.201305555
Online-Version: http://dx.doi.org/10.1002/ange.201305555

Contact:
Prof. Clemens Richert, University of Stuttgart, Institute of Organic Chemistry, Tel. 0711/685-64311,
Email: lehrstuhl-2 (at) oc.uni-stuttgart.de
Andrea Mayer-Grenu, University of Stuttgart, Department of University Communication, Tel. 0711/685-82176,
Email: andrea.mayer-grenu (at) hkom.uni-stuttgart.de
 

Top: base pairing of the newly developed nucleoside with thymidine. The various interactions are indicated by dotted lines. Left: double helix containing the new base pair. Right: sequence of the shown double helix. (Graphics: M. Minuth)
To the top of the page