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