Research group leader: Professor Marcus Wilhelmsson
PhD student Pauline Pfeiffer
PostDoc Anna Wypijewska Del Nogal
PostDoc Jesper Nilsson
PostDoc Tom Baladi (collaboration with AstraZeneca, Mölndal)
PostDoc Vinoth Edal Joseph Sundar Rajan
The group develops molecules that can be used to replace the natural DNA/RNA building blocks, the bases, and unlike the bases, which are transparent, has properties that make them fluorescent (emit light) when they are hit by light of the correct colour (300-500 nm). These so called fluorescent base analogues (see review by Wilhelmsson in QRB 2010) have molecular properties that are optimal for being inserted into the natural DNA/RNA structure (Figure 1). They can therefore be used to, on a very detailed level, understand more about essential processes in cells like replication, during cell division, and transcription, during protein synthesis. Fundamental knowledge thereof is vital in order to comprehend cellular processes and errors that could occur and cause several common diseases.
Figure 1. Left: Fluorescent base analogue tC, right, base-pairing with the natural base uanine, left. In the figure we look down the long-axis of a natural DNA duplex. Right: Same ase analogue instead looking along the short-axis of the DNA duplex.
One of the goals is to design and construct new fluorescent base analogues that can replace all the natural bases. This is done by trying to predict structural and spectral properties with the help of quantum chemical methods where after promising candidates are synthesized. Parts of this work is performed in collaboration with Professor Morten Grøtli at Göteborgs Universitet. After the synthesis, the new base analogues are investigated to determine whether they have promising fluorescent properties, where after interesting ones are incorporated into DNA/RNA (often in collaboration with Professor Tom Brown, Oxford, UK) for further characterization. The characterization is performed to understand how well the fluorescent base analogue works as a replacement for a natural base, it should not perturb the properties or structure of the DNA/RNA, as well as to establish its spectral and photophysical properties for further use in biochemically and biologically relevant investigations (see, for example, Sci. Rep. 2017 where we developed a cytosine analogue for RNA).
Another goal is to use the novel fluorescent base analogues, to make them available for other researchers as well as to develop biochemical/biophysical/biological methods where the probes can be used. An example thereof is the freeware FRETmatrix that has been developed by the group and can be used to obtain detailed structural information about biomolecules (DNA/RNA and molecules that interact with these). The investigations that can be performed using FRETmatrix have been enabled thanks to a newly developed FRET-pairs that constitutes a unique tool to measure short distances in biomolecular systems (Figure 2). Our first FRET-pair, that was the first of its kind, was published by the group in JACS 2009 and in JACS 2017 we published another FRET-pair based on adenine analogues. This first FRET-pair is now being used by the group in several studies two of which have already been published in PNAS 2012 and NAR 2016. The base analogues are also used to study among other things polymerases (NAR 2009, Biochemistry 2009), cellular molecules that are central at cell division and protein expression.
The Wilhelmsson research group is one of six labs in Sweden involved in the SSF Industrial Research Centre (IRC) FoRmulaEx. In this large academia/industry-collaboration fluorescent base analogues and methodologies in connection to that are developed and used to enhance the understanding regarding the process of cellular uptake, trafficking and endosomal escape of oligonucleotide based drugs. The lab also has activities regarding the use of modified DNA and RNA in nanotechnology together with the Westerlund and Albinsson groups.
Figure 2. Shows how the FRET-pair consisting of two base analogues, tCO-tCnitro, developed by our group at the same time can be used for obtaining distance and orientation information. Red squares show measured steady-state fluorescence values and lue dots the corresponding time-resolved data. Measurements performed using the FRET-pair separated by 2-13 base pairs.
Several of the fluorescent molecules developed by the group are now distributed through a collaboration between the American company GlenResearch Corp., world leading in chemicals related to DNA/RNA, and ModyBase HB, a company founded by Marcus Wilhelmsson.
The group has or has earlier received grants from among other these sources:
The Swedish Research Council (VR)
SSF (Swedish Foundation for Strategic Research); IRC FoRmulaEx
SSF (Korea collaboration; with Prof. B.H. Kim at POSTECH, Pohang)
Olle Engkvist Byggmästare Foundation
Kristina Stenborg’s Foundation
Chalmers Area of Advance Nanoscience and Nanotechnology
Linneaus grant from the Swedish Research Council to the SUPRA project