Welcome

Our group specializes in mesoscopic models for DNA, RNA and modified bases. One of our core methods allows us to obtain estimates about hydrogen bonds from melting temperatures. So far we have sucessfully obtained hydrogen bonds for canonical Watson-Crick DNA and RNA base pairs, deoxyinosine, GU in RNAterminal bases in DNACy3/Cy5 fluorescent dyes attached to DNA and DNA/RNA hybrids.

Are you an experimentalist working in oligonuceotide synthesis? Do you have melting temperatures of your samples and are wondering what to do with them? Perhaps you might be interested in sharing your data with us. There is a possibility that we can say something about the hydrogen bonding and stacking interactions, perhaps you may not even need to perform costly NMR experiments on your samples. If you are interested please contact us for some informal discussion.


News

Check out  our Tm calculator for 23 different sets of NN parameters comprising DNA, RNA and DNA-RNA hybrids. (October 2018)

You will find here some links to my list of publications and to software packages:
  • TfReg A linux program for calculating DNA or RNA melting temperatures and average strand openings. Implements several types of Peyrard-Bishop models. News: version 4.0 is out with parameters for DNA/RNA hybrids (September 2018).
  • VarGibbs a linux program for calculating DNA nearest-neighbour parameters from melting temperatures. News: version 2.2 is available with new DNA/RNA and salt dependent RNA parameters (March 2019)