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 RNA, terminal bases in DNA, Cy3/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 T_m calculator for 32 different sets of nearest-neighbour parameters comprising DNA, RNA and DNA-RNA hybrids. There are many examples available at a click of a button, just check it out and see. (April 2021)

• TfReg A linux program for calculating DNA or RNA melting temperatures and average strand openings. Implements several types of Peyrard-Bishop models. News: version 7.0 is now available with new parameters for metal mediated DNA (February 2022)

• VarGibbs a linux program for calculating nearest-neighbour parameters from melting temperatures. News: version 3.1 is available with new scripts for RNA (August 2021)