This project concerns a number of fundamental problems, some of which primed by earlier discoveries in our laboratory related to the structure and biological function of nucleic acids, mainly DNA. We early postulated that the recognition mechanisms of DNA-binding proteins might involve, in addition to electrostatic interactions also kinetic effects that might be sequence specific, “kinetic recognition”, as well as some sequence specific hydrophobic effects. That such effects indeed exist has been demonstrated for binuclear robust polypyridyl transition metal complexes. An extremely slow (minutes to hours or even days) exchange allowing one of the two metal centers to penetrate through the stack of nucleobases of DNA, a process denoted “thread-intercalation”, is found to sensitively depend on DNA sequence – the threading rate increasing up to 3 orders of magnitude for AT rich sequences. Furthermore, “hydrophobic catalysis” was observed in that large hydrophobic groups could lower the barrier to reaction so that, surprisingly enough, larger groups penetrated more easily than smaller ones.
Another challenge which we have addressed is the question when stretching isolated single DNA molecules of variable sequence, whether defined higher-energy conformations exist or if stretching the DNA just leads to denaturation and strand separation. We have recently shown that applying a force of about 60 pN indeed makes a DNA double helix change into a new, 50% longer conformation, with retained base-pairing. Interestingly, in presence of recombinase proteins the DNA helix is also elongated 50%, in a heterogeneous way with 3 base-pairs stacked as in B-DNA, then followed by a long gap and so on. We may thus speculate that the stretching (as well as the base triplets) may have a biological function: the “genetic code” with base triplets allowing 43=64 different combinations (= amino acids) might thus have evolved from this physical property of nucleic acid instead of being demanded by the variability of protein structure.
How DNA is recognized is still in many contexts an open question, but an important one, whether it be binding of regulatory proteins, or carcinogenic substances or cytostatic drugs. Since most studies are based on crystallographic structures little is known about the role of dynamics (or softness) of the double helix. Recent evidence indicates that bending is of particular relevance; here we have shown how opposite screw forms of a propeller-shaped compound have very different effects on bending upon binding to DNA.
Swedish Research Council - VR grant
the European Research Council - ERC
the King Abdullah University of Science and Technology - the KAUST award
Professor Tom Brown
University of Southhampton