Project without external funding

Measurement and visualization of nucleic acid/protein interactions by scanning force microscopy

Project Details
Project duration: 01/199812/2002

By imaging techniques we have visualized interactions of monoclonal antibodies directed against double stranded RNA with dsRNA. Analysis of RNA-protein complexes unexpectedly revealed preferential binding sites of mAb J2 to the ends and to certain internal sites of different dsRNA species. Internal preferential binding sites have been identified. By site directed mutagenesis, preferential binding has been reduced to average levels. The binding site consists of the sequence motif A2 N7 A3 N7 A2 in which the A residues are spaced in a way that they are all displayed on one face of the A' dsRNA helix. A second mAb (K1) shows a similar preference for end binding but not for the A-rich sequence element.
A RNA backbone structure has been developed which allows for the insertion of sequence elements of interest to investigate RNA-protein interactions. This construct consists of a completely doublestranded and a an incompletely doublestranded part . It thus provides a direct comparison of specific and non-specific binding. This backbone has been used to study binding of IRE-BP to the iron responsive element. See also for details, figures and publications Atomic force spectroscopy is being used to determine binding forces between complementary DNAs and RNAs.

Principal Investigator

Last updated on 2017-11-07 at 13:44