Interaction between hammerhead ribozyme and RNA substrates measured by a surface plasmon resonance biosensor

Dynamic interactions between hammerhead ribozymes and RNA substrates were m easured using the surface plasmon resonance (SPR) technology. Two in vitro transcribed substrates (non-cleavable and cleavable) were immobilised on st reptavidin-coated dextran matrices and subsequently challenged with non-rel ated yeast tRNA or two hammerhead ribozymes, both of which had previously b een shown to exhibit functional binding and cleavage of complementary targe t RNAs. The target-binding domain of one of the ribozymes was fully complem entary to a 16-ribonucleotide stretch on the immobilised substrates, while the other ribozyme had a nine-ribonucleotide complementarity. The two riboz ymes could readily be differentiated with regard to affinity. Cleavage coul d be measured, using the ribozyme with full target complementarity to the c leavable substrate. In contrast, the ribozyme with lower affinity lacked cl eavage activity. We suggest that SPR will be useful for investigations of r ibozyme-substrate interactions. (C) 2000 Elsevier Science B.V. All rights r eserved.