Covalent and non-covalent binding of platinated vitamin B12-derivatives to a B12 responsive riboswitch

Abstract

The B12 responding btuB riboswitch is a short, non-coding RNA sequence involved in the gene-regulation of an outer membrane B12-transport protein in E. coli. This RNA is characterized by its selective high-affinity binding to coenzyme B12 and by the structural rearrangement it undergoes upon this interaction. Due to their involvement in (mostly) bacterial gene regulation, the btuB riboswitch as well as the further about twenty known classes of riboswitches received much attention in recent years. In case of the btuB riboswitch, the light sensitivity of its ligand, coenzyme B12, poses one of the greater challenges for its investigation. Vitamin B12 derivatives carrying a cyanide-bridged platinum(II) moiety offer an ideal strategy for the design of light stable coenzyme B12 analogs. Developed by Alberto and coworkers in 2005 these conjugates provide the possibility to coordinate an additional nucleobase making them potential coenzyme B12 mimics. However, although these derivatives show a high structural similarity to coenzyme B12, their functionality might differ and offers the opportunity to develop new classes of antibiotic agents. Especially the platinum(II)-complex could interact with RNA in an unexpected way, which is the main question addressed in the work presented here. We characterized the binding of three vitamin B12-platinum(II) complexes to two different RNAs: the B12-specific btuB riboswitch and the short RNA D1-45, which is a non-B12-binder. cisPt(II)VitB12+ (1) and enPt(II)VitB12+ (2) carry both a labile chloride ligand at the platinum(II) moiety whereas dienPt(II)VitB122+ (3), that carries no labile chloride ligand anymore, can be considered chemically inert under the applied conditions. Complexes 1 and 2 covalently bind to both RNAs as monitored by band-shift assays. In the case of the short D1-45 the shifted bands are well separated and were further analyzed by MALDI-MS proving the covalent interaction. Complex 3 is unable to covalently bind any of the two RNAs, which proves the general stability of the Pt(II) complex. However, the presence of this moiety has a dramatic influence on the binding property towards the B12-sensing riboswitch, as was observed in in-line probing assays by comparison to the natural ligand coenzyme B12.