Visualization of membrane RNAs

Abstract

Using fluorescence microscopy, we show that previously isolated membrane-binding RNAs coat artificial phospholipid membranes relatively uniformly, except for a frequent tendency to concentrate at bends, membrane junctions, and other unusual sites. Membrane RNAs can also be visualized as single molecules or isolated complexes by atomic force microscopy (AFM) of free RNAs on mica. Finally, RNAs can be seen within membranes by AFM of RNA-liposomes immobilized on hydrophobic mica surfaces. Monomer RNAs appear globular, as expected for small RNAs. When mixed under conditions in which RNAs bind bilayers, RNA 9 and RNA 10 combine to yield about 80% of RNAs as mainly linear oligomers of ≈2-8 molecules. Once inserted in membranes, the RNAs oligomerize further, yielding larger, irregular ropelike structures that prefer the edges of altered lipid patches. These properties can be interpreted in terms of RNA-RNA loop interactions, and the RNA effects on membranes can be explained in terms of an RNA preference for irregular lipid conformations. The RNA-bilayer system poses new opportunities for combining the properties of membranes and RNA in contemporary cells, and also in the ribocytes of an RNA world.

A membrane transporter for tryptophan composed of RNA

“…RNA molecules readily bind phospholipid bilayers (Khvorova et al 1999;Vlassov et al 2001;Janas and Yarus 2003), probably residing within one of the two polar surface zones that comprise about half the membrane thickness (Wiener and White 1992). By selecting RNAs that chromatograph with liposomes, we have found many RNA complexes composed of ∼ 120 nucleotide monomers which bind to dioleoylphosphatidylcholine bilayers (Vlassov et al 2001).…”

“…By selecting RNAs that chromatograph with liposomes, we have found many RNA complexes composed of ∼ 120 nucleotide monomers which bind to dioleoylphosphatidylcholine bilayers (Vlassov et al 2001). Such membrane RNAs oligomerize when free and, even more strikingly, within the membrane (Janas and Yarus 2003). RNAs we use here bind optimally as a 2:1 complex of RNA 9:RNA 10 with RNA contact via kissing loops (Vlassov et al 2001).…”

“…RNA 9 alone shows weak but detectable membrane affinity, suggesting that it incorporates the phospholipid site. In contrast, RNA 10 has no such activity, and may only be a linker (Janas and Yarus 2003) allowing the specific oligomerization of RNA 9.…”

microRNAs in lipoprotein and lipid metabolism: from biological function to clinical application

“…Interestingly, sphingomyelin (SM) binds RNA and prevents its degradation by RNAses [139,140]. Moreover, a few groups have reported that small RNAs could bind to phospholipid membranes using vesicular models [141][142][143][144]. Whether the plasma membrane SM, enriched into lipid rafts, could also bind miRNA and contribute to its export to HDLs has not been published so far.…”

The selection of aptamers specific for membrane molecular targets

“…Characterizing of the RNA complexes, which were composed of RNA 9 and RNA 10 sequences, revealed small internal loops with partially complementary sequences, leading to the formation of a "kissing-loop" complex. These complexes were further visualized via atomic force microscopy (AFM) and fluorescence microscopy [54].…”