The unfolding of our understanding of RNA structure: a personal reflection

Dielectrophoretic manipulation of ribosomal RNA

The manipulation of ribosomal RNA (rRNA) extracted from E. coli cells by dielectrophoresis (DEP) has been demonstrated over the range of 3 kHz-50 MHz using interdigitated microelectrodes. Quantitative measurement using total internal reflection fluorescence microscopy of the time dependent collection indicated a positive DEP response characterized by a plateau between 3 kHz and 1 MHz followed by a decrease in response at higher frequencies. Negative DEP was observed above 9 MHz. The positive DEP response below 1 MHz is described by the Clausius-Mossotti model and corresponds to an induced dipole moment of 3300 D with a polarizability of 7.8×10(-32) F m(2). The negative DEP response above 9 MHz indicates that the rRNA molecules exhibit a net moment of -250 D, to give an effective permittivity value of 78.5 ε(0), close to that of the aqueous suspending medium, and a relatively small surface conductance value of ∼0.1 nS. This suggests that our rRNA samples have a fairly open structure accessible to the surrounding water molecules, with counterions strongly bound to the charged phosphate groups in the rRNA backbone. These results are the first demonstration of DEP for fast capture and release of rRNA units, opening new opportunities for rRNA-based biosensing devices.

The study of genomic DNA adsorption and subsequent interactions using total internal reflection ellipsometry

The adsorption of genomic DNA and subsequent interactions between adsorbed and solvated DNA was studied using a novel sensitive optical method of total internal reflection ellipsometry (TIRE), which combines spectroscopic ellipsometry with surface plasmon resonance (SPR). Single strands of DNA of two species of fish (herring and salmon) were electrostatically adsorbed on top of polyethylenimine films deposited upon gold coated glass slides. The ellipsometric spectra were recorded and data fitting utilized to extract optical parameters (thickness and refractive index) of adsorbed DNA layers. The further adsorption of single stranded DNA from an identical source, i.e. herring ss-DNA on herring ss-DNA or salmon ss-DNA on salmon ss-DNA, on the surface was observed to give rise to substantial film thickness increases at the surface of about 20-21 nm. Conversely adsorption of DNA from alternate species, i.e. salmon ss-DNA on herring ss-DNA or herring ss-DNA on salmon ss-DNA, yielded much smaller changes in thickness of 3-5 nm. AFM studies of the surface roughness of adsorbed layers were in line with the TIRE data.

The ubiquitous nature of RNA chaperone proteins

RNA chaperones are ubiquitous and abundant proteins found in all living organisms and viruses, where they interact with various classes of RNA. These highly diverse families of nucleic acid-binding proteins possess activities enabling rapid and faithful RNA-RNA annealing, strand transfer, and exchange and RNA ribozyme-mediated cleavage under physiological conditions. RNA chaperones appear to be critical to functions as important as maintenance of chromosome ends, DNA transcription, preRNA export, splicing and modifications, and mRNA translation and degradation. Here we review some of the properties of RNA chaperones in RNA-RNA interactions that take place during cellular processes and retrovirus replication. Examples of cellular and viral proteins are dicussed vis à vis the relationships between RNA chaperone activities in vitro and functions. In this new "genomic era" we discuss the possible use of small RNA chaperones to improve the synthesis of cDNA libraries for use in large screening reactions using DNA chips.