Single molecule identification of homology-dependent interactions between long ssRNA and dsDNA

Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, Harvard University researchers have explored, for the first time, the interaction of long single-stranded (ss) RNAs with cognate homologous double-stranded (ds) DNA in vitro Using magnetic tweezers, they measured the effects of ssRNA on force extension curves for dsDNA. They observed that the presence of ssRNA impedes the extension of dsDNA, specifically at low forces, dependent on homology between the RNA and DNA species, and dependent on ssRNA lengths (≥1 kb). The observed effect also depends on the concentration of ssRNA and is abolished by overstretching of the dsDNA. These findings show that significant homologous contacts can occur between long ssRNA and dsDNA in the absence of protein and that these contacts alter the mechanical properties of the dsDNA.

Schematic diagram of the experimental design


(A) Schematic representation of the assay for measuring the extension of dsDNA due to the binding of RNA. (B) Sequences to which analyzed RNAs are homologous. 6L = 6,396-nt low G+C content RNA and 6H = 6,107-nt high G+C content RNA; positions shown relative to full length λ DNA template (black line). 1K = a 1025-nt subsegment of 6L. 416, 130 and 40 are subsegments of 1K. Gray lines denote ssRNAs. A predicted nucleic acid triple helices target site in the 40nt RNA is bold and underlined within the total sequence.

The researchers propose that long ssRNA interacts paranemically with long dsDNA via periodic short homologous interactions, e.g. mediated by RNA/DNA triplex-formation, and that dsDNA extension is impeded by formation of RNA secondary structure in the intervening unbound regions. Analogous interactions in vivo would permit lncRNAs to mediate the juxtaposition of two or more DNA regions on the same or different chromosomes.

Liu C, Danilowicz C, Kleckner N, Prentiss M. (2016) Single molecule identification of homology-dependent interactions between long ssRNA and dsDNA. Nucleic Acids Res [Epub ahead of print]. [article]

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