Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking

We have found strong supporting evidence for the helical structures of single-stranded nucleic acids by stretching individual molecules of polyadenylic acid [poly(A)] and polycytidylic acid [poly(C)]. Analyzing the force versus extension data using a two-state elastic model in which random-coil domains alternate with rigid helical domains allows one to extract the thermodynamic and structural properties. In addition, it also yields moderate to low cooperativity of the helix-coil transition for poly(A) and poly(C), respectively.

Figure 1

Two examples of $F\mathrm{\text{−}}x$ curves for poly(A) (solid square) and poly(C) (open circle) and fits (solid line). A $F\mathrm{\text{−}}x$ curve for poly(U) is also shown (open triangle), offset by $+100\mathrm{nm}$ along the horizontal axis.

Figure 2

A schematic of a single-stranded helix stabilized by base-stacking interactions ( gray boxes). $b$ is the rise per nucleotide in the helix. The random-coil domains are modeled as freely-jointed chains in which the base associated with each chain segment is oriented randomly with respect to its neighbors. Each Kuhn segment of the chain contains $2\lambda /a$ bases, with $a$ the interphosphate distance per nucleotide in the random coil, and $\lambda$ the persistence length.

Figure 3

Rescaled $F\mathrm{\text{−}}x$ curves for 7 poly(A) and 7 poly(C) chains (inset).