Figure 1.

Schematic representation of plasmid DNA (pDNA), messenger RNA (mRNA), small interfering RNA (siRNA) and end-to-end stacked blunt short DNA. The contour length L represents the total length of the macromolecules, and the persistence length l_p represents the length in which the polymer chain remains approximately straight. The l_p for DNA (double stranded) at moderate ionic strength is ca. 50 nm, whereas for mRNA (single stranded) is ~2 nm. siRNA is an essentially rigid molecule (l_p > L) and typically contains two unpaired bases on each strand. All these polymers are anionic and highly charged. The counterion cloud with a condensed counterion layer closer to the nucleic acid backbone (Manning condensation) is explicitly shown for pDNA and omitted for the remaining nucleic acids (NAs) for clarity. Small DNA fragments without unpaired bases (blunt) stacked end-to-end via hydrophobic interactions between the nucleobases are also shown.