Stretching Single Stranded DNA, a Model Polyelectrolyte

Abstract

The elastic properties of single stranded (ss)DNA, studied by pulling on an isolated molecule, are shown to agree with a recent model of ssDNA that takes into account base pairings and screened electrostatic repulsion of the phosphodiester backbone. By an appropriate physicochemical treatment, the pairing interactions were suppressed and ssDNA used as an experimental model for a generic polyelectrolyte. The elastic behavior of such an altered ssDNA deviates strongly from the behavior of an ideal polymer. This deviation is shown to result from the elasticity of the chain and its electrostatic selfavoiding interactions.

Single-stranded nucleic acid elasticity arises from internal electrostatic tension

“…Our empirical finding that b does not depend on I directly contradicts prior modeling of high-force ssNA elasticity (20,21) based upon an electrostatics-dependent persistence length (17)(18)(19). Such models relied upon a highly salt-dependent charge density (22) inappropriately obtained from an effective-charge DH model (42)(43)(44)(45) valid only in the far field and not suitable for treating interactions between neighboring charges.…”

“…Intermediate elasticity has been previously explained with models incorporating an electrostatics-dependent persistence length (17)(18)(19). Some experimental agreement has been seen with these models (20,21), but only for studies at a single salt concentration and only when invoking a strongly saltdependent charge density (22).…”

“…Such models relied upon a highly salt-dependent charge density (22) inappropriately obtained from an effective-charge DH model (42)(43)(44)(45) valid only in the far field and not suitable for treating interactions between neighboring charges. This charge density was seemingly validated through experiments (20,21), but those studies were not conducted over a broad range of I and thus were not well suited to critically test salt-dependent effects. In SI Appendix, Fig.…”

Honey, I shrunk the DNA: DNA length as a probe for nucleic‐acid enzyme activity

“…Doublestranded DNA is considerably stiffer than single-stranded DNA, as indicated by their different persistence lengths, $50 nm for duplex DNA 39,51 and 0.8-3 nm for the singlestranded form (with a strong dependence on the ionic strength of the solution). 50,52 The energy required to bend a stretch of DNA of a certain length over a certain angle is linearly dependent on the bending persistence length: the shorter the persistence length, the less energy required to bend. As a consequence, a polymer with a short bending persistence length will adopt a more compact random-coil structure with an average end-to-end distance much shorter than its contour length.…”

“…Base pairing and electrostatic self-avoiding effects make the WLC model break down for single-stranded DNA at lower forces. 50 (b) Below the crossover point, singlestranded DNA is shorter than the duplex DNA. Enzymatically catalyzed conversions between the two states can be visualized by changes in DNA length.…”