Abstract
Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.
Highlights
Understanding the elastic behavior of single-stranded DNA is of great relevance because of its major role in many biological processes, such as replication, recombination, repair, transcription and transposition of DNA [1]
The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA
We systematically explored a range of different concentration of monovalent and divalent salts observing the formation of a plateau in the force-extension curves (FECs) of the Single-stranded DNA (ssDNA), which we interpret as evidence of secondary structure formation
Summary
Understanding the elastic behavior of single-stranded DNA (ssDNA) is of great relevance because of its major role in many biological processes, such as replication, recombination, repair, transcription and transposition of DNA [1]. The entropic effect to close 30 bases within a loop and the large persistence length of the dsDNA segment in the loop region creates a large kinetic barrier that must be overcome, thereby inhibiting the refolding of the native structure This methodology allows us to study the stretching response of ssDNA over a wide range of forces and salt conditions and should be useful to study the interaction of ssDNA with proteins, peptides and other chemical compounds [24]. Our work contributes to a better understanding of the elastic parameters describing the FECs of ssDNA at different monovalent and divalent salt conditions using analytically tractable formulas This knowledge should be most useful to extract the base pairing free energies of dsDNA in the presence of divalent ions from mechanical unzipping experiments. This information has already been shown to be essential to characterize the thermodynamics of hybridization of DNA in monovalent salt from unzipping experiments [25]
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