Effects of temperature on the mechanical properties of single stranded DNA

Force-induced melting of DNA hairpin: Unfolding pathways and phase diagrams

Using the exact enumeration technique, we have studied the force-induced melting of a DNA hairpin on the face centered cubic lattice for two different sequences which differ in terms of loop closing base pairs. The melting profiles obtained from the exact enumeration technique is consistent with the Gaussian network model and Langevin dynamics simulations. Probability distribution analysis based on the exact density of states revealed the microscopic details of the opening of the hairpin. We showed the existence of intermediate states near the melting temperature. We further showed that different ensembles used to model single-molecule force spectroscopy setups may give different force-temperature diagrams. We delineate the possible reasons for the observed discrepancies.

Energy/entropy partition of force at DNA stretching

We compute by molecular simulation the energy/entropic partition of the force in a stretched double-stranded (ds)DNA molecule that is not yet available from the single-molecule measurements. Simulation using the coarse-grained wormlike chain (WLC) model predicts a gradual decrease in the internal (bending) energy of DNA at stretching. The ensuing negative energy contribution to force f_U is outweighed by the positive entropy contribution f_S . The ratio f_U /f, used to assess the polymer elasticity, is about -1 at the moderate extension of DNA. At the high extension, the extra energy expenses due to the contour length elongation make the ratio f_U /f less negative. The simulation findings of the hybrid energy/entropy nature of DNA elasticity at weak and moderate forces are supported by computations using the thermoelastic method mimicking the polymer experiments in bulk. It is contended that the observation of the negative energy elasticity in DNA can be generalized to other semiflexible polymers described by the WLC model.

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, we 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, we measured the effects of ssRNA on force extension curves for dsDNA. We observe 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. We 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.

Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy

We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence.

A Temperature-Jump Optical Trap for Single-Molecule Manipulation

To our knowledge, we have developed a novel temperature-jump optical tweezers setup that changes the temperature locally and rapidly. It uses a heating laser with a wavelength that is highly absorbed by water so it can cover a broad range of temperatures. This instrument can record several force-distance curves for one individual molecule at various temperatures with good thermal and mechanical stability. Our design has features to reduce convection and baseline shifts, which have troubled previous heating-laser instruments. As proof of accuracy, we used the instrument to carry out DNA unzipping experiments in which we derived the average basepair free energy, entropy, and enthalpy of formation of the DNA duplex in a range of temperatures between 5°C and 50°C. We also used the instrument to characterize the temperature-dependent elasticity of single-stranded DNA (ssDNA), where we find a significant condensation plateau at low force and low temperature. Oddly, the persistence length of ssDNA measured at high force seems to increase with temperature, contrary to simple entropic models.

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

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.

Comparison of the stem-loop and linear probe-based electrochemical DNA sensors by alternating current voltammetry and cyclic voltammetry

Here we systematically characterized the sensor performance of the stem-loop probe (SLP) and linear probe (LP) electrochemical DNA sensors using alternating current voltammetry (ACV) and cyclic voltammetry (CV), with the goal of generating the set of operational criteria that best suits each sensor architecture, in addition to elucidating the signaling mechanism behind these sensors. Although the LP sensor shows slightly better % signal suppression (SS) upon hybridization with the perfect match target at 10 Hz, our frequency-dependent study suggests that it shows optimal % SS only in a very limited AC frequency range. Similar results are observed in CV studies in which the LP sensor, when compared to the SLP sensor, displays a narrower range of voltammetric scan rates where the optimal % SS can be achieved. More importantly, the difference between the two sensors' performance is particularly pronounced if the change in integrated charge (Q) upon target hybridization, rather than the peak current (I), is measured in CV. The temperature-dependent study further highlights the differences between the two sensors, where the LP sensor, owing to the flexible linear probe architecture, is more readily perturbed by temperature changes. Both SLP and LP sensors, however, show a loss of % SS when operated at elevated temperatures, despite the significant improvement in the hybridization kinetics. In conjunction with the ACV, CV, and temperature-dependent studies, the electron-transfer kinetics study provides further evidence in support of the proposed signaling mechanism of these two sensors, in which the SLP sensor's signaling efficiency and sensor performance is directly linked to the hybridization-induced conformational change in the redox-labeled probe, whereas the performance of the LP sensor relies on the hybridization-induced change in probe dynamics.

Role of loop entropy in the force induced melting of DNA hairpin

Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the force-temperature diagram differs significantly with the theoretical prediction.

Theory of Biopolymer Stretching at High Forces

We provide a unified theory for the high force entropic elasticity of biopolymers solely in terms of the persistence length, ξ_p , and the monomer spacing, a. When the force f>ℱ _h ~ k_BTξ_p /a² the biopolymers behave as freely jointed chains (FJCs) while in the range ℱ _l ~ k_BT/ξ_p <f<ℱ _h the worm-like chain (WLC) is a better model. We show that ξ_p can be estimated from the force extension curve (FEC) at the extension x ≈ ¹/₂ (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for x ≥ ¹/₂. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the f-dependent elasticity be fully described.

Adsorption of externally stretched two-dimensional flexible and semiflexible polymers near an attractive wall

We study analytically a model of a two-dimensional partially directed flexible or semiflexible polymer, attached to an attractive wall which is perpendicular to the preferred direction. In addition, the polymer is stretched by an externally applied force. We find that the wall has a dramatic effect on the polymer. For wall attraction epsilon1 smaller than the nonsequential nearest-neighbor attraction epsilon, the fraction of monomers at the wall is zero and the model is the same as that of a polymer without a wall. However, for epsilon1 greater than epsilon, the fraction of monomers at the wall undergoes a first-order transition from unity at low temperature and small force, to zero at higher temperatures and forces. We present phase diagram for this transition. Our results are confirmed by Monte Carlo simulations.

Pulling self-interacting polymers in two dimensions

We investigate a two-dimensional problem of an isolated self-interacting end-grafted polymer, pulled by one end. In the thermodynamic limit, we find that the model has only two different phases, namely a collapsed phase and a stretched phase. We show that the phase diagram obtained by Kumar [Phys. Rev. Lett. 98, 128101 (2007)] for small systems, where differences between various statistical ensembles play an important role, differs from the phase diagram obtained here in the thermodynamic limit.

Force-induced stretched state: effects of temperature

A model of self-avoiding walks with suitable constraint has been developed to study the effect of temperature on a single-stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction coordinate) may increase or decrease with the temperature depending on the applied force. The simple model developed here, which incorporates semimicroscopic details of base direction, provides an explanation of the force-induced transitions in ssDNA as observed in experiments.