A quantitative model of a cooperative two-state equilibrium in DNA: experimental tests, insights, and predictions

Stretching and twisting of double-stranded RNA under forces: Unwinding mechanism and base-pair dependent elasticity

We used all-atom molecular dynamics simulations to investigate the mechanical response of double-stranded RNA (dsRNA) by applying various forces. We used the helical rise and helical twist, as well as a newly defined helical diameter, to characterize the stretching and twisting of dsRNA. The results indicate that dsRNA unwinds when stretched, accompanied by a linear increase in helical rise and helical diameter. Then, we utilized the normal modes, which are linear combinations of helical modes, to elucidate the underlying mechanism of dsRNA unwinding from an energetic perspective. On the other hand, we employed a stiffness matrix based on a rigid base pair model to examine the base-pair dependence of twist elasticity for dsRNA, as well as stretch elasticities with respect to the helical rise and helical diameter. The results show that the force induces variations in the local elasticities and their couplings of dsRNA, which are closely related to the distributions of base pairs. The mean stretch and twist elasticities can be considered as constants within the measurement uncertainties; however, their couplings demonstrate a slight linear dependency on applied force.

Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.

Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations

RNA plays critical roles in the transmission and regulation of genetic information and is increasingly used in biomedical and biotechnological applications. Functional RNAs contain extended double-stranded regions, and the structure of double-stranded RNA (dsRNA) has been revealed at high resolution. However, the dependence of the properties of the RNA double helix on environmental effects, notably temperature, is still poorly understood. Here, we use single-molecule magnetic tweezer measurements to determine the dependence of the dsRNA twist on temperature. We find that dsRNA unwinds with increasing temperature, even more than DNA, with ΔTwRNA = -14.4 ± 0.7°/(°C·kbp), compared to ΔTwDNA = -11.0 ± 1.2°/(°C·kbp). All-atom molecular dynamics (MD) simulations using a range of nucleic acid force fields, ion parameters, and water models correctly predict that dsRNA unwinds with rising temperature but significantly underestimate the magnitude of the effect. These MD data, together with additional MD simulations involving DNA and DNA-RNA hybrid duplexes, reveal a linear correlation between the twist temperature decrease and the helical rise, in line with DNA but at variance with RNA experimental data. We speculate that this discrepancy might be caused by some unknown bias in the RNA force fields tested or by as yet undiscovered transient alternative structures in the RNA duplex. Our results provide a baseline to model more complex RNA assemblies and to test and develop new parametrizations for RNA simulations. They may also inspire physical models of the temperature-dependent dsRNA structure.

Ion-induced changes in DNA gels

Small angle neutron scattering (SANS) measurements are reported for DNA gels under near physiological conditions in which the concentration of monovalent and divalent counter-ions and the pH are varied. The scattering intensity I(q) is described by a two-term equation, one due to osmotic concentration fluctuations and the other coming from static inhomogeneities frozen in by the cross-links. SANS in the low q range indicates the presence of large clusters and the size of which exceeds the resolution of the experiment. In the intermediate q-range, the intensity increases with the CaCl2 concentration and the slope approaches -1, corresponding to linear (rod-like) scatterers. In the highest q region, the scattering response is governed by the local chain geometry. Screening of electrostatic interactions by sodium chloride causes a moderate increase in the SANS intensity that is accompanied by an increase in the mesh size L of the network. Addition of calcium chloride, or a decrease in pH, produces similar trends, and ultimately leads to phase separation. The scattering intensity at q = 0, estimated from independent measurements of the osmotic pressure Π, is in excellent agreement with I(0) from the SANS measurements. Anomalous small angle X-ray scattering (ASAXS) measurements on the uncross-linked DNA show that the monovalent ion cloud is only weakly influenced by the addition of divalent ions. Conversely, the divalent counter-ion cloud tightly follows the contour of polymer chains.

Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study

We used all-atom molecular dynamics simulation to investigate the elastic properties of double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch, bend, and twist elasticities, as well as the twist-stretch coupling, of the dsDNA over a wide range of temperature. The results showed that the bending and twist persistence lengths, together with the stretch and twist moduli, decrease linearly with temperature. However, the twist-stretch coupling behaves in a positive correction and enhances as the temperature increases. The potential mechanisms of how temperature affects dsDNA elasticity and coupling were investigated by using the trajectories from atomistic simulation, in which thermal fluctuations in structural parameters were analyzed in detail. We analyzed the simulation results by comparing them with previous simulation and experimental data, which are in good agreement. The prediction about the temperature dependence of dsDNA elastic properties provides a deeper understanding of DNA elasticities in biological environments and potentially helps in the further development of DNA nanotechnology.

Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting

The advances in nucleic acid nanotechnology have given rise to various elegantly designed structural complexes fabricated from DNA, RNA, chemically modified RNA strands, and their mixtures. The structural properties of NA nanoparticles (NANP) generally dictate and significantly impact biological function; and thus, it is critical to extract information regarding relative stabilities of the different structural forms. The adequate stability assessment requires knowledge of thermodynamic parameters that can be empirically derived using conventional UV-melting technique. The focus of this chapter is to describe methodology to evaluate thermodynamic data of NANPs complexation based on DNA 12 base-pair (bp) duplex formation as an example.