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 phase diagram differs significantly with the theoretical prediction.
The role of loop stacking in the dynamics of DNA hairpin formation
我们使用一个核苷酸水平的DNA粗粒度模型oxDNA研究DNA发夹形成的动力学。特别是，我们探讨了环堆积相互作用和非天然碱基配对对发夹闭合时间的影响。我们发现发夹闭合时间随温度的非单调变化，与Wallace等人的实验工作一致。Sci. USA 2001，98，5584-5589]。发夹闭合过程包括茎之间的一个或两个键的初始核的形成，随后茎的快速拉链化。在高温下，通常高于发夹熔化温度，观察到有效的负活化焓，因为核具有比开放状态低的焓。相比之下，在低温下，活化焓变为正，主要是由于弯曲环的能量成本增加，该环随着温度降低而变得越来越高度堆叠。我们表明，堆叠必须是非常强大的诱导实验观察到的行为，以及沿着环的存在，只有几个薄弱的堆叠点可以大大抑制it. Non-native碱基对观察到只有一个小的影响，略有加速发夹的形成。
The chirality-induced spin selectivity (CISS), demonstrated in diverse chiral molecules by numerous experimental and theoretical groups, has been attracting extensive and ongoing interest in recent years. As the secondary structure of DNA, the charge transfer along DNA hairpins has been widely studied for more than two decades, finding that DNA hairpins exhibit spin-related effects as reported in recent experiments. Here, we propose a setup to demonstrate directly the CISS effect in DNA hairpins contacted by two nonmagnetic leads at both ends of the stem. Our results indicate that DNA hairpins…
If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte Carlo simulations of co…
We investigate melting transition of DNA sequences embedded in a Langevin fluctuation-dissipation thermal bath. Torsional effects are considered by a twist angle $φ$ between neighboring base pairs stacked along the molecule backbone. Our simulation results show that the increase of twist angle translates linearly the melting temperature with a positive slope. After the so called equilibrium angle $φ_\mathrm{eq}$, the DNA chain becomes very rigid against opening and accordingly very high temperatures are required to initiate the melting process. In such cases however, the biofunctionality of DN…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we evaluate the melting profile of DNA of different length in two geometries: conical and cylindrical. Our results show that not only the confinement but also the geometry of the confined space plays a prominent role in the stability and opening manner of the molecule.
We study the effect of crowders on the melting profile of homogeneous and heterogeneous DNA molecules. We find out the melting profile of short DNA molecules and compare our findings with the experiments. We consider some random distribution of crowders along the chain, and by finding out the best match with the experiments, we attempt to identify the location of crowders in the experimental findings of Ghosh \cite{Ghosh_PNAS_2020}. We also study the melting of homogeneous DNA molecules of different lengths (25, 50, 75) in the presence of only one crowder in the chain. By varying the location …
A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets obscured by large population kinetics at the macroscale, associating equilibrium pathway to the unravelling landscape. In this work, we capture evidence of fluctuation energetics with picoliter samples in a microfluidic cantilever. We exploit nanomechanical resonance to measure the NE energy exchanges through dissipation, revealing a crucial pre-melting tran…
Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induced melting have been correctly described by Rouzina and Bloomfield \cite{RouzinaBloomfield2001a}, neither force threshold has been exactly calculated by theory. In this work, a detailed analysis of the force-extension curve is presented, based on a description of single-stranded DNA in terms of the discrete Kratky-Porod model, consistent with (i) t…
Near the melting transition the bending elastic constant, $κ$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $κ$ with temperature is determined by the denatured bubbles for a continuous transition, e.g., when the two strands are gaussian, but by the broken bonds near the open end in a Y-like configuration for a first-order transition as for strands with excluded volume interactions. In the latter case, a lever rule is operational implying a phase coexistence although dsDNA is known to be a single phase.
Using Langevin dynamics simulations, we study the hysteresis in unzipping of longer double stranded DNA chains whose ends are subjected to a time dependent periodic force with frequency $ω$ and amplitude $G$ keeping the other end fixed. We find that the area of the hysteresis loop, $A_{loop}$, scales as $1/ω$ at higher frequencies, whereas it scales as $(G-G_c)^αω^β$ with exponents $α=1$ and $β=1.25$ in the low frequency regime. These values are same as the exponents obtained in Monte Carlo simulation studies of a directed self avoiding walk model of a homopolymer DNA [R. Kapri, Phys. Rev. E 9…
