DNA Base Pair Mismatches Induce Structural Changes and Alter the Free Energy Landscape of Base Flip

Supercoiling DNA locates mismatches

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.5 pN force and show that, under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under …

DNA hybridization to mismatched templates: a chip study

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from hybridizing the target RNA to two nearly identical templates: a perfect match (PM) and a single mismatch (MM) probe. It has been observed that a large fraction of MM probes repeatably bind targets better than the PMs, against the usual expectation from sequence-specific hybridization; this is difficult to interpret in terms of the underlying physics. We examine thi…

特定太赫兹场能否诱导DNA中的集体碱基翻转？基于新型介观模型的随机平均与共振增强研究

Can Specific THz Fields Induce Collective Base-Flipping in DNA? A Stochastic Averaging and Resonant Enhancement Investigation Based on a New Mesoscopic Model

该研究构建含螺旋性、偶极耦合、黏度与热噪声的介观DNA模型，结合随机平均和共振增强理论，估计约0.28 THz、450 kV/cm的太赫兹场可诱导集体碱基翻转，并与实验相符。

单轨迹贝叶斯建模揭示MSH滑动夹的多态扩散

Single-Trajectory Bayesian Modeling Reveals Multi-State Diffusion of the MSH Sliding Clamp

本文通过单粒子追踪实验和贝叶斯单轨迹建模分析ATP结合态MSH滑动夹的扩散动力学，发现其运动由三个具有不同扩散系数的状态交替构成，揭示了比简单布朗运动更复杂的构象变化驱动的多态扩散机制。

DNA复制错配修复中依赖ATP的错配识别

ATP-Dependent Mismatch Recognition in DNA Replication Mismatch Repair

针对DNA错配修复中错配识别机制不明的问题，本文提出依赖ATP的三能级量子假想酶模型，通过低能级能隙及其翻转实现正确匹配与错配的指数概率判别，并建立能量成本与识别错误的关系。

Characterizing the bending and flexibility induced by bulges in DNA duplexes

Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly…