论文标题
较弱的张力会加速杂交和短寡核苷酸的脱杂交
Weak tension accelerates hybridization and dehybridization of short oligonucleotides
论文作者
论文摘要
DNA受张力的杂交和脱缩合与基本遗传过程以及基于DNA的机械生物学测定法的设计有关。虽然强张力会加速DNA熔化并减速DNA退火，但较弱的张力弱的效果尚不清楚。在这项研究中，我们开发了一种DNA弓测定法，该测定方法使用双链DNA（DSDNA）的弯曲刚度在2 pn至6 pn的范围内在单链DNA（SSDNA）靶标上发挥弱张力。将此测定与单分子特品格相结合，我们测量了在张力下和8-9 NT寡核的15 nt ssDNA之间的杂交和脱杂交动力学，并发现杂交和脱缩率均单调速率随着测试的各种核苷酸序列而单调而增加。这些发现表明，其过渡状态的成核双链体比纯dsDNA或ssDNA对应物更扩展。我们使用粗粒牛NNA2模型的模拟表明，过渡态的扩展增加是由于未配对的ssDNA区域之间的排除相互作用彼此紧密近。这项研究突出了一个例子，其中理想的类似蠕虫样链模型无法解释低力状态下DNA的动力学行为。
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing, the effects of tension weaker than 5 pN are less clear. In this study, we developed a DNA bow assay, which uses the bending rigidity of double-stranded DNA (dsDNA) to exert weak tension on a single-stranded DNA (ssDNA) target in the range of 2 pN to 6 pN. Combining this assay with single-molecule FRET, we measured the hybridization and dehybridization kinetics between a 15 nt ssDNA under tension and a 8-9 nt oligo, and found that both the hybridization and dehybridization rates monotonically increase with tension for various nucleotide sequences tested. These findings suggest that the nucleated duplex in its transition state is more extended than the pure dsDNA or ssDNA counterpart. Our simulations using the coarse-grained oxDNA2 model indicate that the increased extension of the transition state is due to exclusion interactions between unpaired ssDNA regions in close proximity to one another. This study highlights an example where the ideal worm-like chain models fail to explain the kinetic behavior of DNA in the low force regime.
