Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.
Homi Bhabha National Institute, Mumbai 400094, India.
J Phys Chem B. 2023 May 25;127(20):4351-4363. doi: 10.1021/acs.jpcb.3c00778. Epub 2023 May 10.
While the double helix is the most stable conformation of DNA inside cells, its transient unwinding and subsequent partial separation of the two complementary strands yields an intermediate single-stranded DNA (ssDNA). The ssDNA is involved in all major DNA transactions such as replication, transcription, recombination, and repair. The process of DNA unwinding and translocation is shouldered by helicases that transduce the chemical energy derived from nucleotide triphosphate (NTP) hydrolysis to mechanical energy and utilize it to destabilize hydrogen bonds between complementary base pairs. Consequently, a comprehensive understanding of the molecular mechanisms of these enzymes is essential. In the last few decades, a combination of single-molecule techniques (force-based manipulation and visualization) have been employed to study helicase action. These approaches have allowed researchers to study the single helicase-DNA complex in real-time and the free energy landscape of their interaction together with the detection of conformational intermediates and molecular heterogeneity during the course of helicase action. Furthermore, the unique ability of these techniques to resolve helicase motion at nanometer and millisecond spatial and temporal resolutions, respectively, provided surprising insights into their mechanism of action. This perspective outlines the contribution of single-molecule methods in deciphering molecular details of helicase activities. It also exemplifies how each technique was or can be used to study the helicase action of RecD2 in recombination DNA repair.
虽然双螺旋是细胞内 DNA 最稳定的构象,但它的短暂解旋和随后两条互补链的部分分离产生了中间的单链 DNA(ssDNA)。ssDNA 参与所有主要的 DNA 代谢过程,如复制、转录、重组和修复。DNA 解旋和易位的过程由解旋酶承担,解旋酶将核苷酸三磷酸(NTP)水解产生的化学能转化为机械能,并利用它来破坏互补碱基对之间的氢键。因此,全面了解这些酶的分子机制至关重要。在过去的几十年中,单分子技术(基于力的操作和可视化)的结合已被用于研究解旋酶的作用。这些方法使研究人员能够实时研究单个解旋酶-DNA 复合物,并检测其相互作用的自由能景观,以及在解旋酶作用过程中构象中间体和分子异质性的检测。此外,这些技术各自具有在纳米和毫秒空间和时间分辨率下解析解旋酶运动的独特能力,为其作用机制提供了令人惊讶的见解。本观点概述了单分子方法在破译解旋酶活性的分子细节方面的贡献。它还举例说明了每种技术如何或可以用于研究 RecD2 在重组 DNA 修复中的解旋酶作用。