Bandyopadhyay Debolina, Mishra Padmaja P
Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India.
HBNI, Mumbai, India.
Front Mol Biosci. 2021 Sep 3;8:725541. doi: 10.3389/fmolb.2021.725541. eCollection 2021.
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
除了经典的双螺旋形式外，已知DNA还可外推成其他几种二级结构模式，这些模式涉及分子间和分子内的氢键作用。核酸的二级结构经历多个复杂且可相互转换的异构构象阶段。DNA在这些构象之间的转变具有重要意义，并且已经进行了全面监测，以建立关于未折叠、折叠、错误折叠和部分折叠状态之间转变的定性和定量信息。在这种结构相互转换过程中，总是存在特定数量的中间体，它们寿命短暂，有时甚至不会在异构群体中积累，使用传统的整体技术很难对其进行表征。单分子荧光共振能量转移（sm-FRET）显微光谱方法具有克服这些局限性的优势，能够监测以可测量的高速率随机且平衡地随时间发生的生物现象。因此，追踪特定分子的时间轨迹能够直接测量每个转变步骤的速率常数，包括由于浓度低而隐藏在整体水平下的中间体。本综述重点关注单分子福斯特共振能量转移（sm-FRET）的应用优势，该方法对于了解DNA所采用的各种二级结构的动态结构和结构转变非常有价值，同时不会让一个分子的供体与任何其他分子的受体发生串扰。我们强调了为探索几种核酸二级结构（例如DNA发夹、霍利迪连接体、G-四链体和i-基序）的折叠和展开状态而进行的研究。
