Völker Jens, Gindikin Vera, Breslauer Kenneth J
Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Rd, Piscataway, NJ 08854, USA.
The Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA.
Biomolecules. 2024 Nov 29;14(12):1532. doi: 10.3390/biom14121532.
We demonstrate that a short oligonucleotide complementary to a G-quadruplex domain can invade this iconic, noncanonical DNA secondary structure in ways that profoundly influence the properties and differential occupancies of the resulting DNA polymorphic products. Our spectroscopic mapping of the conformational space of the associated reactants and products, both before and after strand invasion, yield unanticipated outcomes which reveal several overarching features. First, strand invasion induces the disruption of DNA secondary structural elements in both the invading strand (which can assume an iDNA tetrad structure) and the invaded species (a G-quadruplex). The resultant cascade of coupled alterations represents a potential pathway for the controlled unfolding of kinetically trapped DNA states, a feature that may be characteristic of biological regulatory mechanisms. Furthermore, the addition of selectively designed, exogenous invading oligonucleotides can enable the manipulation of noncanonical DNA conformations for biomedical applications. Secondly, our results highlight the importance of metastability, including the interplay between slower and faster kinetic processes in determining preferentially populated DNA states. Collectively, our data reveal the importance of sample history in defining state populations, which, in turn, determine preferred pathways for further folding steps, irrespective of the position of the thermodynamic equilibrium. Finally, our spectroscopic data reveal the impact of topological constraints on the differential stabilities of base-paired domains. We discuss how our collective observations yield insights into the coupled and uncoupled cascade of strand-invasion-induced transformations between noncanonical DNA forms, potentially as components of molecular wiring diagrams that regulate biological processes.
我们证明，与G-四链体结构域互补的短寡核苷酸能够以深刻影响所得DNA多态性产物的性质和差异占有率的方式侵入这种标志性的非经典DNA二级结构。我们对链侵入前后相关反应物和产物构象空间的光谱测绘产生了意想不到的结果，揭示了几个总体特征。首先，链侵入会导致侵入链（可呈现iDNA四联体结构）和被侵入物种（G-四链体）中的DNA二级结构元件被破坏。由此产生的一系列耦合变化代表了一种潜在途径，可用于控制动力学捕获的DNA状态的展开，这一特征可能是生物调节机制所特有的。此外，添加经过选择性设计的外源侵入寡核苷酸能够为生物医学应用操纵非经典DNA构象。其次，我们的结果突出了亚稳性的重要性，包括较慢和较快动力学过程之间的相互作用在确定优先占据的DNA状态方面的作用。总体而言，我们的数据揭示了样品历史在定义状态群体中的重要性，而状态群体又决定了进一步折叠步骤的首选途径，无论热力学平衡的位置如何。最后，我们的光谱数据揭示了拓扑约束对碱基配对结构域差异稳定性的影响。我们讨论了我们的总体观察结果如何深入了解非经典DNA形式之间由链侵入诱导的耦合和解耦级联转变，这些转变可能作为调节生物过程的分子布线图的组成部分。
