Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois.
Biophys J. 2024 Jan 16;123(2):118-133. doi: 10.1016/j.bpj.2023.11.022. Epub 2023 Nov 24.
Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base-pairing on each side of the AP site. The barrier induces fraying of the short segment when an AP site is near the termini. Shifting the AP site inward promotes a transition from short-segment fraying to fully encompassing the barrier into the thermodynamics of hybridization, leading to further destabilization of the duplex. Nucleobase sequence determines the length scale for this transition by tuning the barrier height and base-pair stability of the short segment, and certain sequences enable out-of-register base-pairing to minimize the barrier height.
局部 DNA 碱基配对稳定性的改变，如损伤和化学修饰，可以改变整个寡核苷酸的稳定性和动力学。末端效应可能导致短双链体中破坏位置影响双链体稳定性和结构动力学，但核酸修饰的这一方面经常被忽视。我们研究了碱基缺失（AP 位点）的位置如何影响短 DNA 双链体的稳定性和动力学。通过稳态和时间分辨光谱以及分子动力学模拟的结合，我们揭示了 AP 位点位置与核碱基序列之间的相互作用，这种相互作用控制着双链体的能量和动态破坏。AP 位点两侧的碱基配对熵垒将双链体打断成两个片段。当 AP 位点靠近末端时，该势垒会诱导短片段的磨损。将 AP 位点向内移动会促使短片段的磨损从短片段的磨损转变为完全包含势垒进入杂交热力学，从而进一步使双链体失稳。核碱基序列通过调整短片段的势垒高度和碱基配对稳定性来确定这种转变的长度尺度，某些序列可以实现非对齐碱基配对以最小化势垒高度。
