Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes
Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes
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DOI：
10.1002/admi.202000353
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发表时间：
2020-06-08
影响因子：
5.4
通讯作者：
Vukovi, Lela
中科院分区：
文献类型：
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作者：
Alizadehmojarad, Ali A.;Zhou, Xingcheng;Vukovi, Lela
DNA聚合物包裹的单壁碳纳米管（SWNTs）在各种纳米技术应用中得到了广泛的应用。分子动力学（MD）模拟和实验被用来探索的结构构象，结合亲和力和动力学稳定性的短单链寡核苷酸吸附在单壁碳纳米管之间的关系。通过计算筛选（9，4）SWNT上36个寡核苷酸序列的构象，其中选择聚合物长度，以便聚合物可以在一级近似下围绕SWNT圆周缠绕一次。所鉴定的构象可大致分为“环”和“非环”。然后，通过温度复制交换计算获得所选序列的二维构象自由能景观。“环”构象的倾向主要由序列化学和聚合物形成紧凑结构的能力驱动。然而，发现成环概率与寡核苷酸与单壁碳纳米管结合的自由能（增量G（结合））无关。寡核苷酸的构象分析，计算的自由能结合的寡核苷酸单壁碳纳米管，和实验确定的动力学稳定性测量表明，增量G（结合）是动力学稳定性的主要相关。序列采用紧凑的环状构象的概率被证明发挥次要作用，仍然有助于可测量的和积极的动力学稳定性。
DNA polymer-wrapped single-walled carbon nanotubes (SWNTs) finds a widespread use in a variety of nanotechnology applications. Molecular dynamics (MD) simulations and experiments are used to explore the relationship between structural conformation, binding affinity, and kinetic stability for short single-stranded oligonucleotides adsorbed on SWNTs. The conformation of 36 oligonucleotide sequences on (9,4) SWNT is computationally screened, where the polymer lengths are selected so the polymers can, to a first approximation, wrap once around the SWNT circumference. The identified conformations can be broadly classified into "rings" and "non-rings." Then, 2D conformational free energy landscapes for selected sequences are obtained by temperature replica exchange calculations. Propensity for "ring" conformations are driven primarily by sequence chemistry and the ability of the polymer to form compact structures. However, ring-formation probability is found to be uncorrelated with free energy of oligonucleotide binding to SWNTs ( increment G(bind)). Conformational analyses of oligonucleotides, computed free energy of binding of oligonucleotides to SWNTs, and experimentally determined kinetic stability measurements show that increment G(bind) is the primary correlate for kinetic stability. The probability of the sequence to adopt a compact, ring-like conformation is shown to play a secondary role that still contributes measurably and positively to kinetic stability.