Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.
Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.
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DOI：
10.1021/nl8022143
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发表时间：
2008-12
期刊：
影响因子：
10.8
通讯作者：
Vezenov DV
中科院分区：
文献类型：
--
作者：
Manohar S;Mantz AR;Bancroft KE;Hui CY;Jagota A;Vezenov DV
我们使用化学力显微镜测量了从单晶石墨中剥离单链DNA分子所需的力。用寡核苷酸化学修饰的尖端回缩过程中的力轨迹显示出特征性的高原和突变力跳跃，我们将其解释为一个稳定的剥离过程，其间有一个或多个分子的完全脱离。我们能够区分嘧啶均聚物中的碱基-多胸腺嘧啶和多胞嘧啶的剥离力分别为85.3±4.7pN和60.8±5.5pN，基本上与盐浓度和脱落率无关。我们建立了一个从石墨表面剥离自由连接链的模型，并估算了胸腺嘧啶和胞嘧啶核苷酸的平均单体结合能分别为11.5±0.6KBT和8.3±0.7KBT。用分子动力学模拟的平衡自由能谱对胸腺嘧啶核苷的势垒为18.9kBT，表明非静电相互作用占主导地位。实验和理论之间的差异表明，并不是所有的碱都吸附在表面上，或者存在大量的碱基吸附在其中。使用与AFM尖端共价连接的寡核苷酸的力光谱提供了一种灵活而明确的手段来量化DNA与一些底物之间的相互作用强度，可能包括纳米材料，如碳纳米管。
We measured the force required to peel single-stranded DNA molecules from single-crystal graphite using chemical force microscopy. Force traces during retraction of a tip chemically modified with oligonucleotides displayed characteristic plateaus with abrupt force jumps, which we interpreted as a steady state peeling process punctuated by complete detachment of one or more molecules. We were able to differentiate between bases in pyrimidine homopolymers – peeling forces were 85.3±4.7 pN for polythymine and 60.8±5.5 pN for polycytosine, substantially independent of salt concentration and the rate of detachment. We developed a model for peeling a freely jointed chain from the graphite surface and estimated the average binding energy per monomer to be 11.5±0.6 kBT and 8.3±0.7 kBT in the cases of thymine and cytosine nucleotides. The equilibrium free-energy profile simulated using molecular dynamics had a potential well of 18.9 kBT for thymidine, showing that non-electrostatic interactions dominate the binding. The discrepancy between the experiment and theory indicates that not all bases are adsorbed on the surface or that there is a population of conformations in which they adsorb. Force spectroscopy using oligonucleotides covalently linked to AFM tips provides a flexible and unambiguous means to quantify the strength of interactions between DNA and a number of substrates, potentially including nanomaterials such as carbon nanotubes.
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