Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments
Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments
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DOI：
10.1093/nar/gkx1161
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发表时间：
2017-12-15
影响因子：
14.9
通讯作者：
Ritort, Felix
中科院分区：
文献类型：
--
作者：
Maria Huguet, Josep;Ribezzi-Crivellari, Marco;Ritort, Felix
DNA杂交是生物学中重要的分子反应，具有广泛的应用。核酸的最近邻（NN）模型使用不同碱基对基序的能量值来预测DNA热力学。这些值是从一价盐和二价盐的熔融实验中得到的，并用于预测低聚物在几度内的熔融温度。然而，目前的生物技术应用仍需要改进神经网络能量值及其在镁中的盐依赖性的测定，以寻求合成dna杂交的高选择性。我们开发了一种基于单分子解压缩实验的方法，以获得准确的神经网络能量值和DNA的起始因子。在一系列温度和盐条件下，镁结合离子之间的相关效应较弱，导出了一组新的镁值，再现了解压缩数据，并改进了所有可用寡核苷酸长度的熔化温度预测。结果表明，神经网络盐校正参数与神经网络基序的GC含量相关。我们的研究显示了单分子力谱分析揭示核酸新特征的能力，如序列依赖性盐校正。
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.