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首页> 外文期刊>Journal of Biomolecular Structure and Dynamics >Methylene Blue Binding to DNA with Alternating AT Base Sequence: Minor Groove Binding is Favored over Intercalation.
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Methylene Blue Binding to DNA with Alternating AT Base Sequence: Minor Groove Binding is Favored over Intercalation.

机译：亚甲基蓝以交替的AT碱基序列与DNA结合：小沟槽结合比插层更有利。

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摘要

The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5'-YpR-3' intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute-solvent interactions, which are assumed to be nearly constant for the compared complexes of MB with DNA, seem to be justified by the results.
机译：本文介绍的亚甲基蓝（MB）与AT交替碱基序列与DNA结合的结果补充了MB与GC交替DNA结合的两个以前模型研究中获得的数据。鉴于两个系统的大量实验数据，此理论研究集中于详细的能量分析和比较，以了解它们的不同行为。由于复合物的实验高分辨率结构不可用，因此该分析基于在不同结合模式下复合物的能量最小化结构模型。对于这两个序列，已经提出了四种不同的插入结构和两种用于小沟和大沟中MB结合的模型。使用静电连续理论将溶剂的静电效应包括在能量分析中，并通过求解非线性Poisson-Boltzmann方程研究MB结合对盐浓度的依赖性。我们发现，对于两个序列，不同配合物的相对稳定性相似，这与光谱数据的解释是一致的。然而，在能量分解中观察到细微的差异，这可以归因于盐浓度增加，从对称的5'-YpR-3'插入到较小的凹槽结合的变化，这是通过实验观察到，AT序列的盐浓度低于盐浓度。 GC序列。根据我们的结果，这种差异是由于带有AT交替DNA的小沟复合物的非静电能量明显较低，而与该序列的结合能量稍低是由于DNA的较高变形能引起的。含能数据与不同光谱学研究得出的结论一致，也可以在建模的复合物的基础上进行结构解释。结果表明，简单的静态建模技术以及对熵项和非静电溶质-溶剂相互作用的忽略（对于MB与DNA的比较复合物而言假定为几乎恒定）似乎是合理的。

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