Unfolding thermodynamics of DNA pyrimidine triplexes with different molecularities
Unfolding thermodynamics of DNA pyrimidine triplexes with different molecularities
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DOI：
10.1021/jp710926h
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发表时间：
2008-04-17
影响因子：
3.3
通讯作者：
Marky, Luis A.
中科院分区：
文献类型：
--
作者：
Lee, Hui-Ting;Arciniegas, Santiago;Marky, Luis A.
核酸寡核苷酸（ODNs）作为一种药物，具有高度的选择性和亲和力，可用于反基因和反义策略来控制基因表达。在这项工作中，我们试图回答以下问题：DNA三链体的分子结构如何影响其整体稳定性和熔解行为？为此，我们使用了温度依赖性紫外光谱和量热（差示扫描量热法）技术相结合，以调查的熔融行为的DNA三链体具有类似的螺旋茎，TC+TC+ TC+T/AGAGAGA/TCTCTCT，但形成不同的链分子。我们确定了标准的热力学配置文件和差分结合的质子和反离子伴随着他们的展开。三链体的形成伴随着有利的自由能项，这是由有利的熵-不利的熵贡献的典型补偿引起的，即，特定三链体的折叠是由焓驱动的。有利的焓贡献的大小对应于所形成的碱基-三重态堆叠的数量和强度，这是由于引入悬挂末端或环而得到堆叠贡献的帮助。三链体稳定性按以下顺序：单分子>双分子>三分子;这是根据由于包含环的额外堆叠贡献来解释的。正如预期的那样，酸性pH通过允许第三链中的胞嘧啶质子化来稳定所有三链体;然而，质子化的百分比随着分子度的降低而增加。这些结果有助于选择适当的溶液条件，用于研究含有不同比例的CGC（+）和达特碱基三联体的三联体，并有助于设计寡核苷酸序列作为靶向试剂，可以有效地与涉及人类疾病的mRNA序列反应，从而增加使用反义策略用于治疗目的的可行性。
Nucleic acid oligonucleotides (ODNs), as drugs, present an exquisite selectivity and affinity that can be used in antigene and antisense strategies for the control of gene expression. In this work we try to answer the following question: How does the molecularity of a DNA triplex affect its overall stability and melting behavior? To this end, we used a combination of temperature-dependent UV spectroscopy and calorimetric (differential scanning calorimetry) techniques to investigate the melting behavior of DNA triplexes with a similar helical stem, TC+TC+TC+T/AGAGAGA/TCTCTCT, but formed with different strand molecularity. We determined standard thermodynamic profiles and the differential binding of protons and counterions accompanying their unfolding. The formation of a triplex is accompanied by a favorable free energy term, resulting from the typical compensation of favorable enthalpy-unfavorable entropy contributions, i.e., the folding of a particular triplex is enthalpy driven. The magnitude of the favorable enthalpy contributions corresponds to the number and strength of the base-triplet stacks formed, which are helped by stacking contributions due to the incorporation of dangling ends or loops. Triplex stability is in the following order: monomolecular > bimolecular > trimolecular; this is explained in terms of additional stacking contributions due to the inclusion of loops. As expected, acidic pH stabilized all triplexes by allowing protonation of the cytosines in the third strand; however, the percentage of protonation increases as the molecularity decreases. The results help to choose adequate solution conditions for the study of triplexes containing different ratios of CGC(+) and TAT base triplets and to aid in the design of oligonucleotide sequences as targeting reagents that could effectively react with mRNA sequences involved in human diseases, thereby increasing the feasibility of using the antisense strategy for therapeutic purposes.