Loop Sequence Context Influences the Formation and Stability of the i-Motif for DNA Oligomers of Sequence (CCCXXX)4, where X = A and/or T, under Slightly Acidic Conditions
Loop Sequence Context Influences the Formation and Stability of the i-Motif for DNA Oligomers of Sequence (CCCXXX)4, where X = A and/or T, under Slightly Acidic Conditions
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DOI：
10.1021/acs.jpcb.6b04561
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发表时间：
2016-08-11
影响因子：
3.3
通讯作者：
Sheardy, Richard D.
中科院分区：
文献类型：
--
作者：
McKim, Mikeal;Buxton, Alexander;Sheardy, Richard D.
DNA的结构和稳定性高度依赖于碱基（A、G、C和T）的序列背景和制备DNA的环境（例如，缓冲液、温度、pH、离子强度）。了解影响i-基序构象的结构和稳定性的因素可以导致具有高度可调性质的DNA序列的设计。我们一直在使用光谱方法研究pH和温度对DNA序列（CCCXXX）（4）的所有排列的构象和稳定性的影响，其中X = A和/或T。所有低聚物经历从单链结构在pH 7.0的转变，在pH 5.0的i-基序构象证明了圆二色性（CD）的研究。这些折叠结构具有通过5 '-XXX-3'环连接的堆叠的C：CH+碱基对。虽然在过渡的中点的pH值（pH值（mp））略有不同的环序列，pH值和log K之间的联系质子诱导的过渡是高度环序列依赖性。当温度从25 ℃升高至95 ℃时，所有低聚物在pH 5.0下也经历热诱导的i-基序至单链的转变。在该转变的中点处的温度（T-m）也高度依赖于环序列上下文效应。对于八种可能的排列中的七种，pH诱导的和热诱导的转变似乎是高度合作的和两种状态。通过范特霍夫方法的CD光学熔解曲线的分析揭示了序列依赖的热力学参数的展开以及。总之，这些数据表明，i-基序构象表现出精致的敏感性，以环序列上下文的形成和稳定性。
The structure and stability of DNA is highly dependent upon the sequence context of the bases (A, G, C, and T) and the environment under which the DNA is prepared (e.g., buffer, temperature, pH, ionic strength). Understanding the factors that influence structure and stability of the i-motif conformation can lead to the design of DNA sequences with highly tunable properties. We have been investigating the influence of pH and temperature on the conformations and stabilities for all permutations of the DNA sequence (CCCXXX)(4), where X = A and/or T, using spectroscopic approaches. All oligomers undergo transitions from single-stranded structures at pH 7.0 to i-motif conformations at pH 5.0 as evidenced by circular dichroism (CD) studies. These folded structures possess stacked C:CH+ base pairs joined by loops of 5'-XXX-3'. Although the pH at the midpoint of the transition (pH(mp)) varies slightly with loop sequence, the linkage between pH and log K for the proton induced transition is highly loop sequence dependent. All oligomers also undergo the thermally induced i-motif to single-strand transition at pH 5.0 as the temperature is increased from 25 to 95 degrees C. The temperature at the midpoint of this transition (T-m) is also highly dependent on loop sequence context effects. For seven of eight possible permutations, the pH induced, and thermally induced transitions appear to be highly cooperative and two state. Analysis of the CD optical melting profiles via a van't Hoff approach reveals sequence-dependent thermodynamic parameters for the unfolding as well. Together, these data reveal that the i-motif conformation exhibits exquisite sensitivity to loop sequence context with respect to formation and stability.