Hysteresis in poly‐2′‐deoxycytidine i‐motif folding is impacted by the method of analysis as well as loop and stem lengths,Biopolymers

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Hysteresis in poly‐2′‐deoxycytidine i‐motif folding is impacted by the method of analysis as well as loop and stem lengths
Biopolymers ( IF 3.2 ) Pub Date : 2020-07-18 , DOI: 10.1002/bip.23389
R Aaron Rogers ₁ , Madeline R Meyer ₁ , Kayla M Stewart ₁ , Gabriela M Eyring ₁ , Aaron M Fleming ₁ , Cynthia J Burrows ₁

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In DNA, i‐motif (iM) folds occur under slightly acidic conditions when sequences rich in 2′‐deoxycytidine (dC) nucleotides adopt consecutive dC self base pairs. The pH stability of an iM is defined by the midpoint in the pH transition (pHT) between the folded and unfolded states. Two different experiments to determine pHT values via circular dichroism (CD) spectroscopy were performed on poly‐dC iMs of length 15, 19, or 23 nucleotides. These experiments demonstrate two points: (1) pHT values were dependent on the titration experiment performed, and (2) pH‐induced denaturing or annealing processes produced isothermal hysteresis in the pHT values. These results in tandem with model iMs with judicious mutations of dC to thymidine to favor particular folds found the hysteresis was maximal for the shorter poly‐dC iMs and those with an even number of base pairs, while the hysteresis was minimal for longer poly‐dC iMs and those with an odd number of base pairs. Experiments to follow the iM folding via thermal changes identified thermal hysteresis between the denaturing and annealing cycles. Similar trends were found to those observed in the CD experiments. The results demonstrate that the method of iM analysis can impact the pHT parameter measured, and hysteresis was observed in the pHT and Tm values.

中文翻译：

聚-2'-脱氧胞苷 i-基序折叠的滞后受分析方法以及环和茎长度的影响

在 DNA 中，当富含 2'-脱氧胞苷 (dC) 核苷酸的序列采用连续的 dC 自身碱基对时，i-motif (iM) 折叠发生在弱酸性条件下。iM 的 pH 稳定性由折叠和未折叠状态之间的 pH 转变 (pHT) 的中点定义。在长度为 15、19 或 23 个核苷酸的 poly-dC iM 上进行了两个不同的实验，通过圆二色性 (CD) 光谱确定 pHT 值。这些实验证明了两点：（1）pHT 值取决于所进行的滴定实验，以及（2）pH 诱导的变性或退火过程在 pHT 值中产生等温滞后。这些结果与具有 dC 到胸苷的明智突变以有利于特定折叠的模型 iM 串联，发现对于较短的 poly-dC iM 和具有偶数个碱基对的那些，滞后最大，而对于较长的 poly-dC，滞后最小iMs 和具有奇数个碱基对的那些。通过热变化跟踪 iM 折叠的实验确定了变性和退火循环之间的热滞后。发现了与 CD 实验中观察到的趋势相似的趋势。结果表明，iM 分析方法可以影响测量的 pHT 参数，并且在 pHT 和 Tm 值中观察到滞后。通过热变化跟踪 iM 折叠的实验确定了变性和退火循环之间的热滞后。发现了与 CD 实验中观察到的趋势相似的趋势。结果表明，iM 分析方法可以影响测量的 pHT 参数，并且在 pHT 和 Tm 值中观察到滞后。通过热变化跟踪 iM 折叠的实验确定了变性和退火循环之间的热滞后。发现了与 CD 实验中观察到的趋势相似的趋势。结果表明，iM 分析方法可以影响测量的 pHT 参数，并且在 pHT 和 Tm 值中观察到滞后。

更新日期：2020-07-18

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