Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States.
J Am Chem Soc. 2017 Apr 5;139(13):4682-4689. doi: 10.1021/jacs.6b10117. Epub 2017 Mar 21.
Strands of DNA with four or more contiguous runs of 2'-deoxycytidine (dC) nucleotides have the potential to adopt i-motif folds, generally under mildly acidic conditions. Analysis of dC homo-oligonucleotide strands ranging in length from 10 to 30 nucleotides by five different pH-dependent methods identified a pattern in strand length vs stability. Beginning with dC, which does not fold, the transition pH (pH) increased with chain length with the addition of up to four nucleotides, after which the stability dramatically decreased, and the trend repeated this cycle up to dC. The analysis found dC strands of length 15, 19, 23, and 27 nucleotides (i.e., 4n-1) to have pH values >7.2 and thermal stabilities >37 °C at pH 7.0. Model studies using thymidine nucleotides to lock in i-motif loop lengths support the conclusion that the most stable dC i-motifs possess one nucleotide in each of the three loops and a core built of an even number of base pairs. The pattern identified from the model studies occurs with a frequency of four nucleotides at lengths of 15, 19, 23, and 27 in accordance with the results obtained for the dC strands. This observation led us to interrogate the human genome for dC runs. Inspection of the human genome indicates that dC runs are enriched in critical regions of the genome (promoters, UTRs, and introns), while being depleted in coding and intergenic regions, and these findings may have biological implications. Lastly, the ability to tune i-motif stabilities by the length of the strand might be harnessed for stimulus-responsive applications in DNA scaffolds, sensors, nanotechnology, and other chemical applications.
具有四个或更多连续的 2'-脱氧胞嘧啶 (dC) 核苷酸的 DNA 链有形成 i 型结构的潜力，通常在轻度酸性条件下。通过五种不同的 pH 依赖性方法对长度在 10 到 30 个核苷酸的 dC 同聚核苷酸链进行分析，确定了链长与稳定性之间的关系。从不折叠的 dC 开始，随着链长的增加，转变 pH 值 (pH) 增加至四个核苷酸，之后稳定性急剧下降，并且这种趋势重复了这个循环，直到 dC。分析发现，长度为 15、19、23 和 27 个核苷酸的 dC 链（即 4n-1）的 pH 值大于 7.2，在 pH 7.0 时的热稳定性大于 37°C。使用胸苷核苷酸锁定 i 型结构环长度的模型研究支持了这样的结论，即最稳定的 dC i 型结构在三个环中每个环都有一个核苷酸，并且核心由偶数个碱基对组成。模型研究中确定的模式以 15、19、23 和 27 个长度的 4 个核苷酸的频率出现，这与从 dC 链获得的结果一致。这一观察结果促使我们在人类基因组中寻找 dC 重复序列。对人类基因组的检查表明，dC 重复序列在基因组的关键区域（启动子、UTR 和内含子）中富集，而在编码和基因间区域中减少，这些发现可能具有生物学意义。最后，通过链长来调节 i 型结构的稳定性的能力可能会被用于 DNA 支架、传感器、纳米技术和其他化学应用中的刺激响应应用。
