Dai Jixun, Ambrus Attila, Hurley Laurence H, Yang Danzhou
College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, USA.
J Am Chem Soc. 2009 May 6;131(17):6102-4. doi: 10.1021/ja900967r.
I-motifs are four-stranded DNA secondary structures formed in C-rich DNA sequences and consist of parallel-stranded DNA duplexes zipped together in an antiparallel orientation by intercalated, hemiprotonated cytosine(+)-cytosine base pairs. I-motif structures have been indicated to form in various regions of the human genome as well as in nanotechnological applications. While NMR is a major tool for structural studies of I-motifs, the determination of the folding topologies of unimolecular I-motifs has been a challenging and arduous task using conventional NMR spectral assignment strategies, due to the inherent sequence redundancy of the C-rich strands in the formation of unimolecular I-motif structures. We report here a direct and nondestructive method that can be utilized to unambiguously determine the hemiprotonated C(+)-C base pairs and thus the folding topology of unimolecular I-motif structures formed from native C-rich DNA sequences. The reported approach uses affordable low-enrichment site-specific labeling. More significantly, the reported method can directly and unambiguously determine the equilibrating multiple conformations coexisting in a single DNA sequence, which would be a very difficult task using conventional assignment strategies. Additionally, this method can be applied to the direct detection of the base-paired thymines that are involved in the capping structures.
I-基序是在富含C的DNA序列中形成的四链DNA二级结构，由通过插入的半质子化胞嘧啶（+）-胞嘧啶碱基对以反平行方向拉链在一起的平行链DNA双链体组成。I-基序结构已被证明在人类基因组的各个区域以及纳米技术应用中形成。虽然核磁共振（NMR）是研究I-基序结构的主要工具，但由于在单分子I-基序结构形成过程中富含C的链具有固有的序列冗余性，使用传统的NMR光谱归属策略来确定单分子I-基序的折叠拓扑结构一直是一项具有挑战性和艰巨的任务。我们在此报告一种直接且无损的方法，该方法可用于明确确定半质子化的C（+）-C碱基对，从而确定由天然富含C的DNA序列形成的单分子I-基序结构的折叠拓扑结构。所报道的方法使用了经济实惠的低丰度位点特异性标记。更重要的是，所报道的方法可以直接且明确地确定存在于单个DNA序列中的平衡共存的多种构象，而使用传统的归属策略这将是一项非常困难的任务。此外，该方法可应用于直接检测参与封端结构的碱基配对胸腺嘧啶。
