Introduction
In the last decades, a variety of DNA secondary structures other than the canonical Watson–Crick duplex, have been documented. Such structural polymorphism depends on sequence, hydration, ions and/or ligands and superhelical stress; it occurs during biological processes such as replication and transcription, thus having an impact on genetic stability. [1]
在过去的几十年中，已经记录了除规范的Watson-Crick双链体以外的各种DNA二级结构。这种结构的多态性取决于序列，水合，离子和/或配体以及超螺旋应力。它在复制和转录等生物学过程中发生，因此对遗传稳定性有影响。 [1]
Non-canonical DNA structures include hairpins, cruciforms, triplexes, G-quadruplexes (G4s), and i-motifs (i-DNAs). [2–7] i DNA was first observed in 1993 for the hexamer sequence d(TCCCCC) under acidic conditions. [8]
It consists of two intercalated parallel-stranded duplexes held together by hemi-protonated cytosine–cytosine + (C:C + ) base pairs (Fig ure 1A). [8, 9]
i-DNA formation at physiological pH has been recently reported. [10, 11]
Moreover, the generation of an anti body able to detect i-DNA has proved its presence in the nucleus of human cells, arguing for regulatory roles in the genome, e.g., at proto-oncogene promoters and telomeres, [12] making this DNA structure a potential target for anticancer therapy.
Putative i-DNA-forming sequences occur in C-rich strands complementary to G-rich regions that may form G4s.
However, if the G4 counterpart folding conditions have already been extensively studied, i-DNA s optimal features for its formation near physiological pH in vitro are still under investigation.
In fact, several studies have been conducted recently to better understand the influence of external conditions, such as presence of metals [13, 14] or ligands, [15–17] molecular crowding, [11, 18, 19] cation type and ionic strength, [20] on i-DNA formation.
However, i-DNA stability also depends on sequence composition. A typical formula of an intra molecular i-DNA-forming sequence is (CnXN)3Cn, where X can be either a C or non-C (T, A, G); the presence of four C tracts (Cn) allows the generation of a C-stem, while the three spacers (XN), connect the four cytosine tracts (C-tracts) and form the loops (Figure 1 B).
Much attention has been paid to the influence of the loops length and composition as well as to the length of the C-tracts. In general, it was found that thymines confer a higher i-DNA stability compared to other non-C deoxynucleo tides. [21, 22]
Very recently, the Vorlickova s group reported a systematic investigation of sequence requirements for i-DNA formation.
They found that the lower number of residues are present in the spacers, the more i-DNA is destabilized. This is due to the loss of C:C+ base pairs as several Cs need to be incorporated into the loops to compensate for the short linkers.
非规范的DNA结构包括发夹，十字形，三链体，G-四链体（G4）和i-基序（i-DNA）。 [2-7]在酸性条件下，1993年首次发现六聚体序列d（TCCCCC）的i DNA。 [8] 它由通过半质子化的胞嘧啶-胞嘧啶+（C：C +）碱基对连接在一起的两个插入的平行链双链体组成（图1A）。 [8，9] 最近已经报道了在生理pH下i-DNA的形成。 [10，11] 此外，一种能够检测i-DNA的抗体的产生已证明其存在于人类细胞的核中，争论着其在基因组中的调控作用，例如在原癌基因启动子和端粒中的作用[12]。抗癌治疗的潜在目标。推定的i-DNA形成序列出现在富含C的链中，与可能形成G4的富含G的区域互补。但是，如果已经广泛研究了G4对应折叠条件，则仍在研究i-DNA在体外生理pH值附近形成i-DNA的最佳功能。实际上，最近进行了一些研究，以更好地了解外部条件的影响，例如金属[13、14]或配体的存在，[15-17]分子拥挤，[11、18、19]阳离子类型和离子i-DNA形成的强度[20]。
但是，i-DNA的稳定性也取决于序列的组成。分子内i-DNA形成序列的典型公式是（CnXN）3 C n，其中X可以是C或非C（T，A，G）；四个C区域（Cn）的存在允许生成C-茎，而三个间隔基（XN）连接四个胞嘧啶区域（C区域）并形成环（图1 B）。已经对环长度和组成以及C线长度的影响给予了很多关注。通常，发现与其他非C脱氧核苷酸相比，胸腺嘧啶具有更高的i-DNA稳定性。 [21，22]最近，Vorlickova小组报告了对i-DNA形成所需序列的系统研究。他们发现间隔物中存在的残基数量越少，i-DNA越不稳定。这是由于丢失了C：C +碱基对，因为需要将几个C合并到环路中以补偿短连接子。
