Kaushik Mahima, Kukreti Shrikant
Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi 110007, India.
Nucleic Acids Res. 2006 Jul 19;34(12):3511-22. doi: 10.1093/nar/gkl456. Print 2006.
Structural polymorphism of DNA is a widely accepted property. A simple addition to this perception has been our recent finding, where a single nucleotide polymorphism (SNP) site present in a quasipalindromic sequence of beta-globin LCR exhibited a hairpin-duplex equilibrium. Our current studies explore that secondary structures adopted by individual complementary strands compete with formation of a perfect duplex. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation, circular dichroism (CD) techniques, we have demonstrated the structural transitions within a perfect duplex containing 11 bp quasipalindromic stretch (TGGGG(G/C)CCCCA), to hairpins and bulge duplex forms. The extended version of the 11 bp duplex, flanked by 5 bp on both sides also demonstrated conformational equilibrium between duplex and hairpin species. Gel-electrophoresis confirms that the duplex coexists with hairpin and bulge duplex/cruciform species. Further, in CD spectra of duplexes, presence of two overlapping positive peaks at 265 and 285 nm suggest the features of A- as well as B-type DNA conformation and show oligomer concentration dependence, manifested in A --> B transition. This indicates the possibility of an architectural switching at quasipalindromic region between linear duplex to a cruciform structure. Such DNA structural variations are likely to be found in the mechanics of molecular recognition and manipulation by proteins.
DNA的结构多态性是一种被广泛认可的特性。我们最近的发现为这一认知增添了新内容，即β-珠蛋白LCR准回文序列中存在的单核苷酸多态性（SNP）位点呈现出发夹-双链体平衡。我们目前的研究探索了单个互补链所采用的二级结构与完美双链体形成之间的竞争。通过凝胶电泳、紫外（UV）-热变性、圆二色性（CD）技术，我们证明了在一个包含11个碱基对准回文片段（TGGGG(G/C)CCCCA）的完美双链体内向发夹和凸起双链体形式的结构转变。两侧各有5个碱基对的11个碱基对双链体的扩展版本也展示了双链体和发夹物种之间的构象平衡。凝胶电泳证实双链体与发夹、凸起双链体/十字形物种共存。此外，在双链体的CD光谱中，265和285纳米处两个重叠的正峰表明了A-型以及B-型DNA构象的特征，并显示出寡聚物浓度依赖性，表现为A向B的转变。这表明在准回文区域可能存在从线性双链体到十字形结构的结构转换。这种DNA结构变化很可能存在于蛋白质的分子识别和操纵机制中。
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