Radhakrishnan I, Patel D J
Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032.
Structure. 1994 Jan 15;2(1):17-32. doi: 10.1016/s0969-2126(00)00005-8.
Under certain conditions, homopyrimidine oligonucleotides can bind to complementary homopurine sequences in homopurine-homopyrimidine segments of duplex DNA to form triple helical structures. Besides having biological implications in vivo, this property has been exploited in molecular biology applications. This approach is limited by a lack of knowledge about the recognition by the third strand of pyrimidine residues in Watson-Crick base pairs.
We have therefore determined the solution structure of a pyrimidine.purine.pyrimidine (Y.RY) DNA triple helix containing a guanine residue in the third strand which was postulated to specifically recognize a thymine residue in a Watson-Crick TA base pair. The structure was solved by combining NMR-derived restraints with molecular dynamics simulations conducted in the presence of explicit solvent and counter ions. The guanine of the G-TA triple is tilted out of the plane of its target TA base pair towards the 3'-direction, to avoid a steric clash with the thymine methyl group. This allows the guanine amino protons to participate in hydrogen bonds with separate carbonyls, forming one strong bond within the G-TA triple and a weak bond to an adjacent T.AT triple. Dramatic variations in helical twist around the guanine residue lead to a novel stacking interaction. At the global level, the Y.RY DNA triplex shares several structural features with the recently solved solution structure of the R.RY DNA triplex.
The formation of a G.TA triple within an otherwise pyrimidine.purine.pyrimidine DNA triplex causes conformational realignments in and around the G.TA triple. These highlight new aspects of molecular recognition that could be useful in triplex-based approaches to inhibition of gene expression and site-specific cleavage of genomic DNA.
在特定条件下，同嘧啶寡核苷酸可与双链DNA同嘌呤 - 同嘧啶片段中的互补同嘌呤序列结合，形成三螺旋结构。除了在体内具有生物学意义外，这一特性已在分子生物学应用中得到利用。这种方法受到对沃森 - 克里克碱基对中嘧啶残基的第三条链识别缺乏了解的限制。
因此，我们确定了一种嘧啶·嘌呤·嘧啶（Y.RY）DNA三螺旋的溶液结构，该三螺旋在第三条链中含有一个鸟嘌呤残基，据推测该残基可特异性识别沃森 - 克里克TA碱基对中的胸腺嘧啶残基。通过将核磁共振衍生的约束与在明确溶剂和抗衡离子存在下进行的分子动力学模拟相结合来解析该结构。G-TA三联体中的鸟嘌呤从其目标TA碱基对的平面倾斜向3'方向，以避免与胸腺嘧啶甲基发生空间冲突。这使得鸟嘌呤氨基质子能够与单独的羰基形成氢键，在G-TA三联体内形成一个强键，并与相邻的T.AT三联体形成一个弱键。围绕鸟嘌呤残基的螺旋扭曲的显著变化导致了一种新的堆积相互作用。在整体水平上，Y.RY DNA三链体与最近解析的R.RY DNA三链体的溶液结构具有几个结构特征。
在其他方面为嘧啶·嘌呤·嘧啶DNA三链体的G.TA三联体的形成会导致G.TA三联体及其周围的构象重新排列。这些突出了分子识别的新方面，这可能有助于基于三链体的基因表达抑制和基因组DNA位点特异性切割方法。
