Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489, Greifswald, Germany.
Chemistry. 2024 May 23;30(29):e202400722. doi: 10.1002/chem.202400722. Epub 2024 Apr 9.
A guanine-rich oligonucleotide based on a human telomeric sequence but with the first three-nucleotide intervening stretch replaced by a putative 15-nucleotide hairpin-forming sequence shows a pH-dependent folding into different quadruplex-duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair-type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem-loop occurs. NMR-derived high-resolution structures reveal that an adenine protonation is prerequisite for the formation of a non-canonical base quartet, capping the outer G-tetrad at the quadruplex-duplex interface and stabilizing the antiparallel chair conformation in an acidic environment. Being directly associated with interactions at the quadruplex-duplex interface, this unique pH-dependent topological transition is fully reversible. Coupled with a conformation-sensitive optical readout demonstrated as a proof of concept using the fluorescent dye thiazole orange, the present quadruplex-duplex hybrid architecture represents a potentially valuable pH-sensing system responsive in a physiological pH range of 7±1.
基于人类端粒序列的富含鸟嘌呤的寡核苷酸，但前三个核苷酸的间隔区被一个假定的 15 个核苷酸发夹形成序列取代，在含有钾的缓冲液中显示出 pH 依赖性折叠成不同的四链体-双链杂交体。在略酸性 pH 下，四链体结构域采用椅式构象。随着 pH 的增加，会发生一种转变，其中点接近中性 pH，形成主要和次要（3+1）杂交拓扑结构，其中双链茎环呈同轴堆叠或正交取向。NMR 衍生的高分辨率结构表明，腺嘌呤质子化是形成非规范碱基四联体的前提，在外层 G-四联体与四链体-双链体界面处封端，并在酸性环境中稳定反平行椅式构象。与四链体-双链体界面的相互作用直接相关，这种独特的 pH 依赖性拓扑转变是完全可逆的。结合构象敏感的光学读出，使用荧光染料噻唑橙作为概念验证进行证明，目前的四链体-双链杂交结构代表了一种潜在有价值的 pH 感应系统，可在生理 pH 范围 7±1 内响应。
