Duplex DNA Is Weakened in Nanoconfinement
Duplex DNA Is Weakened in Nanoconfinement
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DOI：
10.1021/jacs.0c01978
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发表时间：
2020-06-03
影响因子：
15
通讯作者：
Mao, Hanbin
中科院分区：
文献类型：
--
作者：
Jonchhe, Sagun;Pandey, Shankar;Mao, Hanbin
对于蛋白质和DNA二级结构，如g -四plex和i-motif，纳米限制可以促进它们的折叠并增加结构稳定性。然而，生理上普遍存在的B-DNA双工的性质尚未在纳米腔内阐明。在这里，我们使用一个17-bp的DNA双链，以发夹茎的形式，在DNA折纸纳米腔中探测了发夹DNA双链的折叠和展开转变。与自由溶液相比，15 × 15 nm横截面的纳米笼内DNA发夹的力学稳定性（20 - bbb90pn）和热力学稳定性（25 - >6kcal /mol）显著降低。自由能谱显示，发夹DNA双链解压缩的活化能显著降低（28 - 8 kcal/mol），而过渡态在纳米笼内向未折叠态靠拢。所有这些都表明，纳米限制在意想不到的程度上削弱了发夹DNA双链的稳定性。在包含互补端粒g -四重体（GQ）和i-基序（iM）形成序列的茎构成的DNA发夹中，GQ或iM上的Hoogsteen碱基对的形成优于DNA发夹中的Watson-Crick碱基对。这些结果揭示了DNA在纳米通道、纳米孔或各种自然或合成机器中的行为。它还阐明了在纳米空腔丰富的细胞环境中，非规范DNA在B-DNA上填充的另一种途径。
For proteins and DNA secondary structures such as G-quadruplexes and i-motifs, nanoconfinement can facilitate their folding and increase structural stabilities. However, the properties of the physiologically prevalent B-DNA duplex have not been elucidated inside the nanocavity. Using a 17-bp DNA duplex in the form of a hairpin stem, here, we probed folding and unfolding transitions of the hairpin DNA duplex inside a DNA origami nanocavity. Compared to the free solution, the DNA hairpin inside the nanocage with a 15 x 15 nm cross section showed a drastic decrease in mechanical (20 -> 9 pN) and thermodynamic (25 -> 6 kcal/mol) stabilities. Free energy profiles revealed that the activation energy of unzipping the hairpin DNA duplex decreased dramatically (28 -> 8 kcal/mol), whereas the transition state moved closer to the unfolded state inside the nanocage. All of these indicate that nanoconfinement weakens the stability of the hairpin DNA duplex to an unexpected extent. In a DNA hairpin made of a stem that contains complementary telomeric G-quadruplex (GQ) and i-motif (iM) forming sequences, formation of the Hoogsteen base pairs underlining the GQ or iM is preferred over the Watson-Crick base pairs in the DNA hairpin. These results shed light on the behavior of DNA in nanochannels, nanopores, or nanopockets of various natural or synthetic machineries. It also elucidates an alternative pathway to populate noncanonical DNA over B-DNA in the cellular environment where the nanocavity is abundant.