金属离子驱动的DNA分子折叠及其协助下的链替换反应
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摘要
富含胸腺嘧啶(T)碱基与胞嘧啶碱基(C)的长单链DNA分子是一种柔性很强的生物大分子。它能够在汞离子与银离子的驱动下通过形成T-Hg-T以及C-Ag-C的金属-碱基对从而发生分子内折叠形成特殊结构。在本论文中,我们采用等温滴定微量热技术(ITC)监测了汞离子与富T碱基长单链DNA的相互作用并测定了二者结合的各项热力学参数。结合圆二色谱的结果我们发现这种相互作用是放热过程且伴随着熵减小——体系由无序化转向有序化的过程——长链富T碱基DNA分子在汞离子驱动下能够发生自我折叠形成发夹结构。同时我们发现,外界环境促发DNA无规单链强行折叠成发夹的过程中,DNA趋向于尽量使得发夹双臂的链接环存有4或5个碱基的链段。
进一步的,我们利用得出的DNA单链发夹折叠原则设计了一种富含T、C碱基的DNA序列。我们利用ITC、CD、荧光等技术手段探究了这种DNA序列在汞离子与银离子的驱动下发生构象转变的机理,这种探究拓展了我们对于金属-DNA复合物的理解。DNA在这两种离子的驱动下都能发生分子折叠成为发夹。这种分子折叠存在着两种路径——发生在发夹尾端的高熵变的路径与发生在靠近发夹环内部的低熵变路径。这两种路径的最终产物都只有一个。与汞离子反应后的DNA-Hg复合物能与银离子发生相互作用形成更为稳定而完美的发夹结构,而这种结合就发生在发夹不完美的部分。UV滴定数据佐证了ITC的结合位点数是正确的,CD与荧光的表征手段验证了中间过程与最终形态的发夹构象。
更改离子的加入顺序,DNA会有不同的发夹折叠方式,这对于离子驱动的DNA分子机器与含有离子参与的DNA纳米技术都有着非凡的意义。DNA的折叠是个非常复杂的过程,同样的离子改变加样顺序结果都会不同。在银离子条件下,DNA采取了一种新发现的不同于传统的C-Ag-C的金属-碱基配对：T-Ag-C。这种配对方式形成了更多的金属-碱基对,使得DNA采取了一种不完美的发夹折叠方式。它同时也封闭住了体系中大多数的T碱基,在大大提升了DNA与银离子结合能力的同时,也大大的降低甚至是基本上杜绝了DNA与汞离子反应的活性——汞离子的后续加入不再能使DNA链段发生有效的折叠。这种发夹结构是不完美的但是却是稳定的。
最后一章中,我们提出了一种新型的可用于调控DNA链替换反应速率的新方法。我们引入了一个全新的概念：metallo-toehold,并利用其构建了汞离子驱动DNA链替换反应的体系。我们发现利用汞离子浓度的不同我们可以很方便且很灵敏的对单一目标DNA体系调控其链替换反应的速率。通过形成稳定的T-Hg-T金属碱基对弥补了碱基错配所带来的障碍,合适的汞离子浓度会极大地促进DNA链替换反应的进行。但是物极必反,过高浓度的汞离子浓度会因为封闭T碱基而阻滞DNA分支迁移的进行。这种抑制作用可以随着汞离子被其他强结合物质(如DTT)捕缚而得到解放。这种在汞离子不同浓度下,metallo-toehold DNA体系的特性让我们调控其链替换反应速度与效率提供了可能。这种DNA链替换反应驱动体现出了极佳的离子选择性。我们还可以通过对链段的设计实现其他特征金属离子(如银离子)对DNA链替换反应的驱动。该方法不仅在离子检测上有着一席之地,还具有着构建金属-DNA纳米结构的潜质。由于与当今两大热门领域：离子-DNA相互作用以及DNA链替换反应联系紧密,因此在DNA分子机器领域将大有可为。
Thymine-cytosine-rich DNA is a kind of strongly flexible biopolymer. It can specifically bind with Hg(Ⅱ) or Ag(Ⅰ) ions to generate metal-mediated base pairs (T-Hg-T and C-Ag-C) in hairpin-like structure from a random coil structure. Isothermal titration calorimetry experiments were performed to reveal the detail of whole binding process. The observed negative ΔH was favorable for the specific binding between the Hg(Ⅱ) ion and the T:T mismatched base pair, while negative AS values demonstrate that the oligonucleotide conformation changes from a random coil to a regular, stable hairpin when Hg(Ⅱ) ions are added. Moreover, we found that in the process of hairpin folding from random coil induced by external environment, DNA tended to make the link ring of hairpin a segment of four or five bases.
Furthermore, we reported the mechanism of the formation of hairpin structure of thymine-cytosine-rich oligonucleotides induced by Hg(Ⅱ) and Ag(Ⅰ) ions. The study also confirmed and extended our understanding of the nature of metal-DNA adducts. Designed thymine-cytosine-rich oligonucleotides can significantly change in structure upon the addition of Hg(Ⅱ) ions, which converts the random coil single-strand to an anti-parallel hairpin-like folded structure. The ITC-derived thermodynamic parameters exhibited two possible pathways:one with the binding in the inner hairpin and another with the binding in the terminal hairpin. These two different binding pathways resulted in identical final products. Obvious results were observed when Ag(Ⅰ) ions were then added, confirming the existence of the spacing C-base loop of the hairpin-like formation of the Hg-DNA complex as well as the interactions between the Ag(Ⅰ) ions and the C:C mismatched base pairs that highly strengthened the structure. The result demonstrates that isothermal titration calorimetry is a powerful tool to study mechanism of DNA folding, induced by ions as well. Excellent agreement was found in coupled CD and UV measurements.
DNA folding is a very complex process. The same ion, different order will make different results in DNA folding. Under the condition of silver ions, DNA had adopted a new found metallo-basepair, T-Ag-C, which is totally different from the traditional C-Ag-C pair. T-Ag-C formed more metallo-basepairs, which also blocked most of the T bases of the DNA. It greatly promoted the ability of silver ions in combination with DNA, but at the same time, reduced reactivity of DNA on mercury ions. The hairpin structure is not perfect but it is stable.
In the last chapter, we present for the first time a new concept:metallo-toeholds. We have discovered that metal ions (Hg2+) that specifically interact with mismatched base pairs (T:T) can be employed with metallo-toeholds to intentionally trigger strand displacement in DNA devices. Using this concept, we have developed a mechanism that allows increased control over the kinetics of strand displacement. Using metal ions (Hg2+) as a regulatory factor, the metallo-toeholds allowed effective tuning of the rate of strand displacement. Through additional design of the sequence of the toeholds, we could also regulate the range of reaction rates. Mismatched base pairs between the toehold and displacement domains induced an obstacle between toehold binding and strand displacement, slowing down the reaction. The insertion of Hg2+ions provided the metallo-toeholds with perfect complementary, driving the strand displacement successfully. Too many Hg2+ions presumably led to blocking of the T sites on the toeholds, impeding the reaction. But the blocking system could be emancipated by dithiothreitol (DTT), which can sequestrate Hg2+ions in solution. Strand displacement has already been used as the basis for the operation of many synthetic molecular machines. We expect that this novel concept might be applicable to strategies for the design of molecular machines that function based on toehold-mediated strand displacement reactions in the presence of metal ions.
进一步的,我们利用得出的DNA单链发夹折叠原则设计了一种富含T、C碱基的DNA序列。我们利用ITC、CD、荧光等技术手段探究了这种DNA序列在汞离子与银离子的驱动下发生构象转变的机理,这种探究拓展了我们对于金属-DNA复合物的理解。DNA在这两种离子的驱动下都能发生分子折叠成为发夹。这种分子折叠存在着两种路径——发生在发夹尾端的高熵变的路径与发生在靠近发夹环内部的低熵变路径。这两种路径的最终产物都只有一个。与汞离子反应后的DNA-Hg复合物能与银离子发生相互作用形成更为稳定而完美的发夹结构,而这种结合就发生在发夹不完美的部分。UV滴定数据佐证了ITC的结合位点数是正确的,CD与荧光的表征手段验证了中间过程与最终形态的发夹构象。
更改离子的加入顺序,DNA会有不同的发夹折叠方式,这对于离子驱动的DNA分子机器与含有离子参与的DNA纳米技术都有着非凡的意义。DNA的折叠是个非常复杂的过程,同样的离子改变加样顺序结果都会不同。在银离子条件下,DNA采取了一种新发现的不同于传统的C-Ag-C的金属-碱基配对：T-Ag-C。这种配对方式形成了更多的金属-碱基对,使得DNA采取了一种不完美的发夹折叠方式。它同时也封闭住了体系中大多数的T碱基,在大大提升了DNA与银离子结合能力的同时,也大大的降低甚至是基本上杜绝了DNA与汞离子反应的活性——汞离子的后续加入不再能使DNA链段发生有效的折叠。这种发夹结构是不完美的但是却是稳定的。
最后一章中,我们提出了一种新型的可用于调控DNA链替换反应速率的新方法。我们引入了一个全新的概念：metallo-toehold,并利用其构建了汞离子驱动DNA链替换反应的体系。我们发现利用汞离子浓度的不同我们可以很方便且很灵敏的对单一目标DNA体系调控其链替换反应的速率。通过形成稳定的T-Hg-T金属碱基对弥补了碱基错配所带来的障碍,合适的汞离子浓度会极大地促进DNA链替换反应的进行。但是物极必反,过高浓度的汞离子浓度会因为封闭T碱基而阻滞DNA分支迁移的进行。这种抑制作用可以随着汞离子被其他强结合物质(如DTT)捕缚而得到解放。这种在汞离子不同浓度下,metallo-toehold DNA体系的特性让我们调控其链替换反应速度与效率提供了可能。这种DNA链替换反应驱动体现出了极佳的离子选择性。我们还可以通过对链段的设计实现其他特征金属离子(如银离子)对DNA链替换反应的驱动。该方法不仅在离子检测上有着一席之地,还具有着构建金属-DNA纳米结构的潜质。由于与当今两大热门领域：离子-DNA相互作用以及DNA链替换反应联系紧密,因此在DNA分子机器领域将大有可为。
Thymine-cytosine-rich DNA is a kind of strongly flexible biopolymer. It can specifically bind with Hg(Ⅱ) or Ag(Ⅰ) ions to generate metal-mediated base pairs (T-Hg-T and C-Ag-C) in hairpin-like structure from a random coil structure. Isothermal titration calorimetry experiments were performed to reveal the detail of whole binding process. The observed negative ΔH was favorable for the specific binding between the Hg(Ⅱ) ion and the T:T mismatched base pair, while negative AS values demonstrate that the oligonucleotide conformation changes from a random coil to a regular, stable hairpin when Hg(Ⅱ) ions are added. Moreover, we found that in the process of hairpin folding from random coil induced by external environment, DNA tended to make the link ring of hairpin a segment of four or five bases.
Furthermore, we reported the mechanism of the formation of hairpin structure of thymine-cytosine-rich oligonucleotides induced by Hg(Ⅱ) and Ag(Ⅰ) ions. The study also confirmed and extended our understanding of the nature of metal-DNA adducts. Designed thymine-cytosine-rich oligonucleotides can significantly change in structure upon the addition of Hg(Ⅱ) ions, which converts the random coil single-strand to an anti-parallel hairpin-like folded structure. The ITC-derived thermodynamic parameters exhibited two possible pathways:one with the binding in the inner hairpin and another with the binding in the terminal hairpin. These two different binding pathways resulted in identical final products. Obvious results were observed when Ag(Ⅰ) ions were then added, confirming the existence of the spacing C-base loop of the hairpin-like formation of the Hg-DNA complex as well as the interactions between the Ag(Ⅰ) ions and the C:C mismatched base pairs that highly strengthened the structure. The result demonstrates that isothermal titration calorimetry is a powerful tool to study mechanism of DNA folding, induced by ions as well. Excellent agreement was found in coupled CD and UV measurements.
DNA folding is a very complex process. The same ion, different order will make different results in DNA folding. Under the condition of silver ions, DNA had adopted a new found metallo-basepair, T-Ag-C, which is totally different from the traditional C-Ag-C pair. T-Ag-C formed more metallo-basepairs, which also blocked most of the T bases of the DNA. It greatly promoted the ability of silver ions in combination with DNA, but at the same time, reduced reactivity of DNA on mercury ions. The hairpin structure is not perfect but it is stable.
In the last chapter, we present for the first time a new concept:metallo-toeholds. We have discovered that metal ions (Hg2+) that specifically interact with mismatched base pairs (T:T) can be employed with metallo-toeholds to intentionally trigger strand displacement in DNA devices. Using this concept, we have developed a mechanism that allows increased control over the kinetics of strand displacement. Using metal ions (Hg2+) as a regulatory factor, the metallo-toeholds allowed effective tuning of the rate of strand displacement. Through additional design of the sequence of the toeholds, we could also regulate the range of reaction rates. Mismatched base pairs between the toehold and displacement domains induced an obstacle between toehold binding and strand displacement, slowing down the reaction. The insertion of Hg2+ions provided the metallo-toeholds with perfect complementary, driving the strand displacement successfully. Too many Hg2+ions presumably led to blocking of the T sites on the toeholds, impeding the reaction. But the blocking system could be emancipated by dithiothreitol (DTT), which can sequestrate Hg2+ions in solution. Strand displacement has already been used as the basis for the operation of many synthetic molecular machines. We expect that this novel concept might be applicable to strategies for the design of molecular machines that function based on toehold-mediated strand displacement reactions in the presence of metal ions.
引文
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