石墨烯纳米孔DNA测序的分子动力学模拟研究
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摘要
自从人类基因组图谱完成以来,寻找快速而又廉价的DNA测序方法就一直是我们追求的目标。DNA测序指的是分析特定DNA片段的碱基序列,也就是腺嘌呤(A)、胸腺嘧啶(T)、胞嘧啶(C)与鸟嘌呤(G)的排列方式。快速的DNA测序方法极大地推动了生物学和医学领域的研究和发现,其在基础生物学以及众多的应用领域如诊断,生物技术,法医生物学,生物系统学等中均有涉及。其中,固态纳米孔(solid state nanopore)测序被认为是下一代比较有潜力的快速测序方法,在众多的固态纳米孔中,石墨烯(graphene)片层由于其特有的力学性质以及物理性质而特别引人注目。DNA经过纳米孔道或者管道的移位过程是一个集物理,化学,生物等学科于一身的课题,其非常重要却又异常复杂。如溶液的影响,孔厚度以及孔大小对于测序问题的影响等等。利用分子动力学模拟研究DNA分子在纳米孔道中的移位以及动力学过程已经展现出了强大的优势,成为了除实验手段外有力的研究工具。
本论文利用分子动力学(molecular dynamics, MD)先研究单层石墨烯片层的纳米孔道对DNA分子测序的影响因素,这些影响因素包括纳米孔道的大小,溶液离子浓度,外界电场强度等等。在此基础上,我们研究了多层石墨烯片层的纳米孔道对DNA分子测序的影响,主要研究了层数对于DNA分子测序的影响。随后,我们用操控式分子动力学(steered molecular dynamics, SMD)模拟了将单链DNA (single strand DNA, ssDNA)从不同形状构型的石墨烯纳米孔道拉伸出去,研究不同碱基是否可以根据不同的力特征峰值来分辨。最后我们考察了是否可以用不同碱基在纳米孔中的移位时间不同而对DNA测序。本论文的主要研究结果如下：
1.研究不同直径的单层石墨烯纳米孔,盐浓度以及偏压对于poly(A-T)45在纳米孔中移位过程的阻滞电流信号的影响,我们发现纳米孔的直径是影响纳米孔测序精度的关键因素。DNA分子的转移速度随着偏压的减小而减少,从而延长DNA分子在纳米孔道中的滞留时间,使得检测时间有所延长。离子浓度对于电流信号的影响主要包括DNA分子和离子两个方面,在低离子浓度时,DNA穿过纳米孔时的电流比不穿孔时高,然而在高浓度时情况正好相反。通过研究这些因素,我们构建了非占据纳米孔的面积与电流信号之间的关系模型,并且证明非占据纳米孔面积是影响检测DNA穿孔时的电流信号的最重要因素。
2.通过对DNA分子在多层石墨烯纳米孔道中穿孔行为的研究,我们发现多层石墨烯对于DNA测序在精度方面优于单层石墨烯。首先石墨烯层数在一定范围内的增加(1-7层)使得DNA分子穿孔的时间增长。其次,DNA分子通过多层石墨烯时检测电流会有一个阶梯形的变化从而使得电流信号的丰富度增加。在这些研究的基础上,我们构建了检测信号电流与纳米孔体积之间的理论模型,发现检测信号电流与非占据纳米孔道体积息息相关,同时我们的研究还表明DNA分子穿孔的动力学行为与碱基和石墨烯片层之间的相互作用能息息相关。
3.与那些较大的石墨烯纳米孔(>3nm)相比,DNA分子在较小的纳米孔(<2nm)中的穿孔行为显得尤为特殊。由于双链DNA分子的直径较大(~1.8nm),所以其很难自由的通过直径小于1.6nm的纳米孔。通过施加外力,包含有A,T,C,G四种碱基以及5-甲基化胞嘧啶的单链DNA分子片段在通过不同形状的直径都为lnm的石墨烯纳米孔时,不同的碱基在圆形纳米孔中展现出很好的单碱基精度的力的特征峰值；然而,在其他非对称性的纳米孔中(三角形,正方形,菱形)均不能实现。这个表明纳米孔的对称性对于实现石墨烯纳米孔在DNA测序上应用是极其重要以及关键的。
4.在低电场强度下,由于尺度合适的石墨烯纳米孔对于不同碱基的识别性不同,不同碱基穿过石墨烯纳米孔的保留时间有明显的区别,因此我们通过不同碱基在石墨烯纳米孔中的保留时间不同而测序。
Cheap and fast method to sequence DNA needs to be developed due to the increasing need in DNA sequencing. DNA sequencing is to obtain the composition order of DNA which is composed by A (adenine), T (thymine), C (cytosine), and G (guanine). Fast development of DNA sequencing allows us to better understand the relationships among diseases, inheritance, and individuality. Solid state nanopore has been recommended as the next generation platform for DNA sequencing due to its low-cost and high-throughput. Nanopores fabricated from graphene sheets are shown to be extremely thin and structurally robust and have been extensively used in DNA detection in recent years. The translocation process of DNA through a nanopore, which is related to physics, chemistry, and biology, is very important but very complicated issue. Many factors including ion concentration, thickness of the nanopore, nanopore diameter et al could affect the resolution of DNA sequencing. Molecular dynamics (MD) simulation has been another useful tool to study the DNA translocation in nanopore besides experiments.
In this thesis, the DNA translocation under different conditions including different ion concentration, applied voltage, and nanopore diameter through single layer graphene nanopore was studied. Based on this, DNA translocation through multilayer graphene nanopore varied from1to9layers was investigated, and the blockade current and translocation time were analyzed in detail. After that, the ssDNA molecules were pulled out from the smaller different geometry graphene nanopore. The characteristic peak value by different bases was evaluates in different geometry nanopore. In conclusion, the major contributions of this work are as follows:
1. At first, the effects of the bias voltage on the DNA translocation time was investigated, and smaller applied voltage could extend the DNA translocation time in monolayer graphene nanopore. The salt concentration on the corresponding ionic current was studied. In lower ionic concentration (<0.3M), the current was increased as DNA translocation through nanopore; however, the current was decreased as DNA translocation through nanopore in higher ionic concentration (>0.5M). It depends on the contribution of DNA and ions to the current. In addition, a theoretical model was proposed to explore the relationship between the current and the occupied nanopore area. We demonstrated that the DNA translocation time can be prolonged by narrowing the diameter of a nanopore properly, and the reduction of the blockade current depends on the ratio of the unoccupied nanopore area to the total nanopore area.
2. Secondly, DNA translocation through multilayer graphene nanopore was studied to achieve single-base resolution by molecular dynamics simulation. We show that the DNA translocation time could be extended by increasing the graphene layers up to a moderate number (7) and that the current in DNA translocation undergoes a stepwise change upon DNA going through an MLG nanopore. A model was built to account for the relationship between the current change and the unoccupied volume of the MLG nanopore. We demonstrate that the blockade current is closely related to the unoccupied volume. The dynamics of DNA translocation depends specifically on the interaction of nucleotides with the graphene sheet. Thus, our study indicates that the resolution of DNA detection could be improved by increasing the number of graphene layers in a certain range and by modifying the surface of graphene nanopores.
3. Thirdly, the effect of graphene nanopore geometry on the DNA sequence has been assessed by steered molecular dynamics. The DNA fragments including A, T, C, G and5-methylcytosine (MC) was pulled out in different geometry graphene nanopores with diameter down to～1nm by steered molecular dynamics simulation. We demonstrate the bases (A, T, C, G, and MC) could be indentified in single-base resolution by the force peak characteristic value in circle graphene nanopore but not in other geometry graphene nanopores. Axisymmetric nanopore is much better suited to DNA sequence detection via force curve than asymmetric nanopore. It implies that the graphene nanopore surface should be modified as asymmetric as possible to sequence DNA by an atomic force microscope or optical tweezers. It helps us to understand low-cost and time-efficient DNA sequence in narrow nanopore more.
4. At last, the translocation time of different nucleotides to pass through graphene nanopore with a certain diameter was investigated. The translocation time is different for different bases under low electric field. The DNA could be sequenced by retain time to pass through graphene nanopore.
本论文利用分子动力学(molecular dynamics, MD)先研究单层石墨烯片层的纳米孔道对DNA分子测序的影响因素,这些影响因素包括纳米孔道的大小,溶液离子浓度,外界电场强度等等。在此基础上,我们研究了多层石墨烯片层的纳米孔道对DNA分子测序的影响,主要研究了层数对于DNA分子测序的影响。随后,我们用操控式分子动力学(steered molecular dynamics, SMD)模拟了将单链DNA (single strand DNA, ssDNA)从不同形状构型的石墨烯纳米孔道拉伸出去,研究不同碱基是否可以根据不同的力特征峰值来分辨。最后我们考察了是否可以用不同碱基在纳米孔中的移位时间不同而对DNA测序。本论文的主要研究结果如下：
1.研究不同直径的单层石墨烯纳米孔,盐浓度以及偏压对于poly(A-T)45在纳米孔中移位过程的阻滞电流信号的影响,我们发现纳米孔的直径是影响纳米孔测序精度的关键因素。DNA分子的转移速度随着偏压的减小而减少,从而延长DNA分子在纳米孔道中的滞留时间,使得检测时间有所延长。离子浓度对于电流信号的影响主要包括DNA分子和离子两个方面,在低离子浓度时,DNA穿过纳米孔时的电流比不穿孔时高,然而在高浓度时情况正好相反。通过研究这些因素,我们构建了非占据纳米孔的面积与电流信号之间的关系模型,并且证明非占据纳米孔面积是影响检测DNA穿孔时的电流信号的最重要因素。
2.通过对DNA分子在多层石墨烯纳米孔道中穿孔行为的研究,我们发现多层石墨烯对于DNA测序在精度方面优于单层石墨烯。首先石墨烯层数在一定范围内的增加(1-7层)使得DNA分子穿孔的时间增长。其次,DNA分子通过多层石墨烯时检测电流会有一个阶梯形的变化从而使得电流信号的丰富度增加。在这些研究的基础上,我们构建了检测信号电流与纳米孔体积之间的理论模型,发现检测信号电流与非占据纳米孔道体积息息相关,同时我们的研究还表明DNA分子穿孔的动力学行为与碱基和石墨烯片层之间的相互作用能息息相关。
3.与那些较大的石墨烯纳米孔(>3nm)相比,DNA分子在较小的纳米孔(<2nm)中的穿孔行为显得尤为特殊。由于双链DNA分子的直径较大(~1.8nm),所以其很难自由的通过直径小于1.6nm的纳米孔。通过施加外力,包含有A,T,C,G四种碱基以及5-甲基化胞嘧啶的单链DNA分子片段在通过不同形状的直径都为lnm的石墨烯纳米孔时,不同的碱基在圆形纳米孔中展现出很好的单碱基精度的力的特征峰值；然而,在其他非对称性的纳米孔中(三角形,正方形,菱形)均不能实现。这个表明纳米孔的对称性对于实现石墨烯纳米孔在DNA测序上应用是极其重要以及关键的。
4.在低电场强度下,由于尺度合适的石墨烯纳米孔对于不同碱基的识别性不同,不同碱基穿过石墨烯纳米孔的保留时间有明显的区别,因此我们通过不同碱基在石墨烯纳米孔中的保留时间不同而测序。
Cheap and fast method to sequence DNA needs to be developed due to the increasing need in DNA sequencing. DNA sequencing is to obtain the composition order of DNA which is composed by A (adenine), T (thymine), C (cytosine), and G (guanine). Fast development of DNA sequencing allows us to better understand the relationships among diseases, inheritance, and individuality. Solid state nanopore has been recommended as the next generation platform for DNA sequencing due to its low-cost and high-throughput. Nanopores fabricated from graphene sheets are shown to be extremely thin and structurally robust and have been extensively used in DNA detection in recent years. The translocation process of DNA through a nanopore, which is related to physics, chemistry, and biology, is very important but very complicated issue. Many factors including ion concentration, thickness of the nanopore, nanopore diameter et al could affect the resolution of DNA sequencing. Molecular dynamics (MD) simulation has been another useful tool to study the DNA translocation in nanopore besides experiments.
In this thesis, the DNA translocation under different conditions including different ion concentration, applied voltage, and nanopore diameter through single layer graphene nanopore was studied. Based on this, DNA translocation through multilayer graphene nanopore varied from1to9layers was investigated, and the blockade current and translocation time were analyzed in detail. After that, the ssDNA molecules were pulled out from the smaller different geometry graphene nanopore. The characteristic peak value by different bases was evaluates in different geometry nanopore. In conclusion, the major contributions of this work are as follows:
1. At first, the effects of the bias voltage on the DNA translocation time was investigated, and smaller applied voltage could extend the DNA translocation time in monolayer graphene nanopore. The salt concentration on the corresponding ionic current was studied. In lower ionic concentration (<0.3M), the current was increased as DNA translocation through nanopore; however, the current was decreased as DNA translocation through nanopore in higher ionic concentration (>0.5M). It depends on the contribution of DNA and ions to the current. In addition, a theoretical model was proposed to explore the relationship between the current and the occupied nanopore area. We demonstrated that the DNA translocation time can be prolonged by narrowing the diameter of a nanopore properly, and the reduction of the blockade current depends on the ratio of the unoccupied nanopore area to the total nanopore area.
2. Secondly, DNA translocation through multilayer graphene nanopore was studied to achieve single-base resolution by molecular dynamics simulation. We show that the DNA translocation time could be extended by increasing the graphene layers up to a moderate number (7) and that the current in DNA translocation undergoes a stepwise change upon DNA going through an MLG nanopore. A model was built to account for the relationship between the current change and the unoccupied volume of the MLG nanopore. We demonstrate that the blockade current is closely related to the unoccupied volume. The dynamics of DNA translocation depends specifically on the interaction of nucleotides with the graphene sheet. Thus, our study indicates that the resolution of DNA detection could be improved by increasing the number of graphene layers in a certain range and by modifying the surface of graphene nanopores.
3. Thirdly, the effect of graphene nanopore geometry on the DNA sequence has been assessed by steered molecular dynamics. The DNA fragments including A, T, C, G and5-methylcytosine (MC) was pulled out in different geometry graphene nanopores with diameter down to～1nm by steered molecular dynamics simulation. We demonstrate the bases (A, T, C, G, and MC) could be indentified in single-base resolution by the force peak characteristic value in circle graphene nanopore but not in other geometry graphene nanopores. Axisymmetric nanopore is much better suited to DNA sequence detection via force curve than asymmetric nanopore. It implies that the graphene nanopore surface should be modified as asymmetric as possible to sequence DNA by an atomic force microscope or optical tweezers. It helps us to understand low-cost and time-efficient DNA sequence in narrow nanopore more.
4. At last, the translocation time of different nucleotides to pass through graphene nanopore with a certain diameter was investigated. The translocation time is different for different bases under low electric field. The DNA could be sequenced by retain time to pass through graphene nanopore.
引文
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