代尔夫特理工大学教授讲述单分子生物学纳米技术：从纳米孔蛋白质测序到染色体组织

直播时间：2024年8月23日（周五）20:00-21:30

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北京时间2024年8月23日晚八点，iCANX Talks 第200期邀请到了代尔夫特理工大学Cees Dekker教授进行分享！此外，东南大学司伟、南京大学应佚伦、东南大学章寅三位教授担任研讨嘉宾，特文特大学christian A. Niihuis教授担任主持人。

这将是一场汇聚顶尖学者的盛会，共同探讨前沿科技与学术挑战！更多精彩，敬请期待！

【嘉宾介绍】

Dae-Hyeong KimCees Dekker

代尔夫特理工大学

Nanotechnology for single-molecule biology: from nanopore protein sequencing to chromosome organization

【Abstract】

Nanotechnology offers fantastic opportunities to contribute to biology. I will present some recent examples from my lab where nanotech single-molecule tools are used to unravel the biology of cells down to the single-molecule level.

1. A DNA origami turbine powered by nanoscale flow [1]

We recently built artificial nanoscale turbines. We demonstrated driven rotary motion of a nanoscale DNA origami turbine which harnessed energy from a water flow generated by a static chemical or electrical potential gradient in a solid-state nanopore. The origami nanoturbine consisted of a 6-helix DNA bundle that adopted a chiral conformation upon phoretic docking onto the nanopore and subsequently displayed a sustained unidirectional rotary motion of up to 20 revolutions/s. These artificial nano-engines operate autonomously in physiological conditions, converting energy into useful mechanical work.

2. Nanopore-based sequential reading of peptides [2]

We recently demonstrated a nanopore-based single-molecule peptide reader capable of reliably detecting single amino-acid substitutions within individual peptides. A peptide is linked to a DNA molecule and sequentially pulled through a biological nanopore by a DNA helicase in single amino-acid steps. Stepping ion-current signals enable discrimination of single-amino-acid substitutions in single reads. Notably, we demonstrated the capability to ‘rewind’ peptide reads, obtaining indefinitely many independent reads of the same molecule, yielding an undetectably low error rate in single-amino-acid variant identification. Recently, we expanded this concept to discriminating single post-translational modifications within peptides of mixed charge. These proof-of-concept experiments constitute a promising basis for the development of a single-molecule protein sequencer.

3. Real-time imaging of DNA loop extrusion by condensin and cohesin SMC complexes [3]

Structural Maintenance of Chromosomes (SMC) proteins like cohesin and condensin spatially organize chromosomes by extruding DNA into large loops. Using single-molecule assays, we provided unambiguous evidence for loop extrusion by directly visualizing the processive extension of DNA loops by SMCs in real-time. In recent extensions of this work, we showed how this process occurs on supercoiled DNA, that SMCs also can exhibit phase condensation, and that SMC proteins can bypass huge roadblocks of bound proteins on DNA.

References:

[1] X. Shi et al, Nature Physics 18, 1105 (2022); X. Shi et al, Nature Nanotechnology 19, 338 (2024)

[2] H. Brinkerhoff et al, Science 374, 1509 (2021); I. Nova et al, Nature Biotechnology 42, 710 (2024).

[3] Ganji et al, Science 360, 102 (2018); Kim et al, Nature 579, 438 (2020); B. Pradhan et al, Cell Reports 41, 111491(2022).

纳米技术为生物学的发展提供了极好的机会。我将介绍一些来自我的实验室的最近例子，其中纳米技术单分子工具被用来揭开细胞生物学直至单分子层面的秘密。

1.由纳米尺度流动驱动的DNA折纸涡轮机

我们最近构建了人工纳米尺度的涡轮机。我们展示了一个纳米尺度DNA折纸涡轮机的驱动旋转运动，该涡轮机利用固态纳米孔中由静态化学或电势梯度产生的水流能量。折纸纳米涡轮由一个6螺旋DNA束组成，当它在纳米孔上进行光驱动对接时，采用了手性构象，并随后显示出持续的单向旋转运动，高达每秒20转。这些人工纳米引擎在生理条件下自主运行，将能量转化为有用的机械工作。

2.基于纳米孔的多肽序列连续读取

我们最近展示了一种基于纳米孔的单分子肽阅读器，能够可靠地检测单个肽中的单个氨基酸替代。一个肽与一个DNA分子相连，并通过DNA解旋酶以单个氨基酸步骤逐个拉过生物纳米孔。步进离子电流信号使单个氨基酸替代在单次读取中得以区分。值得注意的是，我们展示了“倒带”肽读取的能力，获得同一分子的无限多独立读取，从而在单个氨基酸变体识别中实现了无法检测的低错误率。最近，我们将这一概念扩展到区分多肽中的单个翻译后修饰。这些概念验证实验为开发单分子蛋白质测序器提供了一个有希望的基础。

3.实时成像冷凝蛋白和粘连蛋白SMC复合体的DNA环挤出

像粘连蛋白和冷凝蛋白这样的染色体结构维持(SMC)蛋白通过将DNA挤出成大环来空间组织染色体。使用单分子测定，我们通过直接可视化SMCs实时进行的DNA环的延伸过程，为环挤出提供了明确的证据。在这项工作的最近扩展中，我们展示了这一过程如何在超螺旋DNA上发生，SMCs也可以表现出相位凝聚，并且SMC蛋白可以绕过DNA上大量结合蛋白的路障。

【BIOGRAPHY】

Prof. dr. Cees Dekker (1959) is Distinguished University Professor at Delft University of Technology and KNAW Royal Academy Professor. Trained as a solid-state physicist, he discovered many of the exciting electronic properties of carbon nanotubes in the 1990s. Since 2000 he moved to single-molecule biophysics and nanobiology, with research from studies of DNA loop extrusion and supercoiling to DNA translocation through nanopores. More recently his research has focused on studying chromatin structure and cell division with bacteria on chip, while he is also attempting to ultimately build synthetic cells from the bottom up.

Dekker is an elected member of the Royal Netherlands Academy of Arts and Sciences and fellow to the APS and the IOP. Dekker headed the prestigious Kavli Institute of Nanoscience Delft as Director from 2010-2018. He initiated an entirely new Department of Bionanoscience at Delft and leads the 51M€ NWO Zwaartekracht program NanoFront. He published over 300 papers, received an honorary doctorate, and many prizes such as the 2001 Agilent Europhysics Prize, the 2003 Spinoza award, the 2012 ISNSCE Nanoscience Prize, and the 2017 NanoSmat Prize. In 2006, Delft University appointed him as an Institute Professor. In 2014, Dekker was knighted as Knight in the Order of the Netherlands Lion, and in 2015, he received his second ERC Advanced Grant and the KNAW appointed him as a Royal Academy Professor.

Cees Dekker教授（1959年出生）是代尔夫特理工大学的杰出大学教授和荷兰皇家艺术与科学学院的皇家学院教授。作为一名固体物理学家，他在1990年代发现了碳纳米管的许多激动人心的电子特性。自2000年以来，他转向了单分子生物物理学和纳米生物学，研究从DNA环挤出和超螺旋到DNA通过纳米孔的转位。最近，他的研究集中在使用芯片上的细菌研究染色质结构和细胞分裂，同时他也试图从底部向上构建合成细胞。

Dekker是荷兰皇家艺术与科学学院的当选成员，也是APS和IOP的会员。Dekker从2010年到2018年担任著名的代尔夫特卡夫利纳米科学研究所的主任。他在代尔夫特创立了一个全新的生物纳米科学系，并领导了5100万欧元的NWO Zwaartekracht纳米前沿项目。他发表了300多篇论文，获得了荣誉博士学位和许多奖项，如2001年安捷伦欧洲物理学奖、2003年斯宾诺莎奖、2012年ISNSCE纳米科学奖和2017年纳米智能奖。2006年，代尔夫特大学任命他为研究所教授。2014年，Dekker被封为荷兰狮子勋章骑士，2015年，他获得了他的第二个ERC高级资助，荷兰皇家艺术与科学学院任命他为皇家学院教授。