Latest News

  • JUN 2019

    Welcome to Longfei

    Longfei is joining the Lin lab as a postdoctoral fellow. He recently graduated from the Chengde Mao lab in Purdue University.

  • JUN 2019

    Congratulations to Michael!

    Michael has graduated with a Ph.D. in Cell Biology. He is joining the Farren Isaacs lab as a postdoctoral fellow. Congratulations!

  • FEB 2019

    Congratulations to Michael!

    Michael successfully defended his thesis on ”Vesicle Tubulation with Self-Assembling DNA Nanosprings: Biomimetic Nanotechnology toward the Re-capitulation & Re-purposing of Sub-cellular Functions within an Artificial Framework”. Congratulations!

  • DEC 2018

    New Student: Chun Xie

    Chun is a student from the Huazhong University of Science and Technology (HUST). He will be joining us on an one-year exchange program.

Past Events

  • SEP 2018

    Farewell to Yang

    Yang will be leaving us to start his own lab in the School of Medicine, Shanghai Jiao Tong University. All the best!

  • AUG 2018

    New Exchange Student: Yan Cui

    Yan is a student from Tsinghua University. She will be joining us on an one-year exchange program.

  • JUL 2018

    Farewell to Qi Shen

    Qi will be leaving us to join the Xiong lab at the Department of Molecular Biophysics and Biochemistry, Yale University.

  • JUL 2018

    New Exchange Student: Qi Yan

    Qi is a student from Tsinghua University. She will be joining us on an exchange program for two months.

  • JUN 2018

    Farewell to Zhao Zhang

    Zhao will be leaving us to join the Chapman Lab at the Department of Neuroscience, University of Wisconsin.

  • MAY 2018

    Congratulations to Mark

    Our former undergraduate student, Mark Zhu, graduated as the Class of 2018. Congratulations and all the best!

Current

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    Longfei Liu

    Postdoctoral Fellow

    Longfei graduated from University of Science and Technology of China (USTC) with a Bachelor’s Degree in Chemistry and received his Ph.D. degree at Purdue University. He is now a postdoctoral fellow in the Lin lab and works on DNA-nanotechnology-based membrane science. Outside the lab, he enjoys playing the piano, as well as outdoor activities including basketball and table tennis.

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    Ben Akhuetie-Oni

    Predoctoral Fellow

    Ben is a PhD candidate in the Chenxiang Lin and Farren Isaacs Labs. He holds a B.S. in Biochemistry from the University of Minnesota and a M.S. in Molecular, Cellular, and Developmental Biology (MCDB) from Yale University. His research interests lie at the interface of genome engineering and nucleic acid nanotechnology, where he is developing new tools and technologies for gene-editing based therapies. Outside of lab, Ben spends as much time as he can outside, where he enjoys hiking, swimming, and playing basketball.

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    John Powell

    Predoctoral Fellow

    John is a PhD candidate in the Lin Lab. He works on DNA-origami-based supports for RNA and protein structural studies.

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    Nathan Williams

    Predoctoral Fellow

    Nathan is a PhD candidate in the Lin Lab. He works on DNA-origami-based fluorescence standards.

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    Qiancheng Xiong

    Predoctoral Fellow

    Qiancheng graduated from the University of Cambridge with a major in Genetics and worked as a Research Officer at the Institute of Molecular and Cell Biology (A*STAR, Singapore). He is a third year graduate student in the Lin lab and works on engineering membrane encapsulated DNA origami structures. Outside the laboratory, he also experiments with caffeine extraction and yeast fermentation.

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    Chun Xie

    Exchange Student

    Chun got his B.S. with a major in applied mathematics in Northwestern Polytechnical University and now a forth year PhD candidate in Huazhong University of Science and Technology. Right now he is having fun with his phage and plasmid.

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    Yan Cui

    Exchange Student

    Yan Cui received her B.A. from China Agricultural University in biology and is a 5th year graduate student from Tsinghua University. Yan's work focuses on the construction and application of DNA origami nanostructures. She's in Yale for her research on DNA-templated liposome transformation.

Alumni

Patrick Fisher

PhD in Cell Biology (2017)

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Zhao Zhang

Postdoctoral Fellow

Qi Shen

Postdoctoral Fellow

Qi Yan

2018 Summer Exchange Student

Yang Yang

Postdoctoral Fellow

Michael Grome

PhD in Cell Biology (2019)

Publications

For a full list of Prof Lin's publications, please click here.

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A Programmable DNA-Origami Platform for Studying Lipid Transfer between Bilayers

Xin Bian, Zhao Zhang, Qiancheng Xiong, Pietro De Camilli, Chenxiang Lin
Journal PaperNature Chemical Biology, Volume 15, 18 July 2019, Pages 830–837

Abstract

Non-vesicular lipid transport between bilayers at membrane contact sites plays important physiological roles. Mechanistic insight into the action of lipid-transport proteins localized at these sites requires determination of the distance between bilayers at which this transport can occur. Here we developed DNA-origami nanostructures to organize size-defined liposomes at precise distances and used them to study lipid transfer by the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain of extended synaptotagmin 1 (E-Syt1). Pairs of DNA-ring-templated donor and acceptor liposomes were docked through DNA pillars, which determined their distance. The SMP domain was anchored to donor liposomes via an unstructured linker, and lipid transfer was assessed via a Förster resonance energy transfer (FRET)-based assay. We show that lipid transfer can occur over distances that exceed the length of an SMP dimer, which is compatible with the shuttle model of lipid transport. The DNA nanostructures developed here can also be adapted to study other processes occurring where two membranes are closely apposed to each other.

Stiffness and Membrane Anchor Density Modulate DNA-Nanospring-Induced Vesicle Tubulation

Michael W Grome, Zhao Zhang, Chenxiang Lin
Journal PaperACS Applied Materials & Interfaces, Volume 11, Issue 26, 21 June 2019, Pages 22987-22992

Abstract

DNA nanotechnology provides an avenue for the construction of rationally designed artificial assemblages with well-defined and tunable architectures. Shaped to mimic natural membrane-deforming proteins and equipped with membrane anchoring molecules, curved DNA nanostructures can reproduce subcellular membrane remodeling events such as vesicle tubulation in vitro. To systematically analyze how structural stiffness and membrane affinity of DNA nanostructures affect the membrane remodeling outcome, here we build DNA-origami curls with varying thickness and amphipathic peptide density, and have them polymerize into nanosprings on the surface of liposomes. We find that modestly reducing rigidity and maximizing the number of membrane anchors not only promote membrane binding and remodeling but also lead to the formation of lipid tubules with better defined diameters, highlighting the ability of programmable DNA-based constructs to controllably deform the membrane.

Quantification of Biomolecular Dynamics Inside Real and Synthetic Nuclear Pore Complexes Using Time-Resolved Atomic Force Microscopy

George J. Stanley, Bernice Akpinar, Qi Shen, Patrick D. Ellis Fisher, C. Patrick Lusk, Chenxiang Lin, Bart W. Hoogenboom
Journal PaperACS Nano, 26 June 2019

Abstract

Over the past decades, atomic force microscopy (AFM) has emerged as an increasingly powerful tool to study the dynamics of biomolecules at nanometer length scales. However, the more stochastic the nature of such biomolecular dynamics, the harder it becomes to distinguish them from AFM measurement noise. Rapid, stochastic dynamics are inherent to biological systems comprising intrinsically disordered proteins. One role of such proteins is in the formation of the transport barrier of the nuclear pore complex (NPC): the selective gateway for macromolecular traffic entering or exiting the nucleus. Here, we use AFM to observe the dynamics of intrinsically disordered proteins from two systems: the transport barrier of native NPCs and the transport barrier of a mimetic NPC made using a DNA origami scaffold. Analyzing data recorded with 50-200 ms temporal resolution, we highlight the importance of drift correction and appropriate baseline measurements in such experiments. In addition, we describe an autocorrelation analysis to quantify time scales of observed dynamics and to assess their veracity-an analysis protocol that lends itself to the quantification of stochastic fluctuations in other biomolecular systems. The results reveal the surprisingly slow rate of stochastic, collective transitions inside mimetic NPCs, highlighting the importance of FG-nup cohesive interactions.

Vesicle Tubulation with Self‐Assembling DNA Nanosprings

Michael W. Grome, Zhao Zhang, Frédéric Pincet, Chenxiang Lin
Journal PaperAngewandte Chemie International Edition in English, Volume 57, Issue 19, 04 May 2018, Pages 5330-5334

Abstract

A major goal of nanotechnology and bioengineering is to build artificial nanomachines capable of generating specific membrane curvatures on demand. Inspired by natural membrane‐deforming proteins, we designed DNA‐origami curls that polymerize into nanosprings and show their efficacy in vesicle deformation. DNA‐coated membrane tubules emerge from spherical vesicles when DNA‐origami polymerization or high membrane‐surface coverage occurs. Unlike many previous methods, the DNA self‐assembly‐mediated membrane tubulation eliminates the need for detergents or top‐down manipulation. The DNA‐origami design and deformation conditions have substantial influence on the tubulation efficiency and tube morphology, underscoring the intricate interplay between lipid bilayers and vesicle‐deforming DNA structures.

A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement

Patrick D. Ellis Fisher, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, Thomas J. Melia, Bart W. Hoogenboom, Chenxiang Lin, C. Patrick Lusk
Journal Paper ACS Nano, Volume 12, Issue 2, 19 January 2018, Pages 1508-1518

Abstract

Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.

Directing reconfigurable DNA nanoarrays

Yang Yang, Chenxiang Lin
Journal Paper Science, Volume 357, Issue 6349, 28 July 2017, Pages 352-353

Placing and shaping liposomes with reconfigurable DNA nanocages

Zhao Zhang, Yang Yang, Frederic Pincet, Marc C. Llaguno, Chenxiang Lin
Journal Paper Nature Chemistry, Volume 9, Issue 7, 23 June 2017, Pages 653-659

Abstract

The diverse structure and regulated deformation of lipid bilayer membranes are among a cell's most fascinating features. Artificial membrane-bound vesicles, known as liposomes, are versatile tools for modelling biological membranes and delivering foreign objects to cells. To fully mimic the complexity of cell membranes and optimize the efficiency of delivery vesicles, controlling liposome shape (both statically and dynamically) is of utmost importance. Here we report the assembly, arrangement and remodelling of liposomes with designer geometry: all of which are exquisitely controlled by a set of modular, reconfigurable DNA nanocages. Tubular and toroid shapes, among others, are transcribed from DNA cages to liposomes with high fidelity, giving rise to membrane curvatures present in cells yet previously difficult to construct in vitro. Moreover, the conformational changes of DNA cages drive membrane fusion and bending with predictable outcomes, opening up opportunities for the systematic study of membrane mechanics.

DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching

John T. Powell, Benjamin O. Akhuetie‐Oni, Zhao Zhang, Chenxiang Lin
Journal PaperAngewandte Chemie International Edition in English, Volume 55, Issue 38, 12 September 2016, Pages 11412-11416

Abstract

Mechanically interlocked supramolecular assemblies are appealing building blocks for creating functional nanodevices. Herein, we describe the multistep assembly of large DNA origami rotaxanes that are capable of programmable structural switching. We validated the topology and structural integrity of these rotaxanes by analyzing the intermediate and final products of various assembly routes by electrophoresis and electron microscopy. We further analyzed two structure‐switching behaviors of our rotaxanes, which are both mediated by DNA hybridization. In the first mechanism, the translational motion of the macrocycle can be triggered or halted at either terminus. In the second mechanism, the macrocycle can be elongated after completion of the rotaxane assembly, giving rise to a unique structure that is otherwise difficult to access.

Self-assembly of size-controlled liposomes on DNA nanotemplates

Yang Yang, Jing Wang, Hideki Shigematsu, Weiming Xu, William M. Shih, James E. Rothman, Chenxiang Lin
Journal PaperNature Chemistry, Volume 8, Issue 5, 21 March 2016, Pages 476-483

Abstract

Artificial lipid-bilayer membranes are valuable tools for the study of membrane structure and dynamics. For applications such as the study of vesicular transport and drug delivery, there is a pressing need for artificial vesicles with controlled size. However, controlling vesicle size and shape with nanometre precision is challenging, and approaches to achieve this can be heavily affected by lipid composition. Here, we present a bio-inspired templating method to generate highly monodispersed sub-100-nm unilamellar vesicles, where liposome self-assembly was nucleated and confined inside rigid DNA nanotemplates. Using this method, we produce homogeneous liposomes with four distinct predefined sizes. We also show that the method can be used with a variety of lipid compositions and probe the mechanism of templated liposome formation by capturing key intermediates during membrane self-assembly. The DNA nanotemplating strategy represents a conceptually novel way to guide lipid bilayer formation and could be generalized to engineer complex membrane/protein structures with nanoscale precision.

Our Lab

You can find us at our lab located at the Nanobiology Institute on the Yale West Campus.

  850 West Campus Drive, ISTC #213C, West Haven, CT 06516

There is a free Yale University Shuttle service (Purple Line & Green Line) between the West Campus and the main campus in New Haven.

You may click here for more information.

Our PI

You may also contact Prof Lin directly via email or phone.

  •    office: 203-737-3924
  •    fax: 203-737-3212
  •    chenxiang.lin@yale.edu