Dr Wooli Bae


Lecturer in Experimental Soft Matter Physics
BS, MS and PhD in Physics (KAIST, Republic of Korea)

Academic and research departments

Department of Physics, Soft Matter Group.

Biography

Areas of specialism

DNA, RNA nanotechnology; Single molecule biophysics

My qualifications

2020
Associative Fellow of Higher Education Academy
Advance HE
2014
PhD in Physics
KAIST, Korea

Previous roles

2017 - 2021
Research Associate
Imperial College London. UK
2014 - 2017
Post-doctoral Research Fellow
Ludwig-Maximilians-Universität München, Germany

Research

Research interests

My publications

Publications

Wooli Bae, Tae-Young Yoon, Cherlhyun Jeong (2021)Direct evaluation of self-quenching behavior of fluorophores at high concentrations using an evanescent field, In: PloS one16(2)e0247326 Public Library of Science

The quantum yield of a fluorophore is reduced when two or more identical fluorophores are in close proximity to each other. The study of protein folding or particle aggregation is can be done based on this above-mentioned phenomenon-called self-quenching. However, it is challenging to characterize the self-quenching of a fluorophore at high concentrations because of the inner filter effect, which involves depletion of excitation light and re-absorption of emission light. Herein, a novel method to directly evaluate the self-quenching behavior of fluorophores was developed. The evanescent field from an objective-type total internal reflection fluorescence (TIRF) microscope was used to reduce the path length of the excitation and emission light to ~100 nm, thereby supressing the inner filter effect. Fluorescence intensities of sulforhodamine B, fluorescein isothiocyanate (FITC), and calcein solutions with concentrations ranging from 1 μM to 50 mM were directly measured to evaluate the concentration required for 1000-fold degree of self-quenching and to examine the different mechanisms through which the fluorophores undergo self-quenching.

Javier Cabello-Garcia, Wooli Bae, Guy-Bart Stan, Thomas E Ouldridge (2021)Handhold-Mediated Strand Displacement: A Nucleic Acid Based Mechanism for Generating Far-from-Equilibrium Assemblies through Templated Reactions, In: ACS Nano15(2)pp. 3272-3283 American Chemical Society

The use of templates is a well-established method for the production of sequence-controlled assemblies, particularly long polymers. Templating is canonically envisioned as akin to a self-assembly process, wherein sequence-specific recognition interactions between a template and a pool of monomers favor the assembly of a particular polymer sequence at equilibrium. However, during the biogenesis of sequence-controlled polymers, template recognition interactions are transient; RNA and proteins detach spontaneously from their templates to perform their biological functions and allow template reuse. Breaking template recognition interactions puts the product sequence distribution far from equilibrium, since specific product formation can no longer rely on an equilibrium dominated by selective copy-template bonds. The rewards of engineering artificial polymer systems capable of spontaneously exhibiting nonequilibrium templating are large, but fields like DNA nanotechnology lack the requisite tools; the specificity and drive of conventional DNA reactions rely on product stability at equilibrium, sequestering any recognition interaction in products. The proposed alternative is handhold-mediated strand displacement (HMSD), a DNA-based reaction mechanism suited to producing out-of-equilibrium products. HMSD decouples the drive and specificity of the reaction by introducing a transient recognition interaction, the handhold. We measure the kinetics of 98 different HMSD systems to prove that handholds can accelerate displacement by 4 orders of magnitude without being sequestered in the final product. We then use HMSD to template the selective assembly of any one product DNA duplex from an ensemble of equally stable alternatives, generating a far-from-equilibrium output. HMSD thus brings DNA nanotechnology closer to the complexity of out-of-equilibrium biological systems.

Alicia Climent-Catala, Thomas E Ouldridge, Guy-Bart Stan, WOOLI BAE (2022)Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers, In: ACS synthetic biology11(2)pp. 562-569 AMER CHEMICAL SOC

Synthetic RNA systems offer unique advantages such as faster response, increased specificity, and programmability compared to conventional protein-based networks. Here, we demonstrate an in vitro RNA-based toggle switch using RNA aptamers capable of inhibiting the transcriptional activity of T7 or SP6 RNA polymerases. The activities of both polymerases are monitored simultaneously by using Broccoli and malachite green light up aptamer systems. In our toggle switch, a T7 promoter drives the expression of SP6 inhibitory aptamers, and an SP6 promoter expresses T7 inhibitory aptamers. We show that the two distinct states originating from the mutual inhibition of aptamers can be toggled by adding DNA sequences to sequester the RNA inhibitory aptamers. Finally, we assessed our RNA based toggle switch in degrading conditions by introducing controlled degradation of RNAs using a mix of RNases. Our results demonstrate that the RNA-based toggle switch could be used as a control element for nucleic acid networks in synthetic biology applications.

Tomislav Plesa, Guy-Bart Stan, Thomas E Ouldridge, WOOLI BAE (2021)Quasi-robust control of biochemical reaction networks via stochastic morphing, In: Journal of the Royal Society interface18(177)pp. 20200985-20200985 ROYAL SOC

One of the main objectives of synthetic biology is the development of molecular controllers that can manipulate the dynamics of a given biochemical network that is at most partially known. When integrated into smaller compartments, such as living or synthetic cells, controllers have to be calibrated to factor in the intrinsic noise. In this context, biochemical controllers put forward in the literature have focused on manipulating the mean (first moment) and reducing the variance (second moment) of the target molecular species. However, many critical biochemical processes are realized via higher-order moments, particularly the number and configuration of the probability distribution modes (maxima). To bridge the gap, we put forward the stochastic morpher controller that can, under suitable timescale separations, morph the probability distribution of the target molecular species into a predefined form. The morphing can be performed at a lower-resolution, allowing one to achieve desired multi-modality/multi-stability, and at a higher-resolution, allowing one to achieve arbitrary probability distributions. Properties of the controller, such as robustness and convergence, are rigorously established, and demonstrated on various examples. Also proposed is a blueprint for an experimental implementation of stochastic morpher.

WOOLI BAE, Guy-Bart Stan, Thomas E Ouldridge (2021)In situ Generation of RNA Complexes for Synthetic Molecular Strand-Displacement Circuits in Autonomous Systems, In: Nano letters21(1)pp. 265-271 AMER CHEMICAL SOC

Synthetic molecular circuits implementing DNA or RNA strand-displacement reactions can be used to build complex systems such as molecular computers and feedback control systems. Despite recent advances, application of nucleic acid-based circuits in vivo remains challenging due to a lack of efficient methods to produce their essential components, namely, multistranded complexes known as gates, in situ, i.e., in living cells or other autonomous systems. Here, we propose the use of naturally occurring self-cleaving ribozymes to cut a single-stranded RNA transcript into a gate complex of shorter strands, thereby opening new possibilities for the autonomous and continuous production of RNA strands in a stoichiometrically and structurally controlled way.

WOOLI BAE, Samet Kocabey, Tim Liedl (2019)DNA nanostructures in vitro, in vivo and on membranes, In: Nano today26pp. 98-107 ELSEVIER SCI LTD

Recent developments in DNA nanotechnology brought rich structural and functional diversity. However, for DNA nanostructures to perform in a biologically relevant context, obstacles such as nuclease activity and low divalent ion concentrations have to be addressed. For drug delivery or gene therapy applications, ultimately the lipid membrane barriers must be targeted and overcome. In this article, we highlight efforts and achievements in enhancing the stability of DNA nanostructures including chemical modifications, covalent crosslinking and coating with protective layers composed of polymers or lipids. We then review interactions between DNA nanostructures and lipid membranes, which are often mediated by ligands for membrane receptors or hydrophobic domains incorporated into the structure. Finally, we present applications of DNA nanostructures on and in lipid membranes, including higher order assembly, controlling membrane curvature, targeting and arranging membrane proteins in living cells and DNA-based synthetic lipid channels. (C) 2019 Elsevier Ltd. All rights reserved.

Timon Funck, Tim Liedl, Wooli Bae (2019)Dual Aptamer-Functionalized 3D Plasmonic Metamolecule for Thrombin Sensing, In: Applied Sciences9(15) MDPI

DNA nanotechnology offers the possibility to rationally design structures with emergent properties by precisely controlling their geometry and functionality. Here, we demonstrate a DNA-based plasmonic metamolecule that is capable of sensing human thrombin proteins. The chiral reconfigurability of a DNA origami structure carrying two gold nanorods was used to provide optical read-out of thrombin binding through changes in the displayed plasmonic circular dichroism. In our experiments, each arm of the structure was modified with one of two different thrombin-binding aptamers-thrombin-binding aptamer (TBA) and HD22-in such a way that a thrombin molecule could be sandwiched by the aptamers to lock the metamolecule in a state of defined chirality. Our structure exhibited a K-d of 1.4 nM, which was an order of magnitude lower than those of the individual aptamers. The increased sensitivity arose from the avidity gained by the cooperative binding of the two aptamers, which was also reflected by a Hill coefficient of 1.3 +/- 0.3. As we further exploited the strong plasmonic circular dichroism (CD) signals of the metamolecule, our method allowed one-step, high sensitivity optical detection of human thrombin proteins in solution.

Francesca Nicoli, Anders Barth, WOOLI BAE, Fabian Neukirchinger, Alvaro H Crevenna, D Lamb, Tim Liedl (2017)Directional Photonic Wire Mediated by Homo-Forster Resonance Energy Transfer on a DNA Origami Platform, In: ACS nano11(11)pp. 11264-11272 AMER CHEMICAL SOC

Elaborating efficient strategies and deepening the understanding of light transport at the nanoscale is of great importance for future designs of artificial light-harvesting assemblies and dye-based photonic circuits. In this work, we focus on studying the phenomenon of Forster resonance energy transfer (FRET) among fluorophores of the same kind (homo-FRET) and its implications for energy cascades containing two or three different dye molecules. Utilizing the spatial programmability of DNA origami, we arranged a chain of cyanine 3 (Cy3) dyes flanked at one end with a dye of lower excitation energy, cyanine 5 (Cy5), with or without an additional dye of higher excitation energy, Alexa488, at the other end. We characterized the response of our fluorophore assemblies with bulk and single-molecule spectroscopy and support our measurements by Monte Carlo modeling of energy transfer within the system. We find that, depending on the arrangement of the fluorophores, homo-FRET between the Cy3 dyes can lead to an overall enhanced energy transfer to the acceptor fluorophore. Furthermore, we systematically analyzed the homo-FRET system by addressing the fluorescence lifetime and anisotropy. Finally, we built a homo-FRET-mediated photonic wire capable of transferring energy through the homo-FRET system from the blue donor dye (Alexa488) to the red acceptor fluorophore (Cy5) across a total distance of 16 nm.

Susanne Kempter, Alena Khmelinskaia, Maximilian T Strauss, Petra Schwille, Ralf Jungmann, Tim Liedl, WOOLI BAE (2019)Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami, In: ACS nano13(2)pp. 996-1002 AMER CHEMICAL SOC

DNA nanostructures offer the possibility to mimic functional biological membrane components due to their nanometer-precise shape configurability and versatile biochemical functionality. Here we show that the diffusional behavior of DNA nanostructures and their assembly into higher order membrane-bound lattices can be controlled in a stop-and-go manner and that the process can be monitored with super-resolution imaging. The DNA structures are transiently immobilized on glass-supported lipid bilayers by changing the mono- and divalent cation concentrations of the surrounding buffer. Using DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy, we confirm the fixation of DNA origami structures with different shapes. On mica-supported lipid bilayers, in contrast, we observe residual movement. By increasing the concentration of NaCl and depleting MgCl2, a large fraction of DNA structures restarts to diffuse freely on both substrates. After addition of a set of oligonucleotides that enables three Y-shaped monomers to assemble into a three-legged shape (triskelion), the triskelions can be stopped and super-resolved. Exchanging buffer and adding another set of oligonucleotides triggers the triskelions to diffuse and assemble into hexagonal 2D lattices. This stop-and-go imaging technique provides a way to control and observe the diffusional behavior of DNA nanostructures on lipid membranes that could also lead to control of membrane associated cargos.

Alexander Mario Maier, WOOLI BAE, Daniel Schiffels, Johannes Friedrich Emmerig, Maximilian Schiff, Tim Liedl (2017)Self-Assembled DNA Tubes Forming Helices of Controlled Diameter and Chirality, In: ACS nano11(2)pp. 1301-1306 ACS

Multihelical DNA bundles could enhance the functionality of nanomaterials and serve as model architectures to mimic protein filaments on the molecular and cellular level. We report the self-assembly of micrometer-sized helical DNA nanotubes with widely controllable helical diameters ranging from tens of nanometers to a few micrometers. Nanoscale helical shapes of DNA tile tubes (4-, 6-, 8-, 10-, and 12-helix tile tubes) are achieved by introducing discrete amounts of bending and twist through base pair insertions and/or deletions. Microscale helical diameters, which require smaller amounts of twist and bending, are achieved by controlling the intrinsic "supertwist" present in tile tubes with uneven number of helices (11-, 13-, and 15-helix tile tubes). Supertwist fine-tuning also allows us to produce helical nanotubes of defined chirality.

Samet Kocabey, Susanne Kempter, Jonathan List, YM Xing, WOOLI BAE, Daniel Schiffels, William M Shih, Friedrich C Simmel, Tim Liedl (2015)Membrane-Assisted Growth of DNA Origami Nanostructure Arrays, In: ACS nano9(4)pp. 3530-3539 AMER CHEMICAL SOC

Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors-a three-layered rectangular block and a Y-shaped DNA structure to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of-hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.

Philipp C Nickels, Bettina Wünsch, Phil Holzmeister, WOOLI BAE, Luisa M Kneer, Dina Grohmann, Philip Tinnefeld, Tim Liedl (2016)Molecular force spectroscopy with a DNA origami-based nanoscopic force clamp, In: Science (American Association for the Advancement of Science)354(6310)pp. 305-307

Forces in biological systems are typically investigated at the single-molecule level with atomic force microscopy or optical and magnetic tweezers, but these techniques suffer from limited data throughput and their requirement for a physical connection to the macroscopic world. We introduce a self-assembled nanoscopic force clamp built from DNA that operates autonomously and allows massive parallelization. Single-stranded DNA sections of an origami structure acted as entropic springs and exerted controlled tension in the low piconewton range on a molecular system, whose conformational transitions were monitored by single-molecule Förster resonance energy transfer. We used the conformer switching of a Holliday junction as a benchmark and studied the TATA-binding protein-induced bending of a DNA duplex under tension. The observed suppression of bending above 10 piconewtons provides further evidence of mechanosensitivity in gene regulation.

WOOLI BAE, Kipom Kim, Duyoung Min, Je-Kyung Ryu, Changbong Hyeon, Tae-Young Yoon (2014)Programmed folding of DNA origami structures through single-molecule force control, In: Nature communications5(1)5654 NATURE PUBLISHING GROUP

Despite the recent development in the design of DNA origami, its folding yet relies on thermal or chemical annealing methods. We here demonstrate mechanical folding of the DNA origami structure via a pathway that has not been accessible to thermal annealing. Using magnetic tweezers, we stretch a single scaffold DNA with mechanical tension to remove its secondary structures, followed by base pairing of the stretched DNA with staple strands. When the force is subsequently quenched, folding of the DNA nanostructure is completed through displacement between the bound staple strands. Each process in the mechanical folding is well defined and free from kinetic traps, enabling us to complete folding within 10 min. We also demonstrate parallel folding of DNA nanostructures through multiplexed manipulation of the scaffold DNAs. Our results suggest a path towards programmability of the folding pathway of DNA nanostructures.

WOOLI BAE, Mal-Gi Choi, Changbong Hyeon, Yeon-Kyun Shin, Tae-Young Yoon (2013)Real-Time Observation of Multiple-Protein Complex Formation with Single-Molecule FRET, In: Journal of the American Chemical Society135(43)16242 AMER CHEMICAL SOC
Jiajie Diao, Yuji Ishitsuka, Woo-Ri Bae (2011)Single-molecule FRET study of SNARE-mediated membrane fusion, In: Bioscience Reports31(6)pp. 457-463 Portland Press

Membrane fusion is one of the most important cellular processes by which two initially distinct lipid bilayers merge their hydrophobic cores, resulting in one interconnected structure. Proteins, called SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein receptor), play a central role in the fusion process that is also regulated by several accessory proteins. In order to study the SNARE-mediated membrane fusion, the in vitro protein reconstitution assay involving ensemble FRET (fluorescence resonance energy transfer) has been used over a decade. In this mini-review, we describe several single-molecule-based FRET approaches that have been applied to this field to overcome the shortage of the bulk assay in terms of protein and fusion dynamics.

Additional publications