Honors & Awards
Center for the Molecular Analysis and Design (CMAD) fellowship, Stanford University (2020-2023)
Government Scholarship to Study Abroad (GSSA), Ministry of Education of Taiwan (2019-2021)
Excellent Oral Presentation Award, The Taiwan Society for Biochemistry and Molecular Biology (2018)
Excellent Research Award (Biochemistry Division), The Chinese Chemical Society, Taiwan (2017)
Dr. Yung-Tsai Yen Excellent Research Award, National Taiwan University (2017)
NTU Excellent Teaching Assistants (Top 10% TA), National Taiwan University (2017)
Dean Award (Top 10% Outstanding students), College of Science, National Taiwan University (2017)
Student Presentation Award, The Biophysical Society of Japan (2016)
Excellent Poster Presentation, Department of Chemistry, National Taiwan University (2015)
College Student Research Creativity Award, Ministry of Science and Technology (MoST), Taiwan (2015)
College Student Research Projects Funding, Ministry of Science and Technology (MoST), Taiwan (2014)
ETERNAL Chemical Engineering Corporate Scholarship, ETERNAL CORPORATION, Taiwan (2016)
VE WONG Food Corporate Scholarship, VE WONG CORPORATION, Taiwan (2014)
Excellent Teaching Assistant Award, Department of Chemistry, National Taiwan University (2016)
Education & Certifications
Master of Science, National Taiwan University, Chemistry (Biophysical Chemistry) (2017)
Bachelor of Science, National Taiwan University, Chemistry (Double-major) (2015)
Bachelor of Science, National Taiwan University, Agricultural Chemistry (2015)
Current Research and Scholarly Interests
Bianxiao Cui, (1/31/2019)
Teaching Assistant, National Taiwan University (September 1, 2015 - June 30, 2016)
General Chemistry A (Two-semester course for Agricultural Chemistry/ Atmospheric Science/ Geology students)
Research Assistant, Department of Chemistry, National Taiwan University (August 1, 2017 - July 31, 2018)
Using single-molecule tools to study Biological relevance of Mediators & Anti-recombinases in Eukaryotic Homologous Recombinational DNA Repair and Recombinase-mediated R-loop formation
A NanoCurvS platform for quantitative and multiplex analysis of curvature-sensing proteins.
The cell membrane is characterized by a rich variety of topographical features such as local protrusions or invaginations. Curvature-sensing proteins, including the Bin/Amphiphysin/Rvs (BAR) or epsin N-terminal homology (ENTH) family proteins, sense the bending sharpness and the positive/negative sign of these topographical features to induce subsequent intracellular signaling. A number of assays have been developed to study curvature-sensing properties of proteins in vitro, but it is still challenging to probe low curvature regime with the diameter of curvature from hundreds of nanometers to micrometers. It is particularly difficult to generate negative membrane curvatures with well-defined curvature values in the low curvature regime. In this work, we develop a nanostructure-based curvature sensing (NanoCurvS) platform that enables quantitative and multiplex analysis of curvature-sensitive proteins in the low curvature regime, in both negative and positive directions. We use NanoCurvS to quantitatively measure the sensing range of a negative curvature-sensing protein IRSp53 (an I-BAR protein) and a positive curvature-sensing protein FBP17 (an F-BAR protein). We find that, in cell lysates, the I-BAR domain of IRSp53 is able to sense shallow negative curvatures with the diameter-of-curvature up to 1500 nm, a range much wider than previously expected. NanoCurvS is also used to probe the autoinhibition effect of IRSp53 and the phosphorylation effect of FBP17. Therefore, the NanoCurvS platform provides a robust, multiplex, and easy-to-use tool for quantitative analysis of both positive and negative curvature-sensing proteins.
View details for DOI 10.1039/d2bm01856j
View details for PubMedID 37337788
Membrane curvature regulates the spatial distribution of bulky glycoproteins
View details for DOI 10.1038/s41467-022-30610-2
Swi5–Sfr1 stimulates Rad51 recombinase filament assembly by modulating Rad51 dissociation
Proceedings of the National Academy of Sciences of the United States of America (PNAS)
2018; 115: E10059-E10068
Eukaryotic Rad51 protein is essential for homologous-recombination repair of DNA double-strand breaks. Rad51 recombinases first assemble onto single-stranded DNA to form a nucleoprotein filament, required for function in homology pairing and strand exchange. This filament assembly is the first regulation step in homologous recombination. Rad51 nucleation is kinetically slow, and several accessory factors have been identified to regulate this step. Swi5-Sfr1 (S5S1) stimulates Rad51-mediated homologous recombination by stabilizing Rad51 nucleoprotein filaments, but the mechanism of stabilization is unclear. We used single-molecule tethered particle motion experiments to show that mouse S5S1 (mS5S1) efficiently stimulates mouse RAD51 (mRAD51) nucleus formation and inhibits mRAD51 dissociation from filaments. We also used single-molecule fluorescence resonance energy transfer experiments to show that mS5S1 promotes stable nucleus formation by specifically preventing mRAD51 dissociation. This leads to a reduction of nucleation size from three mRAD51 to two mRAD51 molecules in the presence of mS5S1. Compared with mRAD51, fission yeast Rad51 (SpRad51) exhibits fast nucleation but quickly dissociates from the filament. SpS5S1 specifically reduces SpRad51 disassembly to maintain a stable filament. These results clearly demonstrate the conserved function of S5S1 by primarily stabilizing Rad51 on DNA, allowing both the formation of the stable nucleus and the maintenance of filament length.
View details for DOI 10.1073/pnas.1812753115
View details for PubMedCentralID PMC6205426
Stable Nuclei of Nucleoprotein Filament and High ssDNA Binding Affinity Contribute to Enhanced RecA E38K Recombinase Activity
2017; 7: 14964
RecA plays central roles in the homologous recombination to repair double-stranded DNA break damage in E. coli. A previously identified recA strain surviving high doses of UV radiation includes a dominant RecA E38K mutation. Using single-molecule experiments, we showed that the RecA E38K variant protein assembles nucleoprotein filaments more rapidly than the wild-type RecA. We also used a single-molecule fluorescence resonance energy transfer (smFRET) experiment to compare the nucleation cluster dynamics of wild-type RecA and RecA E38K mutants on various short ssDNA substrates. At shorter ssDNA, nucleation clusters of RecA E38K form dynamically, while only few were seen in wild-type RecA. RecA E38K also forms stable nuclei by specifically lowering the dissociation rate constant, k d . These observations provide evidence that greater nuclei stability and higher ssDNA binding affinity contribute to the observed enhanced recombination activity of the RecA E38K mutant. Given that assembly of RecA nucleoprotein filaments is the first committed step in recombinational repair processes, enhancement at this step gives rise to a more efficient recombinase.
View details for DOI 10.1038/s41598-017-15088-z
View details for Web of Science ID 000414261500081
View details for PubMedID 29097773
View details for PubMedCentralID PMC5668366
RecA-SSB Interaction Modulates RecA Nucleoprotein Filament Formation on SSB-Wrapped DNA
2017; 7: 11876
E. coli RecA recombinase catalyzes the homology pairing and strand exchange reactions in homologous recombinational repair. RecA must compete with single-stranded DNA binding proteins (SSB) for single-stranded DNA (ssDNA) substrates to form RecA nucleoprotein filaments, as the first step of this repair process. It has been suggested that RecA filaments assemble mainly by binding and extending onto the free ssDNA region not covered by SSB, or are assisted by mediators. Using the tethered particle motion (TPM) technique, we monitored individual RecA filament assembly on SSB-wrapped ssDNA in real-time. Nucleation times of the RecA E38K nucleoprotein filament assembly showed no apparent dependence among DNA substrates with various ssDNA gap lengths (from 60 to 100 nucleotides) wrapped by one SSB in the (SSB)65 binding mode. Our data have shown an unexpected RecA filament assembly mechanism in which a RecA-SSB-ssDNA interaction exists. Four additional pieces of evidence support our claim: the nucleation times of the RecA assembly varied (1) when DNA substrates contained different numbers of bound SSB tetramers; (2) when the SSB wrapping mode conversion is induced; (3) when SSB C-terminus truncation mutants are used; and (4) when an excess of C-terminal peptide of SSB is present. Thus, a RecA-SSB interaction should be included in discussing RecA regulatory mechanism.
View details for DOI 10.1038/s41598-017-12213-w
View details for Web of Science ID 000411165100053
View details for PubMedID 28928411
View details for PubMedCentralID PMC5605508
DNA with Different Local Torsional States Affects RecA-Mediated Recombination Progression
2017; 18 (6): 584–90
DNA topology is thought to affect DNA enzyme activity. The helical structure of duplex DNA dictates the change of topological states during strand separation when DNA is constrained. During the repair of DNA double-stranded breaks, the RecA nucleoprotein filament invades DNA and carries out consecutive strand exchange reactions coupled with duplex DNA strand separation. It has been suggested that torsional strain could be generated and its accumulation could inhibit strand exchange. We used hairpin and nicked DNA substrates to test how torsional strain alters the RecA-mediated strand exchange efficiency. Single-molecule tethered particle motion (TPM) experiments showed that torsionally constrained hairpin DNA substrates returned nearly no successful strand exchange events catalyzed by RecA. Surprisingly, the strand exchange efficiencies increase in the presence of DNA nicks or loop disruption. The dwell time of transient RecA events in hairpin is shorter compared to those found in nicked or fork DNA substrates, which suggests a limited strand exchange progression in hairpin substrates. Our observation shows that RecA generates local torsional strain during strand exchange, and the inability to dissipate this torsional strain inhibits homologous recombination progression. DNA topological states are thus important regulation measures of DNA recombination.
View details for DOI 10.1002/cphc.201601281
View details for Web of Science ID 000397578500002
View details for PubMedID 28054431
Single-Molecule Tethered Particle Motion Studies on the DNA Recombinase Filament Assembly and Disassembly.
Methods in molecular biology (Clifton, N.J.)
2021; 2281: 135–49
Bacterial RecA and eukaryotic Rad51 are recombinases indispensable for DNA homologous recombination and repair of double-stranded DNA breaks. Understanding the functions and biophysical properties of the DNA recombinases benefits the research in human medicine such as cancer biology. Single-molecule techniques provide the mechanistic details of complex biological reactions. Tethered particle motion (TPM) experiment is a simple and multiplex single-molecule tool to monitor DNA-protein interactions. We have developed a single-molecule TPM assay to study DNA recombinase filament assembly and disassembly on individual DNA molecules in real time. Characterization of the temporal change of the Brownian motion of DNA tethers during recombinase assembly and disassembly in real time allows the determination of multiple kinetic parameters of nucleation rate, extension rate, dissociation rate, and length of the recombinase-DNA filament.
View details for DOI 10.1007/978-1-0716-1290-3_8
View details for PubMedID 33847956
Microcephaly family protein MCPH1 stabilizes RAD51 filaments
Nucleic Acids Research
View details for DOI 10.1093/nar/gkaa636