Taekjip Ha
@taekjip
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Biophysicist. Howard Hughes Medical Institute. Harvard Medical School. Boston Children’s Hospital. Father of three dragons. Occasional manuscript reviewer.
Joined December 2013
We have a web interface for predicting DNA cyclizability. Entering a PDB ID shows the preferred bending direction around a protein. Widom 601 DNA has strong and weak sides, and indeed intrinsic bending is toward the nucleosome center for the strong side (LH) only. Plz try it out!
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DNA bendability regulates transcription factor binding to nucleosomes.
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N6-methyladenine modification of DNA enhances RecA-mediated homologous recombination | PNAS
pnas.org
Both DNA methylation and homologous recombination (HR) are extensively studied. In bacteria, Dam methylation is the most studied DNA modification, ...
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Structural basis for dual DNA and RNA specificity of the G-quadruplex-.
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RT @xashleefeng: A brief summary/perspective on my recently published PhD work: Nucleosomes constrain 1D DNA diffusion by eukaryotic transc….
nature.com
Nature Structural & Molecular Biology - The transcription factor GAGA factor (GAF) recruits chromatin remodelers to establish and maintain open chromatin for transcription in Drosophila...
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RT @LUMICKS_nl: Discuss single-molecule science with world-renowned Prof. @Taekjip Ha (@Harvard )! Join the upcoming Nature webinar to lear….
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Euchromatin forms condensed domains with short active regions on the surface
biorxiv.org
Technological advances in chromatin structure characterization have continually refined our understanding of transcriptional regulation in eukaryotic systems. Despite these developments, achieving...
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Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues | PNAS
pnas.org
DNA-points accumulation for imaging in nanoscale topography (DNA-PAINT) enables nanoscale imaging with virtually unlimited multiplexing and molecul...
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RT @xashleefeng: My PhD work is online! Huge thanks to my advisors Carl and TJ, and collaborators! @taekjip @maryamyamadi @FuYiben @Mejohn….
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GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion.
nature.com
Nature Structural & Molecular Biology - Single-molecular microscopy shows that GAGA multimeric zinc finger transcription factor searches chromatin for cognate sites through rapid...
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DNA mutagenesis driven by transcription factor competition with mismatch repair: Cell
cell.com
Competition between transcription factors and mismatch repair machinery drives localized hypermutation at regulatory elements, with implications for cancer and genome evolution.
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A conserved coupling of transcriptional ON and OFF periods underlies bursting dynamics | Nature Structural & Molecular Biology.
nature.com
Nature Structural & Molecular Biology - Gene activity levels predict how often and how strongly genes turn on and off. Using live imaging in fruit fly embryos, the authors uncover a conserved...
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RT @NogalesLab: So proud of the smashing success of the International Course in Biophysics co-organized with my @berkeleyMCB colleague Carl….
biophysal.org
First Summer International Advanced Biophysics and Structural Biology Course. Eva Nogales - Carlos Bustamante.
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RT @Fusion_Conf: 🎉 Kicking off #Nucleic25 with an inspiring talk from @taekjip on homology search in 3D genome - setting the tone for an ex….
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RT @tapas1889: Thanks TJ @taekjip for giving me the opportunity to work on this, .“Mechanistic insights into direct DNA and RNA strand tran….
academic.oup.com
Abstract. Single-stranded DNA-binding proteins (SSBs) are essential for genome stability, facilitating replication, repair, and recombination by binding si
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high-throughput single-molecule platform to study DNA supercoiling effect on protein–DNA interactions
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DNA origami-based platform for multi-axial single-molecule force spectroscopy reveals hidden dynamics in Holliday junctions
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Non-disruptive 3D profiling of combinations of epigenetic marks in single cells
biorxiv.org
Recent advancements in single-cell sequencing and spatial omics technologies have enhanced our understanding of diverse cellular identities, compositions, architectures, and functions. However, the...
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Bringing the Genetically Minimal Cell to Life on a Computer in 4D
biorxiv.org
We present a whole-cell spatial and kinetic model for the 100 minute cell cycle of the genetically minimal bacterium, JCVI-syn3A. This is the first simulation of a complete cell cycle in 4D including...
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