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Laman Trip, J.D.S. (author)
Open questions are whether life can be enabled in uninhabitable environments, and whether there is a limit to howmuch one can tune the speed of proliferation. Answering such questions has broad implications. It may reveal whether we can live in unforeseen habitats, whether we can slow down aging, and whether there are limits to lifespan. In this...
doctoral thesis 2022
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Fu, Rongjie (author), He, Wei (author), Dou, Jinzhuang (author), Villarreal, Oscar D. (author), Bedford, Ella (author), Wang, Helen (author), Hou, Connie (author), Zhang, Liang (author), Depken, S.M. (author)
The specificity of CRISPR/Cas9 genome editing is largely determined by the sequences of guide RNA (gRNA) and the targeted DNA, yet the sequence-dependent rules underlying off-target effects are not fully understood. To systematically explore the sequence determinants governing CRISPR/Cas9 specificity, here we describe a dual-target system to...
journal article 2022
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Eslami Mossallam, B. (author), Klein, M. (author), Smagt, Constantijn V.D. (author), Sanden, Koen V.D. (author), Jones, Stephen K. (author), Hawkins, John A. (author), Finkelstein, Ilya J. (author), Depken, S.M. (author)
The S. pyogenes (Sp) Cas9 endonuclease is an important gene-editing tool. SpCas9 is directed to target sites based on complementarity to a complexed single-guide RNA (sgRNA). However, SpCas9-sgRNA also binds and cleaves genomic off-targets with only partial complementarity. To date, we lack the ability to predict cleavage and binding activity...
journal article 2022
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Janissen, R. (author), Eslami Mossallam, B. (author), Artsimovitch, Irina (author), Depken, S.M. (author), Dekker, N.H. (author)
Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high...
journal article 2022
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Severins, I.W.H. (author), Joo, C. (author), van Noort, John (author)
Next-generation sequencing techniques have led to a new quantitative dimension in the biological sciences. In particular, integrating sequencing techniques with biophysical tools allows sequence-dependent mechanistic studies. Using the millions of DNA clusters that are generated during sequencing to perform high-throughput binding affinity...
review 2022
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Gambelli, Lavinia (author), Mesman, Rob (author), Versantvoort, Wouter (author), Diebolder, Christoph A. (author), Engel, A.H. (author), Evers, W.H. (author), Jetten, Mike S.M. (author), Pabst, M. (author), Daum, Bertram (author)
Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed...
journal article 2021
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Seifert, Mona (author), Bera, Subhas C. (author), van Nies, Pauline (author), Kirchdoerfer, Robert N. (author), Shannon, Ashleigh (author), Le, Thi Tuyet Nhung (author), Meng, Xiangzhi (author), Depken, S.M. (author), Dulin, David (author)
The absence of 'shovel-ready' anti-coronavirus drugs during vaccine development has exceedingly worsened the SARS-CoV-2 pandemic. Furthermore, new vaccine-resistant variants and coronavirus outbreaks may occur in the near future, and we must be ready to face this possibility. However, efficient antiviral drugs are still lacking to this day,...
journal article 2021
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Bera, Subhas Chandra (author), Seifert, Mona (author), Kirchdoerfer, Robert N. (author), van Nies, Pauline (author), Wubulikasimu, Yibulayin (author), Quack, Salina (author), Papini, Flávia S. (author), Depken, S.M. (author), Dulin, D. (author)
Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We use a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core...
journal article 2021
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Spoelstra, W.K. (author), van der Sluis, E.O. (author), Dogterom, A.M. (author), Reese, L. (author)
Coacervates are polymer-rich droplets that form through liquid-liquid phase separation in polymer solutions. Liquid-liquid phase separation and coacervation have recently been shown to play an important role in the organization of biological systems. Such systems are highly dynamic and under continuous influence of enzymatic and chemical...
journal article 2020
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Verlinden, E.J. (author), Madadelahi, M. (author), Sarajlic, E. (author), Shamloo, A. (author), Engel, A.H. (author), Staufer, U. (author), Ghatkesar, M.K. (author)
We introduce a two-channel microfluidic atomic force microscopy (AFM) cantilever that combines the nanomechanical sensing functionality of an AFM cantilever with the ability to manipulate fluids of picolitres or smaller volumes through nanoscale apertures near the cantilever tip. Each channel is connected to a separate fluid reservoir, which...
journal article 2020
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Huis In 't Veld, Pim J. (author), Volkov, V. (author), Stender, Isabelle D. (author), Musacchio, Andrea (author), Dogterom, A.M. (author)
Errorless chromosome segregation requires load-bearing attachments of the plus ends of spindle microtubules to chromosome structures named kinetochores. How these end-on kinetochore attachments are established following initial lateral contacts with the microtubule lattice is poorly understood. Two microtubule-binding complexes, the Ndc80 and...
journal article 2019
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McHugh, Toni (author), Zou, Juan (author), Volkov, V. (author), Bertin, Aurélie (author), Talapatra, Sandeep K. (author), Rappsilber, Juri (author), Dogterom, A.M. (author), Welburn, Julie P.I. (author)
Kinesin-13 motors regulate precise microtubule dynamics and limit microtubule length throughout metazoans by depolymerizing microtubule ends. Recently, the kinesin-13 motor family member MCAK (also known Kif2C) has been proposed to undergo large conformational changes during its catalytic cycle, as it switches from being in solution to being...
journal article 2019
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Vendel, K.J.A. (author), Tschirpke, S. (author), Shamsi, F. (author), Dogterom, A.M. (author), Laan, L. (author)
Cell polarity - the morphological and functional differentiation of cellular compartments in a directional manner - is required for processes such as orientation of cell division, directed cellular growth and motility. How the interplay of components within the complexity of a cell leads to cell polarity is still heavily debated. In this...
review 2019
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Deshpande, S.R. (author), Brandenburg, Frank (author), Lau, A.W.H.R. (author), Last, M.G.F. (author), Spoelstra, W.K. (author), Reese, L. (author), Wunnava, Sreekar (author), Dogterom, A.M. (author), Dekker, C. (author)
Liquid-liquid phase separation (LLPS), especially coacervation, plays a crucial role in cell biology, as it forms numerous membraneless organelles in cells. Coacervates play an indispensable role in regulating intracellular biochemistry, and their dysfunction is associated with several diseases. Understanding of the LLPS dynamics would...
journal article 2019
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van de Willige, Dieudonnée (author), Hummel, Jessica J.A. (author), Alkemade, C. (author), Kahn, Olga I. (author), Au, Franco K.C. (author), Qi, Robert Z. (author), Dogterom, A.M. (author), Koenderink, G.H. (author), Hoogenraad, Casper C. (author), Akhmanova, Anna (author)
Crosstalk between the actin and microtubule cytoskeletons underlies cellular morphogenesis. Interactions between actin filaments and microtubules are particularly important for establishing the complex polarized morphology of neurons. Here, we characterized the neuronal function of growth arrest-specific 2-like 1 (Gas2L1), a protein that can...
journal article 2019
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Fanalista, F. (author), Birnie, A.T.F. (author), Maan, R. (author), Burla, Federica (author), Charles usagé Charles-Carty, K.V. (author), Pawlik, G. (author), Deshpande, S.R. (author), Koenderink, Gijsje H. (author), Dogterom, A.M. (author), Dekker, C. (author)
Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is...
journal article 2019
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Aher, Amol (author), Kok, M.W.A. (author), Sharma, Ashwani (author), Rai, Ankit (author), Olieric, Natacha (author), Rodriguez-Garcia, Ruddi (author), Katrukha, Eugene A. (author), Weinert, Tobias (author), Olieric, Vincent (author), Kapitein, Lukas C. (author), Steinmetz, Michel O. (author), Dogterom, A.M. (author), Akhmanova, Anna (author)
The dynamic instability of microtubules plays a key role in controlling their organization and function, but the cellular mechanisms regulating this process are poorly understood. Here, we show that cytoplasmic linker-associated proteins (CLASPs) suppress transitions from microtubule growth to shortening, termed catastrophes, including those...
journal article 2018
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Pavinato Olimpio, E. (author), Dang, Y. (author), Youk, H.O. (author)
Communicating cells can coordinate their gene expressions to form spatial patterns, generating order from disorder. Ubiquitous “secrete-and-sense cells” secrete and sense the same molecule to do so. Here we present a modeling framework—based on cellular automata and mimicking approaches of statistical mechanics—for understanding how secrete-and...
journal article 2018
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Casola, Francesco (author), van der Sar, T. (author), Yacoby, A. (author)
The magnetic fields generated by spins and currents provide a unique window into the physics of correlated-electron materials and devices. First proposed only a decade ago, magnetometry based on the electron spin of nitrogen-vacancy (NV) defects in diamond is emerging as a platform that is excellently suited for probing condensed matter...
review 2018
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Kim, S.H. (author), Ganji, M. (author), Kim, E. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes ...
journal article 2018
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