THE BOERSMA LAB
Welcome to the website of the Arnold Boersma Lab. We are embedded within the DWI Leibniz Institute for Interactive Materials, in Aachen, Germany.
We re-purpose and redesign the beautiful architectures provided by the molecules of Nature as for example sensors, probes, machines, or catalysts.
We use these new molecules in cells and in buffer, and everything in between.
We have a strong focus on engineering biomolecules to
- unravel the biochemical organization inside cells
- transplant cellular organization into synthetic life-like systems
- provide native-like environments to biocatalysts
- miniaturize life-like information processing
RESEARCH
DESIGNING NEW FRET SENSORS TO UNDERSTAND THE INTRACELLULAR ENVIRONMENT
The interior of the cells is obviously not like dilute buffer. Yet, traditionally most biochemistry experiments have been performed in dilute buffer. To understand how the interior of the cell influences biochemical processes, such as biocatalysis and organization of the biopolymers, we need to know what the important parameters in the cell are, and quantify their contribution to the intracellular organization.
By creative design, we developed a series FRET sensors for macromolecular crowding and the ionic strength: Cells are crowded with macromolecules that occupy space, generating a force that influences the organization of biomolecules in cells. The crowding sensors compress akin a polymer in crowded solutions. The sensors provide a readout for the excluded volume in bacteria, yeasts, and mammalian cells. Our efforts are towards improving these sensors, as well as applying them in different species. Further, we apply the sensors in dynamic soft materials.
Further reading:
Nature Methods, 2015, 227-229
Biophys J. 2017, 1929-1939
Nature Rev. Microbiol 2017, 309-318
Collaborators:
Prof. Veenhoff (UMCG Groningen)
Prof. Sheets and Prof. Heikal (Univ Minnesota)
Prof. Fitter (RWTH Aachen)
Dr. Aberg (UMCG Groningen)
Prof. Baldus (Utrecht Univ)
Prof. Poolman (Groningen Univ)
IONIC STRENGTH SENSING
The other sensor that we developed measures the ionic strength. The ionic strength is important for anything charged, which includes pretty much every molecule in the living cell (apart from a few small molecules). Our FRET-based ionic strength sensor allows to determine the ionic strength inside living cells, with all the advantages of FRET-based genetically-encoded sensors, such as high spatiotemporal resolution, and easy targeting to different compartments.
Further reading:
ACS Chem Biol 2017, 2510-2514
BIOCATALYSIS, LIFE-LIKE SYSTEMS, INFORMATION TRANSFER, AND MORE
These exciting topics are just (re)starting in our lab, and we will provide more information soon.
NEWS
MEET THE TEAM
ARNOLD BOERSMA
Principle Investigator
SARA MAVROVA
PhD Student (with Liesbeth Veenhoff)
QI WAN
PhD student
WEIYAN ZUO
PhD student
THEODOROS PITTAS
PhD Student
MILARA KALACHEVA
PhD Student
PUBLISHED WORK
DNA nanotechnology enters cell membranes.
Huo, S.; Li, H.; Boersma, A.J.; Herrmann, A. Adv. Sci. Accepted Manuscript.
Highlighted in Advanced Science News, April 2019.
Decreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress.
Liu, B.; Hasrat, Z.; Poolman, B.; Boersma, A.J. J. Bacteriol. Accepted Manuscript.
Selected as Article of Significant Interest (spotlight) in J. Bacteriol.
Macromolecular Crowding Effects on Energy Transfer Efficiency and Donor-Acceptor Distance of Hetero-FRET Sensors using Time-Resolved Fluorescence.
Schwarz, J; Leopold, H.J.; Leighton, R.; Miller, R.C.; Aplin, C.P.; Boersma, A.J.; Heikal, A.A.; Sheets, E.D. Methods Appl. Fluoresc. Accepted Manuscript.
Crowding Effects on Energy Transfer Efficiencies of hetero-FRET Probes as Measured using Time-Resolved Fluorescence Anisotropy
Leopold, H.; Leighton, R.; Schwarz, J.; Boersma, A.J.; Sheets, E.D.; Heikal, A.A. J. Phys. Chem. B. Accepted Manuscript.
How important is protein diffusion in prokaryotes?
Schavemaker, P.E.; Boersma, A.J.; Poolman, B. Front. Mol. Biosci. 2018, 5, 93
Special issue on biochemical reactions in cytomimetic media edited by A.P. Minton and G. Rivas
Rotational and Translational Diffusion of Size-Dependent Fluorescent Probes in Homogeneous and Heterogeneous Environments
Lee, H.B.; Cong, A.; Leopold, H.; Currie, M.; Boersma, A.J.; Sheets, E.D.; Heikal A.A. Phys. Chem. Chem. Phys. 2018, 20, 24045
The influence of fluorescent protein maturation on FRET measurements in living cells
Liu, B.; Mavrova, S.N.; van den Berg, J.; Kristensen, S.K.; Mantovanelli, L.; Veenhoff, L.M.; Poolman, B.; Boersma, A.J. ACS Sens. 2018, 3, 1735
Genetically encoded FRET-based biosensors studied on the single molecule level.
Höfig, H.; Otten, J.; Steffen, V.; Pohl, M.; Boersma, A. J.; Fitter, J. ACS Sens. 2018, 3, 1462
Ionic strength sensing in living cells.
Liu, B.; Poolman, B.; Boersma, A.J.* ACS Chem. Biol. 2017, 12, 2510.
Highlighted in Chemical & Engineering News, October 2017
Cover image ACS Chem. Biol. October 2017
Meet our authors highlight Boqun Liu
Kinetics model for the wavelength-dependence of excited-state dynamics of hetero-FRET sensors.
Schwarz, J.; Leighton, R.; Leopold, H. J.; Currie, M.; Boersma, A. J.; Sheets, E. D.; Heikal, A. A. Proc. SPIE 2017, 10380, 103800S
Fluorescence dynamics of a FRET probe designed for crowding studies.
Currie, M.; Leopold, H.; Schwarz, J.; Boersma, A. J.; Sheets, E.; Heikal, A. J. Phys. Chem. B 2017, 121, 5688.
Design and properties of genetically encoded probes for sensing macromolecular crowding.
Liu, B.; Aberg, C.; van Eerden, F.; Marrink, S.J.; Poolman, B.; Boersma, A.J.* Biophys. J. 2017, 112, 1929.
Lipid phase separations in the presence of hydrocarbons in giant unilamellar vesicles
Bartelds R.; Barnaud, J.; Boersma, A.J.; Marrink, S.J.; Poolman, B. AIMS Biophys. 2017, 4, 528.
Microorganisms maintain crowding homeostasis.
Van den Berg, J.; Boersma, A.J.; Poolman, B. Nature Rev. Microbiol. 2017, 15, 309.
Semisynthetic nanoreactor for reversible single-molecule covalent chemistry.
Lee, J.; Boersma, A.J.; Boudreau, M.A.; Cheley, S.; Daltrop, O.; Li, J.; Tamagaki, H.; Bayley, H. ACS Nano 2016, 10, 8843.
Highlighted in Nanotechweb.org, 2016.
Associative interactions in crowded solutions of biopolymers counteract depletion effects.
Groen, J.; Foschepoth, D.; te Brinke, E.; Boersma, A.J.; Imamura, H.; Rivas, G.; Heus, H.A.; Huck, W.T.S. J. Am. Chem. Soc. 2015, 40, 13041.
Highlighted in Derek Lowe’s “in the pipeline” blog
The power of four (News & Views)
Boersma, A.J.*; Roelfes, G. Nature Chemistry 2015, 7, 277.
*corresponding author
A sensor for quantification of macromolecular crowding in living cells.
Boersma, A.J.*; Zuhorn, I.S.; Poolman, B. Nature Methods 2015, 12, 227.
*corresponding author
Highlighted in NWO newsletter, 2015
Highlighted in Biophysical Society newsletter (with interview), 2015
News articles in kennislink.nl, University of Groningen website, AzoSensors.com, Science Newsline, Phys.org, Technobahn, EurekAlert!, Science Daily, Bioportfolio, Nanowerk Nanotechnology News, and others.
Characterization of the interactions between substrate, Cu(II) complex and DNA and their role in rate acceleration in DNA-based asymmetric catalysis
Draksharapu, A; Boersma, A.J.; Browne, W.R.; Roelfes, G. Dalton Trans. 2015, 44, 3656.
Binding of copper(II) polypyridyl complexes to DNA and consequences for DNA-based asymmetric catalysis.
Draksharapu, A; Boersma, A.J.; Leising, M.; Meetsma, A.; Browne, W.R.; Roelfes, G. Dalton Trans. 2015, 44, 3647.
Continuous stochastic detection of amino acid enantiomers with a protein nanopore.
Boersma, A.J.; Bayley, H. Angew. Chem. Int. Ed. 2012, 51, 9606.
Real-time detection of multiple neurotransmitters with a protein nanopore.
Boersma, A.J.; Brain, K.L.; Bayley, H. ACS Nano 2012, 6, 5304.
Highlighted in Nanomedicine, 2012.
Ligand denticity controls enantiomeric preference in DNA-based asymmetric catalysis.
Boersma, A.J.; de Bruin, B.; Feringa, B.L.; Roelfes, G. Chem. Commun. 2012, 2394.
Highlighted in Chemistry & Industry, 2012.
Catalytic enantioselective syn hydration of enones in water using a DNA-based catalyst.
Boersma, A.J.; Coquière, D.; Geerdink, D.; Rosati, F.; Feringa, B.L.; Roelfes, G. Nature Chem. 2010, 2, 991.
Highlighted on the NWO website, Chemisch2Weekblad
Synfacts highlight of the month February
Selected in Faculty of 1000
On the role of DNA in DNA-based catalytic enantioselective conjugate addition reactions.
Dijk, E.W.; Boersma, A.J.; Feringa, B.L.; Roelfes, G. Org. Biomol. Chem. 2010, 8, 3868.
DNA-based asymmetric catalysis.
Boersma, A.J.; Megens, R.P.; Feringa, B.L.; Roelfes, G. Chem. Soc. Rev. 2010, 39, 2083.
A kinetic and structural investigation of DNA-based asymmetric catalysis using the first generation ligands.
Rosati, F.; Boersma, A.J.; Klijn, J.E.; Meetsma, A.; Feringa, B.L.; Roelfes, G. Chem. Eur. J. 2009, 15, 9596.
Enantioselective Friedel-Crafts reactions in water using a DNA-based catalyst.
Boersma, A.J.; Feringa, B.L.; Roelfes, G. Angew. Chem. Int. Ed. 2009, 48, 3346.
Highlighted in Synfacts 2009(7)
DNA-based asymmetric catalysis: Sequence-dependent rate acceleration and enantioselectivity.
Boersma, A.J.; Klijn, J.E.; Feringa, B.L.; Roelfes, G. J. Am. Chem. Soc. 2008, 130, 11783.
Highlighted in JACS Select #4
α,β-Unsaturated 2-acyl imidazoles as a practical class of dienophiles for the DNA-based catalytic asymmetric Diels-Alder reaction in water.
Boersma, A.J.; Feringa, B.L.; Roelfes, G. Org. Lett. 2007, 9, 3647.
Highlighted on organic-chemistry.org, august 2008
Highly enantioselective DNA-based catalysis.
Roelfes, G.; Boersma, A.J.; Feringa, B.L. Chem. Commun. 2006, 635.
Hot paper in Chemical Communications.
Highlighted in Chemistry World, march 2006
Highlighted in Nature news & views, 7 dec 2006
Metal-catalyzed cotrimerization of arynes and alkenes.
Quintana, I.; Boersma, A.J.; Peña, D.; Pérez, D.; Guitián, E. Org. Lett. 2006, 8, 3347.
Catalytic enantioselective conjugate addition of dialkylzinc reagents to N-substituted-2,3-dehydro-4-piperidones.
Sebesta, R.; Pizzuti, M.G.; Boersma, A.J.; Minnaard, A.J.; Feringa, B.L. Chem. Commun. 2005, 1711.
CONTACT US
DWI Leibniz Institut für Interaktive Materialien
Forckenbeckstrasse 50
D-52056 Aachen, Germany
boersma[at]dwi.rwth-aachen.de